[{"month":"11","publication_identifier":{"eissn":["2194-041X"],"issn":["2194-0401"]},"project":[{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2207.08293"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1007/s40072-023-00319-4","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/s40072-023-00319-4","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"JuFi"}],"year":"2023","acknowledgement":"The author has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).\r\nThe author thanks Lorenzo Dello Schiavo, Lucio Galeati and Mark Veraar for helpful comments. The author acknowledges Caterina Balzotti for her support in creating the picture. The author\r\nthanks the anonymous referee for helpful comments. ","date_updated":"2023-12-18T07:53:45Z","date_created":"2023-02-02T10:45:47Z","author":[{"full_name":"Agresti, Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","first_name":"Antonio","last_name":"Agresti"}],"scopus_import":"1","day":"28","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Stochastics and Partial Differential Equations: Analysis and Computations","citation":{"ieee":"A. Agresti, “Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations,” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023.","apa":"Agresti, A. (2023). Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-023-00319-4","ista":"Agresti A. 2023. Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations.","ama":"Agresti A. Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations. 2023. doi:10.1007/s40072-023-00319-4","chicago":"Agresti, Antonio. “Delayed Blow-up and Enhanced Diffusion by Transport Noise for Systems of Reaction-Diffusion Equations.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023. https://doi.org/10.1007/s40072-023-00319-4.","short":"A. Agresti, Stochastics and Partial Differential Equations: Analysis and Computations (2023).","mla":"Agresti, Antonio. “Delayed Blow-up and Enhanced Diffusion by Transport Noise for Systems of Reaction-Diffusion Equations.” Stochastics and Partial Differential Equations: Analysis and Computations, Springer Nature, 2023, doi:10.1007/s40072-023-00319-4."},"date_published":"2023-11-28T00:00:00Z","type":"journal_article","abstract":[{"text":"This paper is concerned with the problem of regularization by noise of systems of reaction–diffusion equations with mass control. It is known that strong solutions to such systems of PDEs may blow-up in finite time. Moreover, for many systems of practical interest, establishing whether the blow-up occurs or not is an open question. Here we prove that a suitable multiplicative noise of transport type has a regularizing effect. More precisely, for both a sufficiently noise intensity and a high spectrum, the blow-up of strong solutions is delayed up to an arbitrary large time. Global existence is shown for the case of exponentially decreasing mass. The proofs combine and extend recent developments in regularization by noise and in the Lp(Lq)-approach to stochastic PDEs, highlighting new connections between the two areas.","lang":"eng"}],"title":"Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations","ddc":["510"],"status":"public","_id":"12486","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version"},{"month":"11","day":"16","article_processing_charge":"No","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"scopus_import":"1","date_published":"2023-11-16T00:00:00Z","doi":"10.1109/TIT.2023.3334032","language":[{"iso":"eng"}],"publication":"IEEE Transactions on Information Theory","external_id":{"arxiv":["2211.04408"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04408"}],"citation":{"short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory (2023).","mla":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error Exponents.” IEEE Transactions on Information Theory, IEEE, 2023, doi:10.1109/TIT.2023.3334032.","chicago":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error Exponents.” IEEE Transactions on Information Theory. IEEE, 2023. https://doi.org/10.1109/TIT.2023.3334032.","ama":"Zhang Y, Vatedka S. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. 2023. doi:10.1109/TIT.2023.3334032","ieee":"Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via error exponents,” IEEE Transactions on Information Theory. IEEE, 2023.","apa":"Zhang, Y., & Vatedka, S. (2023). Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2023.3334032","ista":"Zhang Y, Vatedka S. 2023. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory."},"quality_controlled":"1","article_type":"original","abstract":[{"lang":"eng","text":"We derive lower bounds on the maximal rates for multiple packings in high-dimensional Euclidean spaces. For any N > 0 and L ∈ Z ≥2 , a multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L - 1 balls of radius √ nN around points in C . This is a natural generalization of the sphere packing problem. We study the multiple packing problem for both bounded point sets whose points have norm at most √ nP for some constant P > 0, and unbounded point sets whose points are allowed to be anywhere in R n . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied over finite fields. We derive the best known lower bounds on the optimal multiple packing density. This is accomplished by establishing an inequality which relates the list-decoding error exponent for additive white Gaussian noise channels, a quantity of average-case nature, to the list-decoding radius, a quantity of worst-case nature. We also derive novel bounds on the list-decoding error exponent for infinite constellations and closed-form expressions for the list-decoding error exponents for the power-constrained AWGN channel, which may be of independent interest beyond multiple packing."}],"type":"journal_article","author":[{"full_name":"Zhang, Yihan","last_name":"Zhang","first_name":"Yihan","orcid":"0000-0002-6465-6258","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c"},{"first_name":"Shashank","last_name":"Vatedka","full_name":"Vatedka, Shashank"}],"date_created":"2023-12-10T23:01:00Z","date_updated":"2023-12-18T07:46:45Z","oa_version":"Preprint","year":"2023","_id":"14665","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Multiple packing: Lower bounds via error exponents","status":"public","publication_status":"epub_ahead","department":[{"_id":"MaMo"}],"publisher":"IEEE"},{"quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2023/1404","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2023-12-02","start_date":"2023-11-29","location":"Taipei, Taiwan","name":"TCC: Theory of Cryptography"},"doi":"10.1007/978-3-031-48624-1_13","month":"11","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031486234"],"eissn":["1611-3349"]},"publisher":"Springer Nature","department":[{"_id":"KrPi"}],"year":"2023","acknowledgement":"Home Theory of Cryptography Conference paper\r\n(Verifiable) Delay Functions from Lucas Sequences\r\nDownload book PDF\r\nDownload book EPUB\r\nSimilar content being viewed by others\r\n\r\nSlider with three content items shown per slide. Use the Previous and Next buttons to navigate the slides or the slide controller buttons at the end to navigate through each slide.\r\nPrevious slide\r\nGeneric-Group Delay Functions Require Hidden-Order Groups\r\nChapter© 2020\r\n\r\nShifted powers in Lucas–Lehmer sequences\r\nArticle30 January 2019\r\n\r\nA New Class of Trapdoor Verifiable Delay Functions\r\nChapter© 2023\r\n\r\nWeak Pseudoprimality Associated with the Generalized Lucas Sequences\r\nChapter© 2022\r\n\r\nOn the Security of Time-Lock Puzzles and Timed Commitments\r\nChapter© 2020\r\n\r\nGeneration of full cycles by a composition of NLFSRs\r\nArticle08 March 2014\r\n\r\nCryptographically Strong de Bruijn Sequences with Large Periods\r\nChapter© 2013\r\n\r\nOpen Problems on With-Carry Sequence Generators\r\nChapter© 2014\r\n\r\nGenerically Speeding-Up Repeated Squaring Is Equivalent to Factoring: Sharp Thresholds for All Generic-Ring Delay Functions\r\nChapter© 2020\r\n\r\nNext slide\r\nGo to slide 1\r\nGo to slide 2\r\nGo to slide 3\r\n(Verifiable) Delay Functions from Lucas Sequences\r\nCharlotte Hoffmann, Pavel Hubáček, Chethan Kamath & Tomáš Krňák \r\nConference paper\r\nFirst Online: 27 November 2023\r\n83 Accesses\r\n\r\nPart of the Lecture Notes in Computer Science book series (LNCS,volume 14372)\r\n\r\nAbstract\r\nLucas sequences are constant-recursive integer sequences with a long history of applications in cryptography, both in the design of cryptographic schemes and cryptanalysis. In this work, we study the sequential hardness of computing Lucas sequences over an RSA modulus.\r\n\r\nFirst, we show that modular Lucas sequences are at least as sequentially hard as the classical delay function given by iterated modular squaring proposed by Rivest, Shamir, and Wagner (MIT Tech. Rep. 1996) in the context of time-lock puzzles. Moreover, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring. In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring.\r\n\r\nSecond, we demonstrate the feasibility of constructing practically-efficient verifiable delay functions based on the sequential hardness of modular Lucas sequences. Our construction builds on the work of Pietrzak (ITCS 2019) by leveraging the intrinsic connection between the problem of computing modular Lucas sequences and exponentiation in an appropriate extension field.\r\n\r\nKeywords\r\nDelay functions\r\nVerifiable delay functions\r\nLucas sequences\r\nDownload conference paper PDF\r\n\r\n1 Introduction\r\nA verifiable delay function (VDF) \r\n is a function that satisfies two properties. First, it is a delay function, which means it must take a prescribed (wall) time T to compute f, irrespective of the amount of parallelism available. Second, it should be possible for anyone to quickly verify – say, given a short proof \r\n – the value of the function (even without resorting to parallelism), where by quickly we mean that the verification time should be independent of or significantly smaller than T (e.g., logarithmic in T). If we drop either of the two requirements, then the primitive turns out trivial to construct. For instance, for an appropriately chosen hash function h, the delay function \r\n defined by T-times iterated hashing of the input is a natural heuristic for an inherently sequential task which, however, seems hard to verify more efficiently than by recomputing. On the other hand, the identity function \r\n is trivial to verify but also easily computable. Designing a simple function satisfying the two properties simultaneously proved to be a nontrivial task.\r\n\r\nThe notion of VDFs was introduced in [31] and later formalised in [9]. In principle, since the task of constructing a VDF reduces to the task of incrementally-verifiable computation [9, 53], constructions of VDFs could leverage succinct non-interactive arguments of knowledge (SNARKs): take any sequentially-hard function f (for instance, iterated hashing) as the delay function and then use the SNARK on top of it as the mechanism for verifying the computation of the delay function. However, as discussed in [9], the resulting construction is not quite practical since we would rely on a general-purpose machinery of SNARKs with significant overhead.\r\n\r\nEfficient VDFs via Algebraic Delay Functions. VDFs have recently found interesting applications in design of blockchains [17], randomness beacons [43, 51], proofs of data replication [9], or short-lived zero-knowledge proofs and signatures [3]. Since efficiency is an important factor there, this has resulted in a flurry of constructions of VDFs that are tailored with application and practicality in mind. They rely on more algebraic, structured delay functions that often involve iterating an atomic operation so that one can resort to custom proof systems to achieve verifiability. These constructions involve a range of algebraic settings like the RSA or class groups [5, 8, 25, 42, 55], permutation polynomials over finite fields [9], isogenies of elliptic curves [21, 52] and, very recently, lattices [15, 28]. The constructions in [42, 55] are arguably the most practical and the mechanism that underlies their delay function is the same: carry out iterated squaring in groups of unknown order, like RSA groups [47] or class groups [12]. What distinguishes these two proposals is the way verification is carried out, i.e., how the underlying “proof of exponentiation” works: while Pietrzak [42] resorts to an LFKN-style recursive proof system [35], Wesolowski [55] uses a clever linear decomposition of the exponent.\r\n\r\nIterated Modular Squaring and Sequentiality. The delay function that underlies the VDFs in [5, 25, 42, 55] is the same, and its security relies on the conjectured sequential hardness of iterated squaring in a group of unknown order (suggested in the context of time-lock puzzles by Rivest, Shamir, and Wagner [48]). Given that the practically efficient VDFs all rely on the above single delay function, an immediate open problem is to identify additional sources of sequential hardness that are structured enough to support practically efficient verifiability.\r\n\r\n1.1 Our Approach to (Verifiable) Delay Functions\r\nIn this work, we study an alternative source of sequential hardness in the algebraic setting and use it to construct efficient verifiable delay functions. The sequentiality of our delay function relies on an atomic operation that is related to the computation of so-called Lucas sequences [29, 34, 57], explained next.\r\n\r\nLucas Sequences. A Lucas sequence is a constant-recursive integer sequence that satisfies the recurrence relation\r\n\r\nfor integers P and Q.Footnote1 Specifically, the Lucas sequences of integers \r\n and \r\n of the first and second type (respectively) are defined recursively as\r\n\r\nwith \r\n, and\r\n\r\nwith \r\n.\r\n\r\nThese sequences can be alternatively defined by the characteristic polynomial \r\n. Specifically, given the discriminant \r\n of the characteristic polynomial, one can alternatively compute the above sequences by performing operations in the extension field\r\n\r\nusing the identities\r\n\r\nwhere \r\n and its conjugate \r\n are roots of the characteristic polynomial. Since conjugation and exponentiation commute in the extension field (i.e., \r\n), computing the i-th terms of the two Lucas sequences over integers reduces to computing \r\n in the extension field, and vice versa.\r\n\r\nThe intrinsic connection between computing the terms in the Lucas sequences and that of exponentiation in the extension has been leveraged to provide alternative instantiations of public-key encryption schemes like RSA and ElGamal in terms of Lucas sequences [7, 30]. However, as we explain later, the corresponding underlying computational hardness assumptions are not necessarily equivalent.\r\n\r\nOverview of Our Delay Function. The delay function in [5, 25, 42, 55] is defined as the iterated squaring base x in a (safe) RSA groupFootnote2 modulo N:\r\n\r\nOur delay function is its analogue in the setting of Lucas sequences:\r\n\r\nAs mentioned above, computing \r\n can be carried out equivalently in the extension field \r\n using the known relationship to roots of the characteristic polynomial of the Lucas sequence. Thus, the delay function can be alternatively defined as\r\n\r\nNote that the atomic operation of our delay function is “doubling” the index of an element of the Lucas sequence modulo N (i.e., \r\n) or, equivalently, squaring in the extension field \r\n (as opposed to squaring in \r\n). Using the representation of \r\n as \r\n, squaring in \r\n can be expressed as a combination of squaring, multiplication and addition modulo N, since\r\n\r\n(1)\r\nSince \r\n is a group of unknown order (provided the factorization of N is kept secret), iterated squaring remains hard here. In fact, we show in Sect. 3.2 that iterated squaring in \r\n is at least as hard as iterated squaring for RSA moduli N. Moreover, we conjecture in Conjecture 1 that it is, in fact, strictly harder (also see discussion below on advantages of our approach).\r\n\r\nVerifying Modular Lucas Sequence. To obtain a VDF, we need to show how to efficiently verify our delay function. To this end, we show how to adapt the interactive proof of exponentiation from [42] to our setting, which then – via the Fiat-Shamir Transform [22] – yields the non-interactive verification algorithm.Footnote3 Thus, our main result is stated informally below.\r\n\r\nTheorem 1\r\n(Informally stated, see Theorem 2). Assuming sequential hardness of modular Lucas sequence, there exists statistically-sound VDF in the random-oracle model.\r\n\r\nHowever, the modification of Pietrzak’s protocol is not trivial and we have to overcome several hurdles that we face in this task, which we elaborate on in Sect. 1.2. We conclude this section with discussions about our results.\r\n\r\nAdvantage of Our Approach. Our main advantage is the reliance on a potentially weaker (sequential) hardness assumption while maintaining efficiency: we show in Sect. 3.2 that modular Lucas sequences are at least as sequentially-hard as the classical delay function given by iterated modular squaring [48]. Despite the linear recursive structure of Lucas sequences, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring (Conjecture 1). In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring. Even though both assumptions need the group order to be hidden, we believe that there is need for a nuanced analysis of sequential hardness assumptions in hidden order groups, especially because all current delay functions that provide sufficient structure for applications are based on iterated modular squaring. If the iterated modular squaring assumption is broken, our delay function is currently the only practical alternative in the RSA group.\r\n\r\nDelay Functions in Idealised Models. Recent works studied the relationship of group-theoretic (verifiable) delay functions to the hardness of factoring in idealised models such as the algebraic group model and the generic ring model [27, 50]. In the generic ring model, Rotem and Segev [50] showed the equivalence of straight-line delay functions in the RSA setting and factoring. Our construction gives rise to a straight-line delay function and, by their result, its sequentiality is equivalent to factoring for generic algorithms. However, their result holds only in the generic ring model and leaves the relationship between the two assumptions unresolved in the standard model.\r\n\r\nCompare this with the status of the RSA assumption and factoring. On one hand, we know that in the generic ring model, RSA and factoring are equivalent [2]. Yet, it is possible to rule out certain classes of reductions from factoring to RSA in the standard model [11]. Most importantly, despite the equivalence in the generic ring model, there is currently no reduction from factoring to RSA in the standard model and it remains one of the major open problems in number theory related to cryptography since the introduction of the RSA assumption.\r\n\r\nIn summary, speeding up iterated squaring by a non-generic algorithm could be possible (necessarily exploiting the representations of ring elements modulo N), while such an algorithm may not lead to a speed-up in the computation of modular Lucas sequences despite the result of Rotem and Segev [50].\r\n\r\n1.2 Technical Overview\r\nPietrzak’s VDF. Let \r\n be an RSA modulus where p and q are safe primes and let x be a random element from \r\n. At its core, Pietrzak’s VDF relies on the interactive protocol for the statement\r\n\r\n“(N, x, y, T) satisfies \r\n”.\r\n\r\nThe protocol is recursive and, in a round-by-round fashion, reduces the claim to a smaller statement by halving the time parameter. To be precise, in each round, the (honest) prover sends the “midpoint” \r\n of the current statement to the verifier and they together reduce the statement to\r\n\r\n“\r\n satisfies \r\n”,\r\n\r\nwhere \r\n and \r\n for a random challenge r. This is continued till \r\n is obtained at which point the verifier simply checks whether \r\n using a single modular squaring.\r\n\r\nSince the challenges r are public, the protocol can be compiled into a non-interactive one using the Fiat-Shamir transform [22] and this yields a means to verify the delay function\r\n\r\nIt is worth pointing out that the choice of safe primes is crucial for proving soundness: in case the group has easy-to-find elements of small order then it becomes easy to break soundness (see, e.g., [10]).\r\n\r\nAdapting Pietrzak’s Protocol to Lucas Sequences. For a modulus \r\n and integers \r\n, recall that our delay function is defined as\r\n\r\nor equivalently\r\n\r\nfor the discriminant \r\n of the characteristic polynomial \r\n. Towards building a verification algorithm for this delay function, the natural first step is to design an interactive protocol for the statement\r\n\r\n“(N, P, Q, y, T) satisfies \r\n.”\r\n\r\nIt turns out that the interactive protocol from [42] can be adapted for this purpose. However, we encounter two technicalities in this process.\r\n\r\nDealing with elements of small order. The main problem that we face while designing our protocol is avoiding elements of small order. In the case of [42], this was accomplished by moving to the setting of signed quadratic residues [26] in which the sub-groups are all of large order. It is not clear whether a corresponding object exists for our algebraic setting. However, in an earlier draft of Pietrzak’s protocol [41], this problem was dealt with in a different manner: the prover sends a square root of \r\n, from which the original \r\n can be recovered easily (by squaring it) with a guarantee that the result lies in a group of quadratic residues \r\n. Notice that the prover knows the square root of \r\n, because it is just a previous term in the sequence he computed.\r\n\r\nIn our setting, we cannot simply ask for the square root of the midpoint as the subgroup of \r\n we effectively work in has a different structure. Nevertheless, we can use a similar approach: for an appropriately chosen small a, we provide an a-th root of \r\n (instead of \r\n itself) to the prover in the beginning of the protocol. The prover then computes the whole sequence for \r\n. In the end, he has the a-th root of every term of the original sequence and he can recover any element of the original sequence by raising to the a-th power.\r\n\r\nSampling strong modulus. The second technicality is related to the first one. In order to ensure that we can use the above trick, we require a modulus where the small subgroups are reasonably small not only in the group \r\n but also in the extension \r\n. Thus the traditional sampling algorithms that are used to sample strong primes (e.g., [46]) are not sufficient for our purposes. However, sampling strong primes that suit our criteria can still be carried out efficiently as we show in the full version.\r\n\r\nComparing Our Technique with [8, 25]. The VDFs in [8, 25] are also inspired by [42] and, hence, faced the same problem of low-order elements. In [8], this is dealt with by amplifying the soundness at the cost of parallel repetition and hence larger proofs and extra computation. In [25], the number of repetitions of [8] is reduced significantly by introducing the following technique: The exponent of the initial instance is reduced by some parameter \r\n and at the end of an interactive phase, the verifier performs final exponentiation with \r\n, thereby weeding out potential false low-order elements in the claim. This technique differs from the approach taken in our work in the following ways: The technique from [25] works in arbitrary groups but it requires the parameter \r\n to be large and of a specific form. In particular, the VDF becomes more efficient when \r\n is larger than \r\n. In our protocol, we work in RSA groups whose modulus is the product of primes that satisfy certain conditions depending on a. This enables us to choose a parameter a that is smaller than a statistical security parameter and thereby makes the final exponentiation performed by the verifier much more efficient. Further, a can be any natural number, while \r\n must be set as powers of all small prime numbers up a certain bound in [25].\r\n\r\n1.3 More Related Work\r\nTimed Primitives. The notion of VDFs was introduced in [31] and later formalised in [9]. VDFs are closely related to the notions of time-lock puzzles [48] and proofs of sequential work [36]. Roughly speaking, a time-lock puzzle is a delay function that additionally allows efficient sampling of the output via a trapdoor. A proof of sequential work, on the other hand, is a delay “multi-function”, in the sense that the output is not necessarily unique. Constructions of time-lock puzzles are rare [6, 38, 48], and there are known limitations: e.g., that it cannot exist in the random-oracle model [36]. However, we know how to construct proofs of sequential work in the random-oracle model [1, 16, 19, 36].\r\n\r\nSince VDFs have found several applications, e.g., in the design of resource-efficient blockchains [17], randomness beacons [43, 51] and proof of data replication [9], there have been several constructions. Among them, the most notable are the iterated-squaring based construction from [8, 25, 42, 55], the permutation-polynomial based construction from [9], the isogenies-based construction from [13, 21, 52] and the construction from lattice problems [15, 28]. The constructions in [42, 55] are quite practical (see the survey [10]) and the VDF deployed in the cryptocurrency Chia is basically their construction adapted to the algebraic setting of class groups [17]. This is arguably the closest work to ours. On the other hand, the constructions from [21, 52], which work in the algebraic setting of isogenies of elliptic curves where no analogue of square and multiply is known, simply rely on “exponentiation”. Although, these constructions provide a certain form of quantum resistance, they are presently far from efficient. Freitag et al. [23] constructed VDFs from any sequentially hard function and polynomial hardness of learning with errors, the first from standard assumptions. The works of Cini, Lai, and Malavolta [15, 28] constructed the first VDF from lattice-based assumptions and conjectured it to be post-quantum secure.\r\n\r\nSeveral variants of VDFs have also been proposed. A VDF is said to be unique if the proof that is used for verification is unique [42]. Recently, Choudhuri et al. [5] constructed unique VDFs from the sequential hardness of iterated squaring in any RSA group and polynomial hardness of LWE. A VDF is tight [18] if the gap between simply computing the function and computing it with a proof is small. Yet another extension is a continuous VDF [20]. The feasibility of time-lock puzzles and proofs of sequential works were recently extended to VDFs. It was shown [50] that the latter requirement, i.e., working in a group of unknown order, is inherent in a black-box sense. It was shown in [18, 37] that there are barriers to constructing tight VDFs in the random-oracle model.\r\n\r\nVDFs also have surprising connection to complexity theory [14, 20, 33].\r\n\r\nWork Related to Lucas Sequences. Lucas sequences have long been studied in the context of number theory: see for example [45] or [44] for a survey of its applications to number theory. Its earliest application to cryptography can be traced to the \r\n factoring algorithm [56]. Constructive applications were found later thanks to the parallels with exponentiation. Several encryption and signature schemes were proposed, most notably the LUC family of encryption and signatures [30, 39]. It was later shown that some of these schemes can be broken or that the advantages it claimed were not present [7]. Other applications can be found in [32].\r\n\r\n2 Preliminaries\r\n2.1 Interactive Proof Systems\r\nInteractive Protocols. An interactive protocol consists of a pair \r\n of interactive Turing machines that are run on a common input \r\n. The first machine \r\n is the prover and is computationally unbounded. The second machine \r\n is the verifier and is probabilistic polynomial-time.\r\n\r\nIn an \r\n-round (i.e., \r\n-message) interactive protocol, in each round \r\n, first \r\n sends a message \r\n to \r\n and then \r\n sends a message \r\n to \r\n, where \r\n is a finite alphabet. At the end of the interaction, \r\n runs a (deterministic) Turing machine on input \r\n. The interactive protocol is public-coin if \r\n is a uniformly distributed random string in \r\n.\r\n\r\nInteractive Proof Systems. The notion of an interactive proof for a language L is due to Goldwasser, Micali and Rackoff [24].\r\n\r\nDefinition 1\r\nFor a function \r\n, an interactive protocol \r\n is an \r\n-statistically-sound interactive proof system for L if:\r\n\r\nCompleteness: For every \r\n, if \r\n interacts with \r\n on common input \r\n, then \r\n accepts with probability 1.\r\n\r\nSoundness: For every \r\n and every (computationally-unbounded) cheating prover strategy \r\n, the verifier \r\n accepts when interacting with \r\n with probability less than \r\n, where \r\n is called the soundness error.\r\n\r\n2.2 Verifiable Delay Functions\r\nWe adapt the definition of verifiable delay functions from [9] but we decouple the verifiability and sequentiality properties for clarity of exposition of our results. First, we present the definition of a delay function.\r\n\r\nDefinition 2\r\nA delay function \r\n consists of a triple of algorithms with the following syntax:\r\n\r\n:\r\n\r\nOn input a security parameter \r\n, the algorithm \r\n outputs public parameters \r\n.\r\n\r\n:\r\n\r\nOn input public parameters \r\n and a time parameter \r\n, the algorithm \r\n outputs a challenge x.\r\n\r\n:\r\n\r\nOn input a challenge pair (x, T), the (deterministic) algorithm \r\n outputs the value y of the delay function in time T.\r\n\r\nThe security property required of a delay function is sequential hardness as defined below.\r\n\r\nDefinition 3\r\n(Sequentiality). We say that a delay function \r\n satisfies the sequentiality property, if there exists an \r\n such that for all \r\n and for every adversary \r\n, where \r\n uses \r\n processors and runs in time \r\n, there exists a negligible function \r\n such that\r\n\r\nfigure a\r\nA few remarks about our definition of sequentiality are in order:\r\n\r\n1.\r\nWe require computing \r\n to be hard in less than T sequential steps even using any polynomially-bounded amount of parallelism and precomputation. Note that it is necessary to bound the amount of parallelism, as an adversary could otherwise break the underlying hardness assumption (e.g. hardness of factorization). Analogously, T should be polynomial in \r\n as, otherwise, breaking the underlying hardness assumptions becomes easier than computing \r\n itself for large values of T.\r\n\r\n2.\r\nAnother issue is what bound on the number of sequential steps of the adversary should one impose. For example, the delay function based on T repeated modular squarings can be computed in sequential time \r\n using polynomial parallelism [4]. Thus, one cannot simply bound the sequential time of the adversary by o(T). Similarly to [38], we adapt the \r\n bound for \r\n which, in particular, is asymptotically smaller than \r\n.\r\n\r\n3.\r\nWithout loss of generality, we assume that the size of \r\n is at least linear in n and the adversary A does not have to get the unary representation of the security parameter \r\n as its input.\r\n\r\nThe definition of verifiable delay function extends a delay function with the possibility to compute publicly-verifiable proofs of correctness of the output value.\r\n\r\nDefinition 4\r\nA delay function \r\n is a verifiable delay function if it is equipped with two additional algorithms \r\n and \r\n with the following syntax:\r\n\r\n:\r\n\r\nOn input public parameters and a challenge pair (x, T), the \r\n algorithm outputs \r\n, where \r\n is a proof that the output y is the output of \r\n.\r\n\r\n:\r\n\r\nOn input public parameters, a challenge pair (x, T), and an output/proof pair \r\n, the (deterministic) algorithm \r\n outputs either \r\n or \r\n.\r\n\r\nIn addition to sequentiality (inherited from the underlying delay function), the \r\n and \r\n algorithms must together satisfy correctness and (statistical) soundness as defined below.\r\n\r\nDefinition 5\r\n(Correctness). A verifiable delay function \r\n is correct if for all \r\n\r\nfigure b\r\nDefinition 6\r\n(Statistical soundness). A verifiable delay function \r\n is statistically sound if for every (computationally unbounded) malicious prover \r\n there exists a negligible function \r\n such that for all \r\n\r\nfigure c\r\n3 Delay Functions from Lucas Sequences\r\nIn this section, we propose a delay function based on Lucas sequences and prove its sequentiality assuming that iterated squaring in a group of unknown order is sequential (Sect. 3.1). Further, we conjecture (Sect. 3.2) that our delay function candidate is even more robust than its predecessor proposed by Rivest, Shamir, and Wagner [48]. Finally, we turn our delay function candidate into a verifiable delay function (Sect. 4).\r\n\r\n3.1 The Atomic Operation\r\nOur delay function is based on subsequences of Lucas sequences, whose indexes are powers of two. Below, we use \r\n to denote the set of non-negative integers.\r\n\r\nDefinition 7\r\nFor integers \r\n, the Lucas sequences \r\n and \r\n are defined for all \r\n as\r\n\r\nwith \r\n and \r\n, and\r\n\r\nwith \r\n and \r\n.\r\n\r\nWe define subsequences \r\n, respectively \r\n, of \r\n, respectively \r\n for all \r\n as\r\n\r\n(2)\r\nAlthough the value of \r\n depends on parameters (P, Q), we omit (P, Q) from the notation because these parameters will be always obvious from the context.\r\n\r\nThe underlying atomic operation for our delay function is\r\n\r\nThere are several ways to compute \r\n in T sequential steps, and we describe two of them below.\r\n\r\nAn Approach Based on Squaring in a Suitable Extension Ring. To compute the value \r\n, we can use the extension ring \r\n, where \r\n is the discriminant of the characteristic polynomial \r\n of the Lucas sequence. The characteristic polynomial f(z) has a root \r\n, and it is known that, for all \r\n, it holds that\r\n\r\nThus, by iterated squaring of \r\n, we can compute terms of our target subsequences. To get a better understanding of squaring in the extension ring, consider the representation of the root \r\n for some \r\n. Then,\r\n\r\nThen, the atomic operation of our delay function can be interpreted as \r\n, defined for all \r\n as\r\n\r\n(3)\r\nAn Approach Based on Known Identities. Many useful identities for members of modular Lucas sequences are known, such as\r\n\r\n(4)\r\nSetting \r\n we get\r\n\r\n(5)\r\nThe above identities are not hard to derive (see, e.g., Lemma 12.5 in [40]). Indexes are doubled on each of application of the identities in Eq. (5), and, thus, for \r\n, we define an auxiliary sequence \r\n by \r\n. Using the identities in Eq. (5), we get recursive equations\r\n\r\n(6)\r\nThen, the atomic operation of our delay function can be interpreted as \r\n, defined for all \r\n as\r\n\r\n(7)\r\nAfter a closer inspection, the reader may have an intuition that an auxiliary sequence \r\n, which introduces a third state variable, is redundant. This intuition is indeed right. In fact, there is another easily derivable identity\r\n\r\n(8)\r\nwhich can be found, e.g., as Lemma 12.2 in [40]. On the other hand, Eq. (8) is quite interesting because it allows us to compute large powers of an element \r\n using two Lucas sequences. We use this fact in the security reduction in Sect. 3.2. Our construction of a delay function, denoted \r\n, is given in Fig. 1.\r\n\r\nFig. 1.\r\nfigure 1\r\nOur delay function candidate \r\n based on a modular Lucas sequence.\r\n\r\nFull size image\r\nOn the Discriminant D. Notice that whenever D is a quadratic residue modulo N, the value \r\n is an element of \r\n and hence \r\n. By definition, LCS.Gen generates a parameter D that is a quadratic residue with probability 1/4, so it might seem that in one fourth of the cases there is another approach to compute \r\n: find the element \r\n and then perform n sequential squarings in the group \r\n. However, it is well known that finding square roots of uniform elements in \r\n is equivalent to factoring the modulus N, so this approach is not feasible. We can therefore omit any restrictions on the discriminant D in the definition of our delay function LCS.\r\n\r\n3.2 Reduction from RSW Delay Function\r\nIn order to prove the sequentiality property (Definition 3) of our candidate \r\n, we rely on the standard conjecture of the sequentiality of the \r\n time-lock puzzles, implicitly stated in [48] as the underlying hardness assumption.\r\n\r\nDefinition 8\r\n(\r\n delay function). The \r\n delay function is defined as follows:\r\n\r\n: Samples two n-bit primes p and q and outputs \r\n.\r\n\r\n: Outputs an x sampled from the uniform distribution on \r\n.\r\n\r\n: Outputs \r\n.\r\n\r\nTheorem 2\r\nIf the \r\n delay function has the sequentiality property, then the \r\n delay function has the sequentiality property.\r\n\r\nProof\r\nSuppose there exists an adversary \r\n who contradicts the sequentiality of \r\n, where \r\n is a precomputation algorithm and \r\n is an online algorithm. We construct an adversary \r\n who contradicts the sequentiality of \r\n as follows:\r\n\r\nThe algorithm \r\n is defined identically to the algorithm \r\n.\r\n\r\nOn input \r\n, \r\n picks a P from the uniform distribution on \r\n, sets\r\n\r\nand it runs \r\n to compute \r\n. The algorithm \r\n computes \r\n using the identity in Eq. (8).\r\n\r\nNote that the input distribution for the algorithm \r\n produced by \r\n differs from the one produced by \r\n, because the \r\n generator samples Q from the uniform distribution on \r\n (instead of \r\n). However, this is not a problem since the size of \r\n is negligible compared to the size of \r\n, so the statistical distance between the distribution of D produced by \r\n and the distribution of D sampled by \r\n is negligible in the security parameter. Thus, except for a negligible multiplicative loss, the adversary \r\n attains the same success probability of breaking the sequentiality of \r\n as the probability of \r\n breaking the sequentiality of \r\n – a contradiction to the assumption of the theorem. \r\n\r\nWe believe that the converse implication to Theorem 2 is not true, i.e., that breaking the sequentiality of \r\n does not necessarily imply breaking the sequentiality of \r\n. Below, we state it as a conjecture.\r\n\r\nConjecture 1\r\nSequentiality of \r\n cannot be reduced to sequentiality of \r\n.\r\n\r\nOne reason why the above conjecture might be true is that, while the \r\n delay function is based solely only on multiplication in the group \r\n, our \r\n delay function uses the full arithmetic (addition and multiplication) of the commutative ring \r\n.\r\n\r\nOne way to support the conjecture would be to construct an algorithm that speeds up iterated squaring but is not immediately applicable to Lucas sequences. By [49] we know that this cannot be achieved by a generic algorithm. A non-generic algorithm that solves iterated squaring in time \r\n is presented in [4]. The main tool of their construction is the Explicit Chinese Remainder Theorem modulo N. However, a similiar theorem exists also for univariate polynomial rings, which suggests that a similar speed-up can be obtained for our delay function by adapting the techniques in [4] to our setting.\r\n\r\n4 VDF from Lucas Sequences\r\nIn Sect. 3.1 we saw different ways of computing the atomic operation of the delay function. Computing \r\n in the extension field seems to be the more natural and time and space effective approach. Furthermore, writing the atomic operation \r\n as \r\n is very clear, and, thus, we follow this approach throughout the rest of the paper.\r\n\r\n4.1 Structure of \r\nTo construct a VDF based on Lucas sequences, we use an algebraic extension\r\n\r\n(9)\r\nwhere N is an RSA modulus and \r\n. In this section, we describe the structure of the algebraic extension given in Expression (9). Based on our understanding of the structure of the above algebraic extension, we can conclude that using modulus N composed of safe primes (i.e., for all prime factors p of N, \r\n has a large prime divisor) is necessary but not sufficient condition for security of our construction. We specify some sufficient conditions on factors of N in the subsequent Sect. 4.2.\r\n\r\nFirst, we introduce some simplifying notation for quotient rings.\r\n\r\nDefinition 9\r\nFor \r\n and \r\n, we denote by \r\n the quotient ring \r\n, where (m, f(x)) denotes the ideal of the ring \r\n generated by m and f(x).\r\n\r\nObservation 1, below, allows us to restrict our analysis only to the structure of \r\n for prime \r\n.\r\n\r\nObservation 1\r\nLet \r\n be distinct primes, \r\n and \r\n. Then\r\n\r\nProof\r\nUsing the Chinese reminder theorem, we get\r\n\r\nas claimed. \r\n\r\nThe following lemma characterizes the structure of \r\n with respect to the discriminant of f. We use \r\n to denote the standard Legendre symbol.\r\n\r\nLemma 1\r\nLet \r\n and \r\n be a polynomial of degree 2 with the discriminant D. Then\r\n\r\nProof\r\nWe consider each case separately:\r\n\r\nIf \r\n, then f(x) is irreducible over \r\n and \r\n is a field with \r\n elements. Since \r\n is a finite field, \r\n is cyclic and contains \r\n elements.\r\n\r\nIf \r\n, then \r\n and f has some double root \r\n and it can be written as \r\n for some \r\n. Since the ring \r\n is isomorphic to the ring \r\n (consider the isomorphism \r\n), we can restrict ourselves to describing the structure of \r\n.\r\n\r\nWe will prove that the function \r\n,\r\n\r\nis an isomorphism. First, the polynomial \r\n is invertible if and only if \r\n (inverse is \r\n). For the choice \r\n, we have\r\n\r\nThus \r\n is onto. Second, \r\n is, in fact, a bijection, because\r\n\r\n(10)\r\nFinally, \r\n is a homomorphism, because\r\n\r\nIf \r\n, then f(x) has two roots \r\n. We have an isomorphism\r\n\r\nand \r\n. \r\n\r\n4.2 Strong Groups and Strong Primes\r\nTo achieve the verifiability property of our construction, we need \r\n to contain a strong subgroup (defined next) of order asymptotically linear in p. We remark that our definition of strong primes is stronger than the one by Rivest and Silverman [46].\r\n\r\nDefinition 10\r\n(Strong groups). For \r\n, we say that a non-trivial group \r\n is \r\n-strong, if the order of each non-trivial subgroup of \r\n is greater than \r\n.\r\n\r\nObservation 2\r\nIf \r\n and \r\n are \r\n-strong groups, then \r\n is a \r\n-strong group.\r\n\r\nIt can be seen from Lemma 1 that \r\n always contains groups of small order (e.g. \r\n). To avoid these, we descend into the subgroup of a-th powers of elements of \r\n. Below, we introduce the corresponding notation.\r\n\r\nDefinition 11\r\nFor an Abelian group \r\n and \r\n, we define the subgroup \r\n of \r\n in the multiplicative notation and \r\n in the additive notation.\r\n\r\nFurther, we show in Lemma 2 below that \r\n-strong primality (defined next) is a sufficient condition for \r\n to be a \r\n-strong group.\r\n\r\nDefinition 12\r\n(Strong primes). Let \r\n and \r\n. We say that p is a \r\n-strong prime, if \r\n and there exists \r\n, \r\n, such that \r\n and every prime factor of W is greater than \r\n.\r\n\r\nSince a is a public parameter in our setup, super-polynomial a could reveal partial information about the factorization of N. However, we could allow a to be polynomial in \r\n while maintaining hardness of factoring N.Footnote4 For the sake of simplicity of Definition 12, we rather use stronger condition \r\n. The following simple observation will be useful for proving Lemma 2.\r\n\r\nObservation 3\r\nFor \r\n.\r\n\r\nLemma 2\r\nLet p be a \r\n-strong prime and \r\n be a quadratic polynomial. Then, \r\n is a \r\n-strong group.\r\n\r\nProof\r\nFrom definition of the strong primes, there exists \r\n, whose factors are bigger than \r\n and \r\n. We denote \r\n a factor of W. Applying Observation 3 to Lemma 1, we get\r\n\r\nIn particular, we used above the fact that Observation 2 implies that \r\n as explained next. Since \r\n, all divisors of \r\n are divisors of aW. By definition of a and W in Definition 12, we also have that \r\n, which implies that any factor of \r\n divides either a or W, but not both. When we divide \r\n by all the common divisors with a, only the common divisors with W are left, which implies \r\n. The proof of the lemma is now completed by Observation 2.\r\n\r\nCorollary 1\r\nLet p be a \r\n-strong prime, q be a \r\n-strong prime, \r\n, \r\n, \r\n and \r\n. Then \r\n is \r\n-strong.\r\n\r\n4.3 Our Interactive Protocol\r\nOur interactive protocol is formally described in Fig. 3. To understand this protocol, we first recall the outline of Pietrzak’s interactive protocol from Sect. 1.2 and then highlight the hurdles. Let \r\n be an RSA modulus where p and q are strong primes and let x be a random element from \r\n. The interactive protocol in [42] allows a prover to convince the verifier of the statement\r\n\r\n“(N, x, y, T) satisfies \r\n”.\r\n\r\nThe protocol is recursive and in a round-by-round fashion reduces the claim to a smaller statement by halving the time parameter. To be precise, in each round the (honest) prover sends the “midpoint” \r\n of the current statement to the verifier and they together reduce the statement to\r\n\r\n“\r\n satisfies \r\n”,\r\n\r\nwhere \r\n and \r\n for a random challenge r. This is continued until \r\n is obtained at which point the verifier simply checks whether \r\n.\r\n\r\nThe main problem, we face while designing our protocol is ensuring that the verifier can check whether \r\n sent by prover lies in an appropriate subgroup of \r\n. In the first draft of Pietrzak’s protocol [41], prover sends a square root of \r\n, from which the original \r\n can be recovered easily (by simply squaring it) with a guarantee, that the result lies in a group of quadratic residues \r\n. Notice that the prover knows the square root of \r\n, because it is just a previous term in the sequence he computed.\r\n\r\nUsing Pietrzak’s protocol directly for our delay function would require computing a-th roots in RSA group for some arbitrary a. Since this is a computationally hard problem, we cannot use the same trick. In fact, the VDF construction of Wesolowski [54] is based on similar hardness assumption.\r\n\r\nWhile Pietrzak shifted from \r\n to the group of signed quadratic residues \r\n in his following paper [42] to get unique proofs, we resort to his old idea of ‘squaring a square root’ and generalise it.\r\n\r\nThe high level idea is simple. First, on input \r\n, prover computes the sequence \r\n. Next, during the protocol, verifier maps all elements sent by the prover by homomorphism\r\n\r\n(11)\r\ninto the target strong group \r\n. This process is illustrated in Fig. 2. Notice that the equality \r\n for the original sequence implies the equality \r\n for the mapped sequence \r\n.\r\n\r\nFig. 2.\r\nfigure 2\r\nIllustration of our computation of the iterated squaring using the a-th root of \r\n. Horizontal arrows are \r\n and diagonal arrows are \r\n.\r\n\r\nFull size image\r\nRestriction to Elements of \r\n. Mapping Eq. (11) introduces a new technical difficulty. Since \r\n is not injective, we narrow the domain inputs, for which the output of our VDF is verifiable, from \r\n to \r\n. Furthermore, the only way to verify that a certain x is an element of \r\n is to get an a-th root of x and raise it to the ath power. So we have to represent elements of \r\n by elements of \r\n anyway. To resolve these two issues, we introduce a non-unique representation of elements of \r\n.\r\n\r\nDefinition 13\r\nFor \r\n and \r\n, we denote \r\n (an element of \r\n) by [x]. Since this representation of \r\n is not unique, we define an equality relation by\r\n\r\nWe will denote by tilde () the elements that were already powered to the a by a verifier (i.e. ). Thus tilded variables verifiably belong to the target group \r\n.\r\n\r\nIn the following text, the goal of the brackets notation in Definition 13 is to distinguish places where the equality means the equality of elements of \r\n from those places, where the equality holds up to \r\n. A reader can also see the notation in Definition 13 as a concrete representation of elements of a factor group \r\n.\r\n\r\nOur security reduction 2 required the delay function to operate everywhere on \r\n. This is not a problem if the \r\n algorithm is modified to output the set \r\n.\r\n\r\nFig. 3.\r\nfigure 3\r\nOur Interactive Protocol for \r\n.\r\n\r\nFull size image\r\n4.4 Security\r\nRecall here that \r\n is \r\n-strong group, so there exist\r\n\r\n and \r\n such that\r\n\r\n(12)\r\nDefinition 14\r\nFor \r\n and \r\n, we define \r\n as i-th coordinate of \r\n, where \r\n is the isomorphism given by Eq. (12).\r\n\r\nLemma 3\r\nLet \r\n and \r\n. If \r\n, then\r\n\r\n\t(13)\r\nProof\r\nFix \r\n, \r\n and y. Let some \r\n satisfy\r\n\r\n(14)\r\nUsing notation from Definition 14, we rewrite Eq. (14) as a set of equations\r\n\r\nFor every \r\n, by reordering the terms, the j-th equation becomes\r\n\r\n(15)\r\nIf \r\n, then \r\n. Further for every \r\n. It follows that \r\n. Putting these two equations together gives us \r\n, which contradicts our assumption \r\n.\r\n\r\nIt follows that there exists \r\n such that\r\n\r\n(16)\r\nThereafter there exists \r\n such that \r\n divides \r\n and\r\n\r\n(17)\r\nFurthermore, from Eq. (15), \r\n divides \r\n. Finally, dividing eq. Eq. (15) by \r\n, we get that r is determined uniquely (\r\n),\r\n\r\nUsing the fact that \r\n, this uniqueness of r upper bounds number of \r\n, such that Eq. (14) holds, to one. It follows that the probability that Eq. (14) holds for r chosen randomly from the uniform distribution over \r\n is less than \r\n. \r\n\r\nCorollary 2\r\nThe halving protocol will turn an invalid input tuple (i.e. \r\n) into a valid output tuple (i.e. \r\n) with probability less than \r\n.\r\n\r\nTheorem 3\r\nFor any computationally unbounded prover who submits anything other than \r\n such that \r\n in phase 2 of the protocol, the soundness error is upper-bounded by \r\n\r\nProof\r\nIn each round of the protocol, T decreases to \r\n. It follows that the number of rounds of the halving protocol before reaching \r\n is upper bounded by \r\n.\r\n\r\nIf the verifier accepts the solution tuple \r\n in the last round, then the equality \r\n must hold. It follows that the initial inequality must have turned into equality in some round of the halving protocol. By Lemma 3, the probability of this event is bounded by \r\n. Finally, using the union bound for all rounds, we obtain the upper bound (\r\n. \r\n\r\n4.5 Our VDF\r\nAnalogously to the VDF of Pietrzak [42], we compile our public-coin interactive proof given in Fig. 3 into a VDF using the Fiat-Shamir heuristic. The complete construction is given in Fig. 4. For ease of exposition, we assume that the time parameter T is always a power of two.\r\n\r\nFig. 4.\r\nfigure 4\r\n based on Lucas sequences\r\n\r\nFull size image\r\nAs discussed in Sect. 4.3, it is crucial for the security of the protocol that the prover computes a sequence of powers of the a-th root of the challenge and the resulting value (as well as the intermediate values) received from the prover is lifted to the appropriate group by raising it to the a-th power. We use the tilde notation in Fig. 4 in order to denote elements on the sequence relative to the a-th root.\r\n\r\nNote that, by the construction, the output of our VDF is the \r\n-th power of the root of the characteristic polynomial for Lucas sequence with parameters P and Q. Therefore, the value of the delay function implicitly corresponds to the \r\n-th term of the Lucas sequence.\r\n\r\nTheorem 4\r\nLet \r\n be the statistical security parameter. The \r\n VDF defined in Fig. 4 is correct and statistically-sound with a negligible soundness error if \r\n is modelled as a random oracle, against any adversary that makes \r\n oracle queries.\r\n\r\nProof\r\nThe correctness follows directly by construction.\r\n\r\nTo prove its statistical soundness, we proceed in a similar way to [42]. We cannot apply Fiat-Shamir transformation directly, because our protocol does not have constant number of rounds, thus we use Fiat-Shamir heuristic to each round separately.\r\n\r\nFirst, we use a random oracle as the \r\n function. Second, if a malicious prover computed a proof accepted by verifier for some tuple \r\n such that\r\n\r\n(19)\r\nthen he must have succeeded in turning inequality from Eq. (19) into equality in some round. By Lemma 3, probability of such a flipping is bounded by \r\n. Every such an attempt requires one query to random oracle. Using a union bound, it follows that the probability that a malicious prover who made q queries to random oracle succeeds in flipping initial inequality into equality in some round is upper-bounded by \r\n.\r\n\r\nSince q is \r\n, \r\n is a negligible function and thus the soundness error is negligible. \r\n\r\nNotes\r\n1.\r\nNote that integer sequences like Fibonacci numbers and Mersenne numbers are special cases of Lucas sequences.\r\n\r\n2.\r\nThe choice of modulus N is said to be safe if \r\n for safe primes \r\n and \r\n, where \r\n and \r\n are also prime.\r\n\r\n3.\r\nFurther, using the ideas from [14, 20], it is possible to construct so-called continuous VDFs from Lucas sequences.\r\n\r\n4.\r\nSince we set a to be at most polynomial in \r\n, its is possible to go over all possible candidate values for a in time polynomial in \r\n. 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Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, by the European Research Council (ERC) under the European Union’s Horizon Europe research and innovation programme (grant agreement No. 101042417, acronym SPP), and by ISF grant 1789/19.","date_updated":"2023-12-18T09:00:00Z","date_created":"2023-12-17T23:00:54Z","volume":14372,"author":[{"full_name":"Hoffmann, Charlotte","orcid":"0000-0003-2027-5549","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","last_name":"Hoffmann","first_name":"Charlotte"},{"last_name":"Hubáček","first_name":"Pavel","full_name":"Hubáček, Pavel"},{"full_name":"Kamath, Chethan","last_name":"Kamath","first_name":"Chethan"},{"first_name":"Tomáš","last_name":"Krňák","full_name":"Krňák, Tomáš"}],"page":"336-362","publication":"21st International Conference on Theory of Cryptography","citation":{"mla":"Hoffmann, Charlotte, et al. “(Verifiable) Delay Functions from Lucas Sequences.” 21st International Conference on Theory of Cryptography, vol. 14372, Springer Nature, 2023, pp. 336–62, doi:10.1007/978-3-031-48624-1_13.","short":"C. Hoffmann, P. Hubáček, C. Kamath, T. Krňák, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 336–362.","chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Tomáš Krňák. “(Verifiable) Delay Functions from Lucas Sequences.” In 21st International Conference on Theory of Cryptography, 14372:336–62. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48624-1_13.","ama":"Hoffmann C, Hubáček P, Kamath C, Krňák T. (Verifiable) delay functions from Lucas sequences. In: 21st International Conference on Theory of Cryptography. Vol 14372. Springer Nature; 2023:336-362. doi:10.1007/978-3-031-48624-1_13","ista":"Hoffmann C, Hubáček P, Kamath C, Krňák T. 2023. (Verifiable) delay functions from Lucas sequences. 21st International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 14372, 336–362.","apa":"Hoffmann, C., Hubáček, P., Kamath, C., & Krňák, T. (2023). (Verifiable) delay functions from Lucas sequences. In 21st International Conference on Theory of Cryptography (Vol. 14372, pp. 336–362). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-031-48624-1_13","ieee":"C. Hoffmann, P. Hubáček, C. Kamath, and T. Krňák, “(Verifiable) delay functions from Lucas sequences,” in 21st International Conference on Theory of Cryptography, Taipei, Taiwan, 2023, vol. 14372, pp. 336–362."},"date_published":"2023-11-27T00:00:00Z","scopus_import":"1","day":"27","article_processing_charge":"No","status":"public","title":"(Verifiable) delay functions from Lucas sequences","intvolume":" 14372","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14693","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Lucas sequences are constant-recursive integer sequences with a long history of applications in cryptography, both in the design of cryptographic schemes and cryptanalysis. In this work, we study the sequential hardness of computing Lucas sequences over an RSA modulus.\r\nFirst, we show that modular Lucas sequences are at least as sequentially hard as the classical delay function given by iterated modular squaring proposed by Rivest, Shamir, and Wagner (MIT Tech. Rep. 1996) in the context of time-lock puzzles. Moreover, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring. In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring.\r\nSecond, we demonstrate the feasibility of constructing practically-efficient verifiable delay functions based on the sequential hardness of modular Lucas sequences. Our construction builds on the work of Pietrzak (ITCS 2019) by leveraging the intrinsic connection between the problem of computing modular Lucas sequences and exponentiation in an appropriate extension field.","lang":"eng"}]},{"month":"11","publication_identifier":{"isbn":["9783031486203"],"eissn":["1611-3349"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"conference":{"name":"TCC: Theory of Cryptography","start_date":"2023-11-29","location":"Taipei, Taiwan","end_date":"2023-12-02"},"doi":"10.1007/978-3-031-48621-0_10","quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2023/1123","open_access":"1"}],"oa":1,"date_created":"2023-12-17T23:00:53Z","date_updated":"2023-12-18T08:36:51Z","volume":14371,"author":[{"full_name":"Auerbach, Benedikt","orcid":"0000-0002-7553-6606","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","last_name":"Auerbach","first_name":"Benedikt"},{"id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","first_name":"Miguel","last_name":"Cueto Noval","full_name":"Cueto Noval, Miguel"},{"first_name":"Guillermo","last_name":"Pascual Perez","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8630-415X","full_name":"Pascual Perez, Guillermo"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"year":"2023","day":"27","article_processing_charge":"No","scopus_import":"1","date_published":"2023-11-27T00:00:00Z","page":"271-300","publication":"21st International Conference on Theory of Cryptography","citation":{"ista":"Auerbach B, Cueto Noval M, Pascual Perez G, Pietrzak KZ. 2023. On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. 21st International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 14371, 271–300.","ieee":"B. Auerbach, M. Cueto Noval, G. Pascual Perez, and K. Z. Pietrzak, “On the cost of post-compromise security in concurrent Continuous Group-Key Agreement,” in 21st International Conference on Theory of Cryptography, Taipei, Taiwan, 2023, vol. 14371, pp. 271–300.","apa":"Auerbach, B., Cueto Noval, M., Pascual Perez, G., & Pietrzak, K. Z. (2023). On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. In 21st International Conference on Theory of Cryptography (Vol. 14371, pp. 271–300). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-031-48621-0_10","ama":"Auerbach B, Cueto Noval M, Pascual Perez G, Pietrzak KZ. On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. In: 21st International Conference on Theory of Cryptography. Vol 14371. Springer Nature; 2023:271-300. doi:10.1007/978-3-031-48621-0_10","chicago":"Auerbach, Benedikt, Miguel Cueto Noval, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “On the Cost of Post-Compromise Security in Concurrent Continuous Group-Key Agreement.” In 21st International Conference on Theory of Cryptography, 14371:271–300. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48621-0_10.","mla":"Auerbach, Benedikt, et al. “On the Cost of Post-Compromise Security in Concurrent Continuous Group-Key Agreement.” 21st International Conference on Theory of Cryptography, vol. 14371, Springer Nature, 2023, pp. 271–300, doi:10.1007/978-3-031-48621-0_10.","short":"B. Auerbach, M. Cueto Noval, G. Pascual Perez, K.Z. Pietrzak, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 271–300."},"abstract":[{"text":"Continuous Group-Key Agreement (CGKA) allows a group of users to maintain a shared key. It is the fundamental cryptographic primitive underlying group messaging schemes and related protocols, most notably TreeKEM, the underlying key agreement protocol of the Messaging Layer Security (MLS) protocol, a standard for group messaging by the IETF. CKGA works in an asynchronous setting where parties only occasionally must come online, and their messages are relayed by an untrusted server. The most expensive operation provided by CKGA is that which allows for a user to refresh their key material in order to achieve forward secrecy (old messages are secure when a user is compromised) and post-compromise security (users can heal from compromise). One caveat of early CGKA protocols is that these update operations had to be performed sequentially, with any user wanting to update their key material having had to receive and process all previous updates. Late versions of TreeKEM do allow for concurrent updates at the cost of a communication overhead per update message that is linear in the number of updating parties. This was shown to be indeed necessary when achieving PCS in just two rounds of communication by [Bienstock et al. TCC’20].\r\nThe recently proposed protocol CoCoA [Alwen et al. Eurocrypt’22], however, shows that this overhead can be reduced if PCS requirements are relaxed, and only a logarithmic number of rounds is required. The natural question, thus, is whether CoCoA is optimal in this setting.\r\nIn this work we answer this question, providing a lower bound on the cost (concretely, the amount of data to be uploaded to the server) for CGKA protocols that heal in an arbitrary k number of rounds, that shows that CoCoA is very close to optimal. Additionally, we extend CoCoA to heal in an arbitrary number of rounds, and propose a modification of it, with a reduced communication cost for certain k.\r\nWe prove our bound in a combinatorial setting where the state of the protocol progresses in rounds, and the state of the protocol in each round is captured by a set system, each set specifying a set of users who share a secret key. We show this combinatorial model is equivalent to a symbolic model capturing building blocks including PRFs and public-key encryption, related to the one used by Bienstock et al.\r\nOur lower bound is of order k•n1+1/(k-1)/log(k), where 2≤k≤log(n) is the number of updates per user the protocol requires to heal. This generalizes the n2 bound for k=2 from Bienstock et al.. This bound almost matches the k⋅n1+2/(k-1) or k2⋅n1+1/(k-1) efficiency we get for the variants of the CoCoA protocol also introduced in this paper.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","status":"public","title":"On the cost of post-compromise security in concurrent Continuous Group-Key Agreement","intvolume":" 14371","_id":"14691","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Preprint","intvolume":" 14371","title":"Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing","status":"public","_id":"14692","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The generic-group model (GGM) aims to capture algorithms working over groups of prime order that only rely on the group operation, but do not exploit any additional structure given by the concrete implementation of the group. In it, it is possible to prove information-theoretic lower bounds on the hardness of problems like the discrete logarithm (DL) or computational Diffie-Hellman (CDH). Thus, since its introduction, it has served as a valuable tool to assess the concrete security provided by cryptographic schemes based on such problems. A work on the related algebraic-group model (AGM) introduced a method, used by many subsequent works, to adapt GGM lower bounds for one problem to another, by means of conceptually simple reductions.\r\nIn this work, we propose an alternative approach to extend GGM bounds from one problem to another. Following an idea by Yun [EC15], we show that, in the GGM, the security of a large class of problems can be reduced to that of geometric search-problems. By reducing the security of the resulting geometric-search problems to variants of the search-by-hypersurface problem, for which information theoretic lower bounds exist, we give alternative proofs of several results that used the AGM approach.\r\nThe main advantage of our approach is that our reduction from geometric search-problems works, as well, for the GGM with preprocessing (more precisely the bit-fixing GGM introduced by Coretti, Dodis and Guo [Crypto18]). As a consequence, this opens up the possibility of transferring preprocessing GGM bounds from one problem to another, also by means of simple reductions. Concretely, we prove novel preprocessing bounds on the hardness of the d-strong discrete logarithm, the d-strong Diffie-Hellman inversion, and multi-instance CDH problems, as well as a large class of Uber assumptions. Additionally, our approach applies to Shoup’s GGM without additional restrictions on the query behavior of the adversary, while the recent works of Zhang, Zhou, and Katz [AC22] and Zhandry [Crypto22] highlight that this is not the case for the AGM approach.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2023-11-27T00:00:00Z","page":"301-330","citation":{"short":"B. Auerbach, C. Hoffmann, G. Pascual Perez, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 301–330.","mla":"Auerbach, Benedikt, et al. “Generic-Group Lower Bounds via Reductions between Geometric-Search Problems: With and without Preprocessing.” 21st International Conference on Theory of Cryptography, vol. 14371, Springer Nature, 2023, pp. 301–30, doi:10.1007/978-3-031-48621-0_11.","chicago":"Auerbach, Benedikt, Charlotte Hoffmann, and Guillermo Pascual Perez. “Generic-Group Lower Bounds via Reductions between Geometric-Search Problems: With and without Preprocessing.” In 21st International Conference on Theory of Cryptography, 14371:301–30. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48621-0_11.","ama":"Auerbach B, Hoffmann C, Pascual Perez G. Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing. In: 21st International Conference on Theory of Cryptography. Vol 14371. Springer Nature; 2023:301-330. doi:10.1007/978-3-031-48621-0_11","ieee":"B. Auerbach, C. Hoffmann, and G. Pascual Perez, “Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing,” in 21st International Conference on Theory of Cryptography, 2023, vol. 14371, pp. 301–330.","apa":"Auerbach, B., Hoffmann, C., & Pascual Perez, G. (2023). Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing. In 21st International Conference on Theory of Cryptography (Vol. 14371, pp. 301–330). Springer Nature. https://doi.org/10.1007/978-3-031-48621-0_11","ista":"Auerbach B, Hoffmann C, Pascual Perez G. 2023. Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing. 21st International Conference on Theory of Cryptography. , LNCS, vol. 14371, 301–330."},"publication":"21st International Conference on Theory of Cryptography","article_processing_charge":"No","day":"27","scopus_import":"1","volume":14371,"date_updated":"2023-12-18T09:17:03Z","date_created":"2023-12-17T23:00:54Z","author":[{"full_name":"Auerbach, Benedikt","last_name":"Auerbach","first_name":"Benedikt","orcid":"0000-0002-7553-6606","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425"},{"first_name":"Charlotte","last_name":"Hoffmann","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","orcid":"0000-0003-2027-5549","full_name":"Hoffmann, Charlotte"},{"full_name":"Pascual Perez, Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8630-415X","first_name":"Guillermo","last_name":"Pascual Perez"}],"department":[{"_id":"KrPi"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-48621-0_11","quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2023/808","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["0302-9743"],"isbn":["9783031486203"],"eissn":["1611-3349"]},"month":"11"},{"year":"2023","acknowledgement":"The authors are grateful to J. Karcher and A. Mirlin for collaboration on the related project. We thank I. Gruzberg and A. Mirlin for useful discussions and comments. I.S.B. is grateful to M. Parfenov and P. Ostrovsky for collaboration on the related project. The research was supported by Russian Science Foundation (Grant No. 22-42-04416).","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","author":[{"orcid":"0009-0003-7382-8036","id":"41e64307-6672-11ee-b9ad-cc7a0075a479","last_name":"Babkin","first_name":"Serafim","full_name":"Babkin, Serafim"},{"last_name":"Burmistrov","first_name":"I","full_name":"Burmistrov, I"}],"volume":108,"date_updated":"2023-12-18T08:45:28Z","date_created":"2023-12-17T23:00:53Z","article_number":"205429","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2308.16852"}],"oa":1,"external_id":{"arxiv":["2308.16852"]},"quality_controlled":"1","doi":"10.1103/PhysRevB.108.205429","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14690","intvolume":" 108","title":"Boundary multifractality in the spin quantum Hall symmetry class with interaction","status":"public","oa_version":"Preprint","type":"journal_article","issue":"20","abstract":[{"lang":"eng","text":"Generalized multifractality characterizes system size dependence of pure scaling local observables at Anderson transitions in all 10 symmetry classes of disordered systems. Recently, the concept of generalized multifractality has been extended to boundaries of critical disordered noninteracting systems. Here we study the generalized boundary multifractality in the presence of electron-electron interaction, focusing on the spin quantum Hall symmetry class (class C). Employing the two-loop renormalization group analysis within the Finkel'stein nonlinear sigma model, we compute the anomalous dimensions of the pure scaling operators located at the boundary of the system. We find that generalized boundary multifractal exponents are twice larger than their bulk counterparts. Exact symmetry relations between generalized boundary multifractal exponents in the case of noninteracting systems are explicitly broken by the interaction."}],"citation":{"ista":"Babkin S, Burmistrov I. 2023. Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. 108(20), 205429.","ieee":"S. Babkin and I. Burmistrov, “Boundary multifractality in the spin quantum Hall symmetry class with interaction,” Physical Review B, vol. 108, no. 20. American Physical Society, 2023.","apa":"Babkin, S., & Burmistrov, I. (2023). Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.205429","ama":"Babkin S, Burmistrov I. Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. 2023;108(20). doi:10.1103/PhysRevB.108.205429","chicago":"Babkin, Serafim, and I Burmistrov. “Boundary Multifractality in the Spin Quantum Hall Symmetry Class with Interaction.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.205429.","mla":"Babkin, Serafim, and I. Burmistrov. “Boundary Multifractality in the Spin Quantum Hall Symmetry Class with Interaction.” Physical Review B, vol. 108, no. 20, 205429, American Physical Society, 2023, doi:10.1103/PhysRevB.108.205429.","short":"S. Babkin, I. Burmistrov, Physical Review B 108 (2023)."},"publication":"Physical Review B","article_type":"original","date_published":"2023-11-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"15"},{"date_published":"2023-12-01T00:00:00Z","publication":"Nature Genetics","citation":{"ama":"Ing-Simmons E, Machnik NN, Vaquerizas JM. Reply to: Revisiting the use of structural similarity index in Hi-C. Nature Genetics. 2023;55(12):2053-2055. doi:10.1038/s41588-023-01595-5","ista":"Ing-Simmons E, Machnik NN, Vaquerizas JM. 2023. Reply to: Revisiting the use of structural similarity index in Hi-C. Nature Genetics. 55(12), 2053–2055.","ieee":"E. Ing-Simmons, N. N. Machnik, and J. M. Vaquerizas, “Reply to: Revisiting the use of structural similarity index in Hi-C,” Nature Genetics, vol. 55, no. 12. Springer Nature, pp. 2053–2055, 2023.","apa":"Ing-Simmons, E., Machnik, N. N., & Vaquerizas, J. M. (2023). Reply to: Revisiting the use of structural similarity index in Hi-C. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-023-01595-5","mla":"Ing-Simmons, Elizabeth, et al. “Reply to: Revisiting the Use of Structural Similarity Index in Hi-C.” Nature Genetics, vol. 55, no. 12, Springer Nature, 2023, pp. 2053–55, doi:10.1038/s41588-023-01595-5.","short":"E. Ing-Simmons, N.N. Machnik, J.M. Vaquerizas, Nature Genetics 55 (2023) 2053–2055.","chicago":"Ing-Simmons, Elizabeth, Nick N Machnik, and Juan M. Vaquerizas. “Reply to: Revisiting the Use of Structural Similarity Index in Hi-C.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-023-01595-5."},"article_type":"letter_note","page":"2053-2055","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14689","title":"Reply to: Revisiting the use of structural similarity index in Hi-C","status":"public","intvolume":" 55","issue":"12","type":"journal_article","doi":"10.1038/s41588-023-01595-5","language":[{"iso":"eng"}],"external_id":{"pmid":["38052961"]},"quality_controlled":"1","month":"12","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"author":[{"full_name":"Ing-Simmons, Elizabeth","first_name":"Elizabeth","last_name":"Ing-Simmons"},{"full_name":"Machnik, Nick N","last_name":"Machnik","first_name":"Nick N","orcid":"0000-0001-6617-9742","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Juan M.","last_name":"Vaquerizas","full_name":"Vaquerizas, Juan M."}],"date_updated":"2023-12-18T08:51:38Z","date_created":"2023-12-17T23:00:53Z","volume":55,"year":"2023","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"MaRo"}]},{"type":"journal_article","author":[{"first_name":"Lynden A.","last_name":"Archer","full_name":"Archer, Lynden A."},{"last_name":"Bruce","first_name":"Peter G.","full_name":"Bruce, Peter G."},{"first_name":"Ernesto J.","last_name":"Calvo","full_name":"Calvo, Ernesto J."},{"last_name":"Dewar","first_name":"Daniel","full_name":"Dewar, Daniel"},{"full_name":"Ellison, James H. J.","first_name":"James H. J.","last_name":"Ellison"},{"last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Gao, Xiangwen","last_name":"Gao","first_name":"Xiangwen"},{"full_name":"Hardwick, Laurence J.","first_name":"Laurence J.","last_name":"Hardwick"},{"last_name":"Horwitz","first_name":"Gabriela","full_name":"Horwitz, Gabriela"},{"first_name":"Jürgen","last_name":"Janek","full_name":"Janek, Jürgen"},{"full_name":"Johnson, Lee R.","first_name":"Lee R.","last_name":"Johnson"},{"first_name":"Jack W.","last_name":"Jordan","full_name":"Jordan, Jack W."},{"last_name":"Matsuda","first_name":"Shoichi","full_name":"Matsuda, Shoichi"},{"full_name":"Menkin, Svetlana","last_name":"Menkin","first_name":"Svetlana"},{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","last_name":"Mondal","first_name":"Soumyadip","full_name":"Mondal, Soumyadip"},{"first_name":"Qianyuan","last_name":"Qiu","full_name":"Qiu, Qianyuan"},{"full_name":"Samarakoon, Thukshan","first_name":"Thukshan","last_name":"Samarakoon"},{"last_name":"Temprano","first_name":"Israel","full_name":"Temprano, Israel"},{"full_name":"Uosaki, Kohei","last_name":"Uosaki","first_name":"Kohei"},{"full_name":"Vailaya, Ganesh","first_name":"Ganesh","last_name":"Vailaya"},{"full_name":"Wachsman, Eric D.","last_name":"Wachsman","first_name":"Eric D."},{"last_name":"Wu","first_name":"Yiying","full_name":"Wu, Yiying"},{"full_name":"Ye, Shen","first_name":"Shen","last_name":"Ye"}],"oa_version":"None","date_created":"2023-12-20T10:48:09Z","date_updated":"2023-12-20T11:54:06Z","year":"2023","_id":"14701","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Royal Society of Chemistry","department":[{"_id":"StFr"}],"publication_status":"epub_ahead","title":"Towards practical metal–oxygen batteries: General discussion","status":"public","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"article_processing_charge":"No","month":"12","day":"19","keyword":["Physical and Theoretical Chemistry"],"date_published":"2023-12-19T00:00:00Z","doi":"10.1039/d3fd90062b","language":[{"iso":"eng"}],"citation":{"short":"L.A. Archer, P.G. Bruce, E.J. Calvo, D. Dewar, J.H.J. Ellison, S.A. Freunberger, X. Gao, L.J. Hardwick, G. Horwitz, J. Janek, L.R. Johnson, J.W. Jordan, S. Matsuda, S. Menkin, S. Mondal, Q. Qiu, T. Samarakoon, I. Temprano, K. Uosaki, G. Vailaya, E.D. Wachsman, Y. Wu, S. Ye, Faraday Discussions (2023).","mla":"Archer, Lynden A., et al. “Towards Practical Metal–Oxygen Batteries: General Discussion.” Faraday Discussions, Royal Society of Chemistry, 2023, doi:10.1039/d3fd90062b.","chicago":"Archer, Lynden A., Peter G. Bruce, Ernesto J. Calvo, Daniel Dewar, James H. J. Ellison, Stefan Alexander Freunberger, Xiangwen Gao, et al. “Towards Practical Metal–Oxygen Batteries: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3fd90062b.","ama":"Archer LA, Bruce PG, Calvo EJ, et al. Towards practical metal–oxygen batteries: General discussion. Faraday Discussions. 2023. doi:10.1039/d3fd90062b","ieee":"L. A. Archer et al., “Towards practical metal–oxygen batteries: General discussion,” Faraday Discussions. Royal Society of Chemistry, 2023.","apa":"Archer, L. A., Bruce, P. G., Calvo, E. J., Dewar, D., Ellison, J. H. J., Freunberger, S. A., … Ye, S. (2023). Towards practical metal–oxygen batteries: General discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/d3fd90062b","ista":"Archer LA, Bruce PG, Calvo EJ, Dewar D, Ellison JHJ, Freunberger SA, Gao X, Hardwick LJ, Horwitz G, Janek J, Johnson LR, Jordan JW, Matsuda S, Menkin S, Mondal S, Qiu Q, Samarakoon T, Temprano I, Uosaki K, Vailaya G, Wachsman ED, Wu Y, Ye S. 2023. Towards practical metal–oxygen batteries: General discussion. Faraday Discussions."},"publication":"Faraday Discussions","article_type":"review","quality_controlled":"1"},{"author":[{"first_name":"Gary A.","last_name":"Attard","full_name":"Attard, Gary A."},{"first_name":"Ernesto J.","last_name":"Calvo","full_name":"Calvo, Ernesto J."},{"first_name":"Larry A.","last_name":"Curtiss","full_name":"Curtiss, Larry A."},{"last_name":"Dewar","first_name":"Daniel","full_name":"Dewar, Daniel"},{"full_name":"Ellison, James H. J.","last_name":"Ellison","first_name":"James H. J."},{"full_name":"Gao, Xiangwen","last_name":"Gao","first_name":"Xiangwen"},{"last_name":"Grey","first_name":"Clare P.","full_name":"Grey, Clare P."},{"first_name":"Laurence J.","last_name":"Hardwick","full_name":"Hardwick, Laurence J."},{"full_name":"Horwitz, Gabriela","last_name":"Horwitz","first_name":"Gabriela"},{"full_name":"Janek, Juergen","first_name":"Juergen","last_name":"Janek"},{"first_name":"Lee R.","last_name":"Johnson","full_name":"Johnson, Lee R."},{"last_name":"Jordan","first_name":"Jack W.","full_name":"Jordan, Jack W."},{"full_name":"Matsuda, Shoichi","last_name":"Matsuda","first_name":"Shoichi"},{"last_name":"Mondal","first_name":"Soumyadip","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","full_name":"Mondal, Soumyadip"},{"first_name":"Alex R.","last_name":"Neale","full_name":"Neale, Alex R."},{"full_name":"Ortiz-Vitoriano, Nagore","last_name":"Ortiz-Vitoriano","first_name":"Nagore"},{"first_name":"Israel","last_name":"Temprano","full_name":"Temprano, Israel"},{"full_name":"Vailaya, Ganesh","first_name":"Ganesh","last_name":"Vailaya"},{"full_name":"Wachsman, Eric D.","first_name":"Eric D.","last_name":"Wachsman"},{"full_name":"Wang, Hsien-Hau","last_name":"Wang","first_name":"Hsien-Hau"},{"full_name":"Wu, Yiying","last_name":"Wu","first_name":"Yiying"},{"first_name":"Shen","last_name":"Ye","full_name":"Ye, Shen"}],"oa_version":"None","date_created":"2023-12-20T10:49:43Z","date_updated":"2023-12-20T11:58:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14702","year":"2023","publisher":"Royal Society of Chemistry","department":[{"_id":"StFr"}],"status":"public","title":"Materials for stable metal–oxygen battery cathodes: general discussion","publication_status":"epub_ahead","type":"journal_article","date_published":"2023-12-18T00:00:00Z","doi":"10.1039/d3fd90059b","language":[{"iso":"eng"}],"citation":{"mla":"Attard, Gary A., et al. “Materials for Stable Metal–Oxygen Battery Cathodes: General Discussion.” Faraday Discussions, Royal Society of Chemistry, 2023, doi:10.1039/d3fd90059b.","short":"G.A. Attard, E.J. Calvo, L.A. Curtiss, D. Dewar, J.H.J. Ellison, X. Gao, C.P. Grey, L.J. Hardwick, G. Horwitz, J. Janek, L.R. Johnson, J.W. Jordan, S. Matsuda, S. Mondal, A.R. Neale, N. Ortiz-Vitoriano, I. Temprano, G. Vailaya, E.D. Wachsman, H.-H. Wang, Y. Wu, S. Ye, Faraday Discussions (2023).","chicago":"Attard, Gary A., Ernesto J. Calvo, Larry A. Curtiss, Daniel Dewar, James H. J. Ellison, Xiangwen Gao, Clare P. Grey, et al. “Materials for Stable Metal–Oxygen Battery Cathodes: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3fd90059b.","ama":"Attard GA, Calvo EJ, Curtiss LA, et al. Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions. 2023. doi:10.1039/d3fd90059b","ista":"Attard GA, Calvo EJ, Curtiss LA, Dewar D, Ellison JHJ, Gao X, Grey CP, Hardwick LJ, Horwitz G, Janek J, Johnson LR, Jordan JW, Matsuda S, Mondal S, Neale AR, Ortiz-Vitoriano N, Temprano I, Vailaya G, Wachsman ED, Wang H-H, Wu Y, Ye S. 2023. Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions.","apa":"Attard, G. A., Calvo, E. J., Curtiss, L. A., Dewar, D., Ellison, J. H. J., Gao, X., … Ye, S. (2023). Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/d3fd90059b","ieee":"G. A. Attard et al., “Materials for stable metal–oxygen battery cathodes: general discussion,” Faraday Discussions. Royal Society of Chemistry, 2023."},"publication":"Faraday Discussions","article_type":"review","quality_controlled":"1","publication_identifier":{"eissn":["1364-5498"],"issn":["1359-6640"]},"article_processing_charge":"No","month":"12","day":"18","keyword":["Physical and Theoretical Chemistry"]},{"month":"09","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-41173-1","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001087583700008"],"pmid":["37704612"]},"oa":1,"file_date_updated":"2023-09-25T08:22:58Z","article_number":"5644","date_created":"2023-09-24T22:01:10Z","date_updated":"2023-12-21T14:30:01Z","volume":14,"author":[{"last_name":"Sitarska","first_name":"Ewa","full_name":"Sitarska, Ewa"},{"first_name":"Silvia Dias","last_name":"Almeida","full_name":"Almeida, Silvia Dias"},{"last_name":"Beckwith","first_name":"Marianne Sandvold","full_name":"Beckwith, Marianne Sandvold"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A"},{"last_name":"Czuchnowski","first_name":"Jakub","full_name":"Czuchnowski, Jakub"},{"last_name":"Siggel","first_name":"Marc","full_name":"Siggel, Marc"},{"full_name":"Roessner, Rita","last_name":"Roessner","first_name":"Rita"},{"full_name":"Tschanz, Aline","last_name":"Tschanz","first_name":"Aline"},{"full_name":"Ejsing, Christer","first_name":"Christer","last_name":"Ejsing"},{"first_name":"Yannick","last_name":"Schwab","full_name":"Schwab, Yannick"},{"full_name":"Kosinski, Jan","first_name":"Jan","last_name":"Kosinski"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"last_name":"Kreshuk","first_name":"Anna","full_name":"Kreshuk, Anna"},{"first_name":"Anna","last_name":"Erzberger","full_name":"Erzberger, Anna"},{"first_name":"Alba","last_name":"Diz-Muñoz","full_name":"Diz-Muñoz, Alba"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14697"}]},"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL.","pmid":1,"day":"13","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2023-09-13T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"chicago":"Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41173-1.","short":"E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).","mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” Nature Communications, vol. 14, 5644, Springer Nature, 2023, doi:10.1038/s41467-023-41173-1.","apa":"Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41173-1","ieee":"E. Sitarska et al., “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” Nature Communications, vol. 14. Springer Nature, 2023.","ista":"Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644.","ama":"Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 2023;14. doi:10.1038/s41467-023-41173-1"},"abstract":[{"lang":"eng","text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment."}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2725421,"creator":"dernst","access_level":"open_access","file_name":"2023_NatureComm_Sitarska.pdf","checksum":"ad670e3b3c64fc585675948370f6b149","success":1,"date_updated":"2023-09-25T08:22:58Z","date_created":"2023-09-25T08:22:58Z","relation":"main_file","file_id":"14365"}],"ddc":["570"],"status":"public","title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles","intvolume":" 14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14360"},{"volume":8,"date_updated":"2023-12-21T14:30:01Z","date_created":"2023-09-06T08:07:51Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"14279"},{"status":"public","relation":"dissertation_contains","id":"14697"}]},"author":[{"full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko","first_name":"Jonna H"},{"orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","first_name":"Mehmet C","full_name":"Ucar, Mehmet C"},{"full_name":"Canigova, Nikola","first_name":"Nikola","last_name":"Canigova","id":"3795523E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8518-5926"},{"last_name":"Stopp","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A"},{"full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Schwarz"},{"full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K"}],"publisher":"American Association for the Advancement of Science","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","ec_funded":1,"article_number":"adc9584","language":[{"iso":"eng"}],"doi":"10.1126/sciimmunol.adc9584","project":[{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients"},{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/sciimmunol.adc9584"}],"external_id":{"pmid":["37656776"],"isi":["001062110600003"]},"publication_identifier":{"issn":["2470-9468"]},"month":"09","oa_version":"Published Version","intvolume":" 8","title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14274","issue":"87","abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"type":"journal_article","date_published":"2023-09-01T00:00:00Z","article_type":"original","citation":{"ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. American Association for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584","ieee":"J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” Science Immunology, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 2023;8(87). doi:10.1126/sciimmunol.adc9584","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023)."},"publication":"Science Immunology","article_processing_charge":"No","day":"01","keyword":["General Medicine","Immunology"],"scopus_import":"1"},{"_id":"14697","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function","ddc":["570"],"oa_version":"Published Version","file":[{"checksum":"457927165d5d556305d3086f6b83e5c7","date_created":"2023-12-20T09:35:34Z","date_updated":"2023-12-20T09:35:34Z","file_id":"14699","embargo":"2024-12-20","relation":"main_file","creator":"jstopp","content_type":"application/pdf","file_size":51585778,"access_level":"closed","file_name":"Thesis.pdf","embargo_to":"open_access"},{"access_level":"closed","file_name":"Thesis.docx","file_size":69625950,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"jstopp","relation":"source_file","file_id":"14700","checksum":"e8d26449ac461f5e8478a62c9507506f","date_updated":"2023-12-20T10:41:42Z","date_created":"2023-12-20T09:35:35Z"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"citation":{"apa":"Stopp, J. A. (2023). Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14697","ieee":"J. A. Stopp, “Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","ista":"Stopp JA. 2023. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","ama":"Stopp JA. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:10.15479/at:ista:14697","chicago":"Stopp, Julian A. “Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14697.","short":"J.A. Stopp, Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","mla":"Stopp, Julian A. Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14697."},"page":"226","date_published":"2023-12-20T00:00:00Z","day":"20","has_accepted_license":"1","article_processing_charge":"No","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"author":[{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A"}],"related_material":{"record":[{"id":"6328","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"7885"},{"id":"12272","status":"public","relation":"part_of_dissertation"},{"id":"14274","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14360"}]},"date_created":"2023-12-18T19:14:28Z","date_updated":"2023-12-21T14:30:02Z","file_date_updated":"2023-12-20T10:41:42Z","ec_funded":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"doi":"10.15479/at:ista:14697","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"supervisor":[{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"month":"12","publication_identifier":{"isbn":["978-3-99078-038-1"],"issn":["2663 - 337X"]}},{"date_published":"2023-12-12T00:00:00Z","page":"96","citation":{"short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","mla":"Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14651.","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14651.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","apa":"Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria."},"day":"12","has_accepted_license":"1","article_processing_charge":"No","file":[{"relation":"main_file","file_id":"14684","checksum":"520bdb61e95e66070e02824947d2c5fa","success":1,"date_created":"2023-12-13T15:37:55Z","date_updated":"2023-12-13T15:37:55Z","access_level":"open_access","file_name":"Phd_Thesis_LA.pdf","content_type":"application/pdf","file_size":34101468,"creator":"larathoo"},{"date_created":"2023-12-13T15:42:23Z","date_updated":"2023-12-14T08:58:18Z","checksum":"d8e59afd0817c98fba2564a264508e5c","file_id":"14685","relation":"source_file","creator":"larathoo","file_size":31052872,"content_type":"application/zip","file_name":"Phd_Thesis_LA.zip","access_level":"closed"},{"file_id":"14681","relation":"supplementary_material","checksum":"9a778c949932286f4519e1f1fca2820d","date_updated":"2023-12-14T08:58:18Z","date_created":"2023-12-11T19:24:59Z","access_level":"closed","file_name":"Supplementary_Materials.zip","creator":"larathoo","content_type":"application/zip","file_size":10713896}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","_id":"14651","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","degree_awarded":"PhD","supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14651","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"oa":1,"month":"12","publication_identifier":{"issn":["2663 - 337X"]},"date_created":"2023-12-11T19:30:37Z","date_updated":"2023-12-22T11:04:45Z","author":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","first_name":"Louise S","last_name":"Arathoon","full_name":"Arathoon, Louise S"}],"related_material":{"record":[{"id":"11411","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","year":"2023","file_date_updated":"2023-12-14T08:58:18Z","ec_funded":1},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"14703","acknowledgement":"The authors would like to thank Chris Wojtan for his continuous support and several interesting discussions. Part of this research was performed during two visits: one of SI to the BIDSA research center at Bocconi University, and one of HL to the Institute of Science and Technology Austria. Both host institutions are warmly acknowledged for the hospital-\r\nity. HL is partially supported by the MUR-Prin 2022-202244A7YL “Gradient Flows and Non-Smooth Geometric Structures with Applications to Optimization and Machine Learning”, funded by the European Union - Next Generation EU. SI is supported in part by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council.","year":"2023","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publication_status":"submitted","status":"public","title":"Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation","author":[{"id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige","last_name":"Ishida","full_name":"Ishida, Sadashige"},{"last_name":"Lavenant","first_name":"Hugo","full_name":"Lavenant, Hugo"}],"oa_version":"Preprint","date_created":"2023-12-21T10:14:37Z","date_updated":"2023-12-27T13:44:33Z","type":"preprint","article_number":"2312.12213","abstract":[{"lang":"eng","text":"We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.12213","open_access":"1"}],"external_id":{"arxiv":["2312.12213"]},"citation":{"chicago":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2312.12213.","mla":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, 2312.12213, doi:10.48550/arXiv.2312.12213.","short":"S. Ishida, H. Lavenant, ArXiv (n.d.).","ista":"Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv, 2312.12213.","apa":"Ishida, S., & Lavenant, H. (n.d.). Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. https://doi.org/10.48550/arXiv.2312.12213","ieee":"S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” arXiv. .","ama":"Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. doi:10.48550/arXiv.2312.12213"},"oa":1,"publication":"arXiv","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"date_published":"2023-12-19T00:00:00Z","doi":"10.48550/arXiv.2312.12213","language":[{"iso":"eng"}],"keyword":["Optimal transport","Hamilton-Jacobi equation","convex optimization"],"article_processing_charge":"No","month":"12","day":"19"},{"issue":"1","abstract":[{"lang":"eng","text":"Background: Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature.\r\n\r\nResults: In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models’ performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics.\r\n\r\nConclusions: Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers."}],"type":"journal_article","file":[{"file_id":"14723","relation":"main_file","date_created":"2024-01-02T09:09:32Z","date_updated":"2024-01-02T09:09:32Z","success":1,"checksum":"7ff5e95f3496ff663301eb4a13a316d5","file_name":"2023_BMCMicrobiology_Yurtseven.pdf","access_level":"open_access","creator":"dernst","file_size":1979922,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"14716","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 23","ddc":["570"],"title":"Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis","status":"public","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","date_published":"2023-12-01T00:00:00Z","citation":{"short":"A. Yurtseven, S. Buyanova, A.A.A. Agrawal, O. Bochkareva, O.V.V. Kalinina, BMC Microbiology 23 (2023).","mla":"Yurtseven, Alper, et al. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.” BMC Microbiology, vol. 23, no. 1, 404, Springer Nature, 2023, doi:10.1186/s12866-023-03147-7.","chicago":"Yurtseven, Alper, Sofia Buyanova, Amay Ajaykumar A. Agrawal, Olga Bochkareva, and Olga V V. Kalinina. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.” BMC Microbiology. Springer Nature, 2023. https://doi.org/10.1186/s12866-023-03147-7.","ama":"Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 2023;23(1). doi:10.1186/s12866-023-03147-7","apa":"Yurtseven, A., Buyanova, S., Agrawal, A. A. A., Bochkareva, O., & Kalinina, O. V. V. (2023). Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. Springer Nature. https://doi.org/10.1186/s12866-023-03147-7","ieee":"A. Yurtseven, S. Buyanova, A. A. A. Agrawal, O. Bochkareva, and O. V. V. Kalinina, “Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis,” BMC Microbiology, vol. 23, no. 1. Springer Nature, 2023.","ista":"Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. 2023. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 23(1), 404."},"publication":"BMC Microbiology","article_type":"original","file_date_updated":"2024-01-02T09:09:32Z","article_number":"404","author":[{"last_name":"Yurtseven","first_name":"Alper","full_name":"Yurtseven, Alper"},{"id":"2F54A7BC-3902-11EA-AC87-BC9F3DDC885E","first_name":"Sofia","last_name":"Buyanova","full_name":"Buyanova, Sofia"},{"first_name":"Amay Ajaykumar A.","last_name":"Agrawal","full_name":"Agrawal, Amay Ajaykumar A."},{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"full_name":"Kalinina, Olga V V.","last_name":"Kalinina","first_name":"Olga V V."}],"volume":23,"date_updated":"2024-01-02T09:20:57Z","date_created":"2023-12-31T23:01:02Z","pmid":1,"year":"2023","acknowledgement":"Open Access funding enabled and organized by Projekt DEAL. A.Y. and O.V.K. acknowledge financial support from the Klaus Faber Foundation. A.A.A. was funded by the Helmholtz AI project AMR-XAI. The work of O.O.B. is funded by Fonds zur Förderung der Wissenschaftlichen Forschung (FWF), Grant ESP 253-B.","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"eissn":["1471-2180"]},"month":"12","doi":"10.1186/s12866-023-03147-7","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38124060"]},"quality_controlled":"1"},{"type":"conference","abstract":[{"lang":"eng","text":"Binary decision diagrams (BDDs) are one of the fundamental data structures in formal methods and computer science in general. However, the performance of BDD-based algorithms greatly depends on memory latency due to the reliance on large hash tables and thus, by extension, on the speed of random memory access. This hinders the full utilisation of resources available on modern CPUs, since the absolute memory latency has not improved significantly for at least a decade. In this paper, we explore several implementation techniques that improve the performance of BDD manipulation either through enhanced memory locality or by partially eliminating random memory access. On a benchmark suite of 600+ BDDs derived from real-world applications, we demonstrate runtime that is comparable or better than parallelising the same operations on eight CPU cores. "}],"title":"Binary decision diagrams on modern hardware","ddc":["000"],"status":"public","_id":"14718","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","file_size":524321,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_FMCAD_Pastva.pdf","success":1,"checksum":"818d6e13dd508f3a04f0941081022e5d","date_created":"2024-01-02T08:14:23Z","date_updated":"2024-01-02T08:14:23Z","file_id":"14721","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"122-131","citation":{"chicago":"Pastva, Samuel, and Thomas A Henzinger. “Binary Decision Diagrams on Modern Hardware.” In Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, 122–31. TU Vienna Academic Press, 2023. https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20.","mla":"Pastva, Samuel, and Thomas A. Henzinger. “Binary Decision Diagrams on Modern Hardware.” Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, TU Vienna Academic Press, 2023, pp. 122–31, doi:10.34727/2023/isbn.978-3-85448-060-0_20.","short":"S. Pastva, T.A. Henzinger, in:, Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, TU Vienna Academic Press, 2023, pp. 122–131.","ista":"Pastva S, Henzinger TA. 2023. Binary decision diagrams on modern hardware. Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design. FMCAD: Conference on Formal Methods in Computer-aided design, 122–131.","apa":"Pastva, S., & Henzinger, T. A. (2023). Binary decision diagrams on modern hardware. In Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design (pp. 122–131). Ames, IA, United States: TU Vienna Academic Press. https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20","ieee":"S. Pastva and T. A. Henzinger, “Binary decision diagrams on modern hardware,” in Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, Ames, IA, United States, 2023, pp. 122–131.","ama":"Pastva S, Henzinger TA. Binary decision diagrams on modern hardware. In: Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design. TU Vienna Academic Press; 2023:122-131. doi:10.34727/2023/isbn.978-3-85448-060-0_20"},"publication":"Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design","date_published":"2023-10-01T00:00:00Z","ec_funded":1,"file_date_updated":"2024-01-02T08:14:23Z","publisher":"TU Vienna Academic Press","department":[{"_id":"ToHe"}],"publication_status":"published","acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413 and the\r\n“VAMOS” grant ERC-2020-AdG 101020093.","year":"2023","date_created":"2023-12-31T23:01:03Z","date_updated":"2024-01-02T08:16:28Z","author":[{"first_name":"Samuel","last_name":"Pastva","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","orcid":"0000-0003-1993-0331","full_name":"Pastva, Samuel"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"publication_identifier":{"isbn":["9783854480600"]},"month":"10","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.34727/2023/isbn.978-3-85448-060-0_20","conference":{"location":"Ames, IA, United States","start_date":"2023-10-25","end_date":"2023-10-27","name":"FMCAD: Conference on Formal Methods in Computer-aided design"}},{"language":[{"iso":"eng"}],"doi":"10.1093/qmath/haad008","quality_controlled":"1","project":[{"_id":"26A8D266-B435-11E9-9278-68D0E5697425","grant_number":"EP-P026710-2","name":"Between rational and integral points"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2012.04508"]},"oa":1,"month":"12","publication_identifier":{"eissn":["1464-3847"],"issn":["0033-5606"]},"date_updated":"2024-01-02T07:39:55Z","date_created":"2023-12-31T23:01:03Z","volume":74,"author":[{"id":"C8B7BF48-8D81-11E9-BCA9-F536E6697425","first_name":"Tal","last_name":"Horesh","full_name":"Horesh, Tal"},{"last_name":"Karasik","first_name":"Yakov","full_name":"Karasik, Yakov"}],"publication_status":"published","department":[{"_id":"TiBr"}],"publisher":"Oxford University Press","year":"2023","acknowledgement":"This work was done when both authors were visiting Institute of Science and Technology (IST) Austria. T.H. was being supported by Engineering and Physical Sciences Research Council grant EP/P026710/1. Y.K. had a great time there and is grateful for the hospitality. The appendix to this paper is largely based on a mini course T.H. had given at IST in February 2020.","file_date_updated":"2024-01-02T07:37:09Z","date_published":"2023-12-01T00:00:00Z","article_type":"original","page":"1253-1294","publication":"Quarterly Journal of Mathematics","citation":{"short":"T. Horesh, Y. Karasik, Quarterly Journal of Mathematics 74 (2023) 1253–1294.","mla":"Horesh, Tal, and Yakov Karasik. “Equidistribution of Primitive Lattices in ℝn.” Quarterly Journal of Mathematics, vol. 74, no. 4, Oxford University Press, 2023, pp. 1253–94, doi:10.1093/qmath/haad008.","chicago":"Horesh, Tal, and Yakov Karasik. “Equidistribution of Primitive Lattices in ℝn.” Quarterly Journal of Mathematics. Oxford University Press, 2023. https://doi.org/10.1093/qmath/haad008.","ama":"Horesh T, Karasik Y. Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. 2023;74(4):1253-1294. doi:10.1093/qmath/haad008","apa":"Horesh, T., & Karasik, Y. (2023). Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haad008","ieee":"T. Horesh and Y. Karasik, “Equidistribution of primitive lattices in ℝn,” Quarterly Journal of Mathematics, vol. 74, no. 4. Oxford University Press, pp. 1253–1294, 2023.","ista":"Horesh T, Karasik Y. 2023. Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. 74(4), 1253–1294."},"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":724748,"creator":"dernst","access_level":"open_access","file_name":"2023_QuarterlyJourMath_Horesh.pdf","checksum":"bf29baa9eae8500f3374dbcb80712687","success":1,"date_created":"2024-01-02T07:37:09Z","date_updated":"2024-01-02T07:37:09Z","relation":"main_file","file_id":"14720"}],"ddc":["510"],"title":"Equidistribution of primitive lattices in ℝn","status":"public","intvolume":" 74","_id":"14717","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We count primitive lattices of rank d inside Zn as their covolume tends to infinity, with respect to certain parameters of such lattices. These parameters include, for example, the subspace that a lattice spans, namely its projection to the Grassmannian; its homothety class and its equivalence class modulo rescaling and rotation, often referred to as a shape. We add to a prior work of Schmidt by allowing sets in the spaces of parameters that are general enough to conclude the joint equidistribution of these parameters. In addition to the primitive d-lattices Λ themselves, we also consider their orthogonal complements in Zn, A1, and show that the equidistribution occurs jointly for Λ and A1. Finally, our asymptotic formulas for the number of primitive lattices include an explicit bound on the error term."}],"issue":"4","type":"journal_article"},{"author":[{"first_name":"Hamid","last_name":"Mollania","full_name":"Mollania, Hamid"},{"full_name":"Zhang, Chaoqi","first_name":"Chaoqi","last_name":"Zhang"},{"full_name":"Du, Ruifeng","last_name":"Du","first_name":"Ruifeng"},{"full_name":"Qi, Xueqiang","first_name":"Xueqiang","last_name":"Qi"},{"last_name":"Li","first_name":"Junshan","full_name":"Li, Junshan"},{"last_name":"Horta","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","full_name":"Horta, Sharona"},{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"full_name":"Keller, Caroline","first_name":"Caroline","last_name":"Keller"},{"full_name":"Chenevier, Pascale","last_name":"Chenevier","first_name":"Pascale"},{"full_name":"Oloomi-Buygi, Majid","first_name":"Majid","last_name":"Oloomi-Buygi"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"date_created":"2023-12-31T23:01:03Z","date_updated":"2024-01-02T08:35:06Z","volume":15,"acknowledgement":"The authors acknowledge the support from the 2BoSS project of the ERA-MIN3 program with the Spanish grant number PCI2022-132985/AEI/10.13039/501100011033 and the French grant number ANR-22-MIN3-0003-01. J.L. acknowledges the support from the Natural Science Foundation of Sichuan Province 2022NSFSC1229. The authors acknowledge the funding from Generalitat de Catalunya 2021 SGR 01581 and European Union NextGenerationEU/PRTR. This research was supported by the Scientific Service Units (SSU) of ISTA Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF).","year":"2023","publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"doi":"10.1021/acsami.3c14072","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"quality_controlled":"1","month":"12","publication_identifier":{"eissn":["1944-8252"],"issn":["1944-8244"]},"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14719","status":"public","title":"Nanostructured Li₂S cathodes for silicon-sulfur batteries","intvolume":" 15","abstract":[{"lang":"eng","text":"Lithium–sulfur batteries are regarded as an advantageous option for meeting the growing demand for high-energy-density storage, but their commercialization relies on solving the current limitations of both sulfur cathodes and lithium metal anodes. In this scenario, the implementation of lithium sulfide (Li2S) cathodes compatible with alternative anode materials such as silicon has the potential to alleviate the safety concerns associated with lithium metal. In this direction, here, we report a sulfur cathode based on Li2S nanocrystals grown on a catalytic host consisting of CoFeP nanoparticles supported on tubular carbon nitride. Nanosized Li2S is incorporated into the host by a scalable liquid infiltration–evaporation method. Theoretical calculations and experimental results demonstrate that the CoFeP–CN composite can boost the polysulfide adsorption/conversion reaction kinetics and strongly reduce the initial overpotential activation barrier by stretching the Li–S bonds of Li2S. Besides, the ultrasmall size of the Li2S particles in the Li2S–CoFeP–CN composite cathode facilitates the initial activation. Overall, the Li2S–CoFeP–CN electrodes exhibit a low activation barrier of 2.56 V, a high initial capacity of 991 mA h gLi2S–1, and outstanding cyclability with a small fading rate of 0.029% per cycle over 800 cycles. Moreover, Si/Li2S full cells are assembled using the nanostructured Li2S–CoFeP–CN cathode and a prelithiated anode based on graphite-supported silicon nanowires. These Si/Li2S cells demonstrate high initial discharge capacities above 900 mA h gLi2S–1 and good cyclability with a capacity fading rate of 0.28% per cycle over 150 cycles."}],"issue":"50","type":"journal_article","date_published":"2023-12-05T00:00:00Z","publication":"ACS Applied Materials and Interfaces","citation":{"ieee":"H. Mollania et al., “Nanostructured Li₂S cathodes for silicon-sulfur batteries,” ACS Applied Materials and Interfaces, vol. 15, no. 50. American Chemical Society, pp. 58462–58475, 2023.","apa":"Mollania, H., Zhang, C., Du, R., Qi, X., Li, J., Horta, S., … Cabot, A. (2023). Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c14072","ista":"Mollania H, Zhang C, Du R, Qi X, Li J, Horta S, Ibáñez M, Keller C, Chenevier P, Oloomi-Buygi M, Cabot A. 2023. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 15(50), 58462–58475.","ama":"Mollania H, Zhang C, Du R, et al. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 2023;15(50):58462–58475. doi:10.1021/acsami.3c14072","chicago":"Mollania, Hamid, Chaoqi Zhang, Ruifeng Du, Xueqiang Qi, Junshan Li, Sharona Horta, Maria Ibáñez, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” ACS Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c14072.","short":"H. Mollania, C. Zhang, R. Du, X. Qi, J. Li, S. Horta, M. Ibáñez, C. Keller, P. Chenevier, M. Oloomi-Buygi, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 58462–58475.","mla":"Mollania, Hamid, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” ACS Applied Materials and Interfaces, vol. 15, no. 50, American Chemical Society, 2023, pp. 58462–58475, doi:10.1021/acsami.3c14072."},"article_type":"original","page":"58462–58475","day":"05","article_processing_charge":"No","scopus_import":"1"},{"date_published":"2023-12-01T00:00:00Z","citation":{"ama":"Mitrouskas DJ, Pickl P. Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. 2023;64(12). doi:10.1063/5.0172199","ista":"Mitrouskas DJ, Pickl P. 2023. Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. 64(12), 121901.","ieee":"D. J. Mitrouskas and P. Pickl, “Exponential decay of the number of excitations in the weakly interacting Bose gas,” Journal of Mathematical Physics, vol. 64, no. 12. AIP Publishing, 2023.","apa":"Mitrouskas, D. J., & Pickl, P. (2023). Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0172199","mla":"Mitrouskas, David Johannes, and Peter Pickl. “Exponential Decay of the Number of Excitations in the Weakly Interacting Bose Gas.” Journal of Mathematical Physics, vol. 64, no. 12, 121901, AIP Publishing, 2023, doi:10.1063/5.0172199.","short":"D.J. Mitrouskas, P. Pickl, Journal of Mathematical Physics 64 (2023).","chicago":"Mitrouskas, David Johannes, and Peter Pickl. “Exponential Decay of the Number of Excitations in the Weakly Interacting Bose Gas.” Journal of Mathematical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0172199."},"publication":"Journal of Mathematical Physics","article_type":"original","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"file_size":4346922,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_JourMathPhysics_Mitrouskas.pdf","checksum":"66572f718a36465576cf0d6b3f7e01fc","success":1,"date_created":"2024-01-02T08:45:07Z","date_updated":"2024-01-02T08:45:07Z","relation":"main_file","file_id":"14722"}],"_id":"14715","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 64","title":"Exponential decay of the number of excitations in the weakly interacting Bose gas","ddc":["510"],"status":"public","issue":"12","abstract":[{"text":"We consider N trapped bosons in the mean-field limit with coupling constant λN = 1/(N − 1). The ground state of such systems exhibits Bose–Einstein condensation. We prove that the probability of finding ℓ particles outside the condensate wave function decays exponentially in ℓ.","lang":"eng"}],"type":"journal_article","doi":"10.1063/5.0172199","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2307.11062"]},"oa":1,"quality_controlled":"1","publication_identifier":{"eissn":["1089-7658"],"issn":["0022-2488"]},"month":"12","author":[{"id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes"},{"full_name":"Pickl, Peter","first_name":"Peter","last_name":"Pickl"}],"volume":64,"date_created":"2023-12-31T23:01:02Z","date_updated":"2024-01-02T08:51:28Z","acknowledgement":"We thank Lea Boßmann, Phan Thành Nam and Simone Rademacher for helpful remarks. P.P. acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Grant No. SFB/TRR 352 “Mathematics of Many-Body Quantum Systems and Their Collective Phenomena.”","year":"2023","department":[{"_id":"RoSe"}],"publisher":"AIP Publishing","publication_status":"published","file_date_updated":"2024-01-02T08:45:07Z","article_number":"121901"},{"publication":"ACM Transactions on Graphics","citation":{"chicago":"Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations with Dispersive Surface Waves.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3592098.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 42 (2023).","mla":"Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations with Dispersive Surface Waves.” ACM Transactions on Graphics, vol. 42, no. 4, 83, Association for Computing Machinery, 2023, doi:10.1145/3592098.","apa":"Jeschke, S., & Wojtan, C. (2023). Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3592098","ieee":"S. Jeschke and C. Wojtan, “Generalizing shallow water simulations with dispersive surface waves,” ACM Transactions on Graphics, vol. 42, no. 4. Association for Computing Machinery, 2023.","ista":"Jeschke S, Wojtan C. 2023. Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. 42(4), 83.","ama":"Jeschke S, Wojtan C. Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. 2023;42(4). doi:10.1145/3592098"},"article_type":"original","date_published":"2023-08-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14240","status":"public","title":"Generalizing shallow water simulations with dispersive surface waves","ddc":["000"],"intvolume":" 42","oa_version":"Published Version","file":[{"file_id":"14704","relation":"main_file","date_updated":"2023-12-21T12:26:40Z","date_created":"2023-12-21T12:26:40Z","success":1,"checksum":"1d178bb2f8011d9f5aedda6427e18c7a","file_name":"PaperVideo_final.mp4","access_level":"open_access","creator":"sjeschke","content_type":"video/mp4","file_size":511572575},{"access_level":"open_access","file_name":"2023_ACMToG_Jeschke.pdf","creator":"dernst","content_type":"application/pdf","file_size":7469177,"file_id":"14725","relation":"main_file","success":1,"checksum":"a49b2e744d5cd1276bb8b2e0ce6dc638","date_created":"2024-01-02T09:34:27Z","date_updated":"2024-01-02T09:34:27Z"}],"type":"journal_article","abstract":[{"text":"This paper introduces a novel method for simulating large bodies of water as a height field. At the start of each time step, we partition the waves into a bulk flow (which approximately satisfies the assumptions of the shallow water equations) and surface waves (which approximately satisfy the assumptions of Airy wave theory). We then solve the two wave regimes separately using appropriate state-of-the-art techniques, and re-combine the resulting wave velocities at the end of each step. This strategy leads to the first heightfield wave model capable of simulating complex interactions between both deep and shallow water effects, like the waves from a boat wake sloshing up onto a beach, or a dam break producing wave interference patterns and eddies. We also analyze the numerical dispersion created by our method and derive an exact correction factor for waves at a constant water depth, giving us a numerically perfect re-creation of theoretical water wave dispersion patterns.","lang":"eng"}],"issue":"4","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001044671300049"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"doi":"10.1145/3592098","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"month":"08","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"year":"2023","acknowledgement":"We thank Georg Sperl for helping with early research for this paper, Mickael Ly and Yi-Lu Chen for proofreading, and members of the ISTA Visual Computing Group for general feedback. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).\r\nThe motorboat and sailboat were modeled by Sergei and the palmtrees by YadroGames. The environment map was created by Emil Persson.","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"ChWo"}],"author":[{"first_name":"Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan"},{"first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"date_updated":"2024-01-02T09:35:55Z","date_created":"2023-08-27T22:01:17Z","volume":42,"article_number":"83","file_date_updated":"2024-01-02T09:34:27Z"},{"abstract":[{"lang":"eng","text":"The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells."}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14714","checksum":"fd9e9d527c2691f03fbc24031a75a3b3","success":1,"date_updated":"2023-12-27T08:40:43Z","date_created":"2023-12-27T08:40:43Z","access_level":"open_access","file_name":"2023_NatureComm_Curatolo.pdf","file_size":1342319,"content_type":"application/pdf","creator":"kschuh"}],"_id":"14710","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["530"],"title":"A computational toolbox for the assembly yield of complex and heterogeneous structures","intvolume":" 14","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2023-12-01T00:00:00Z","publication":"Nature Communications","citation":{"ama":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 2023;14. doi:10.1038/s41467-023-43168-4","ista":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. 2023. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 14, 8328.","ieee":"A. I. Curatolo, O. Kimchi, C. P. Goodrich, R. K. Krueger, and M. P. Brenner, “A computational toolbox for the assembly yield of complex and heterogeneous structures,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Curatolo, A. I., Kimchi, O., Goodrich, C. P., Krueger, R. K., & Brenner, M. P. (2023). A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-43168-4","mla":"Curatolo, Agnese I., et al. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications, vol. 14, 8328, Springer Nature, 2023, doi:10.1038/s41467-023-43168-4.","short":"A.I. Curatolo, O. Kimchi, C.P. Goodrich, R.K. Krueger, M.P. Brenner, Nature Communications 14 (2023).","chicago":"Curatolo, Agnese I., Ofer Kimchi, Carl Peter Goodrich, Ryan K. Krueger, and Michael P. Brenner. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-43168-4."},"article_type":"original","file_date_updated":"2023-12-27T08:40:43Z","article_number":"8328","author":[{"full_name":"Curatolo, Agnese I.","last_name":"Curatolo","first_name":"Agnese I."},{"full_name":"Kimchi, Ofer","last_name":"Kimchi","first_name":"Ofer"},{"full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","last_name":"Goodrich"},{"first_name":"Ryan K.","last_name":"Krueger","full_name":"Krueger, Ryan K."},{"last_name":"Brenner","first_name":"Michael P.","full_name":"Brenner, Michael P."}],"date_created":"2023-12-24T23:00:53Z","date_updated":"2024-01-02T11:36:46Z","volume":14,"acknowledgement":"We thank Lucy Colwell for suggesting that we use covariance based methods to predict contacts and Yang Hsia, Scott Boyken, Zibo Chen, and David Baker for collaborations on designed protein complexes. We also thank Ned Wingreen for suggesting the alternative derivation of (11). This research was supported by the Office of Naval Research through ONR N00014-17-1-3029, the Simons Foundation the NSF-Simons Center for Mathematical and Statistical Analysis of Biology at Harvard (award number #1764269), the Peter B. Lewis ’55 Lewis-Sigler Institute/Genomics Fund through the Lewis-Sigler Institute of Integrative Genomics at Princeton University, and the National Science Foundation through the Center for the Physics of Biological Function (PHY-1734030).","year":"2023","publication_status":"published","department":[{"_id":"CaGo"}],"publisher":"Springer Nature","month":"12","publication_identifier":{"eissn":["20411723"]},"doi":"10.1038/s41467-023-43168-4","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1"},{"file_date_updated":"2024-01-02T09:23:57Z","author":[{"last_name":"Del Bianco","first_name":"Marta","full_name":"Del Bianco, Marta"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"first_name":"Lucia","last_name":"Strader","full_name":"Strader, Lucia"},{"last_name":"Kepinski","first_name":"Stefan","full_name":"Kepinski, Stefan"}],"date_created":"2023-12-24T23:00:53Z","date_updated":"2024-01-02T09:29:24Z","volume":74,"year":"2023","pmid":1,"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"month":"12","publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"doi":"10.1093/jxb/erad420","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["38038239"]},"quality_controlled":"1","abstract":[{"text":"Amid the delays due to the global pandemic, in early October 2022, the auxin community gathered in the idyllic peninsula of Cavtat, Croatia. More than 170 scientists from across the world converged to discuss the latest advancements in fundamental and applied research in the field. The topics, from signalling and transport to plant architecture and response to the environment, show how auxin research must bridge from the molecular realm to macroscopic developmental responses. This is mirrored in this collection of reviews, contributed by participants of the Auxin 2022 meeting.","lang":"eng"}],"issue":"22","type":"journal_article","file":[{"date_created":"2024-01-02T09:23:57Z","date_updated":"2024-01-02T09:23:57Z","success":1,"checksum":"f66fb960fd791dea53fd0e087f2fbbe8","file_id":"14724","relation":"main_file","creator":"dernst","file_size":425194,"content_type":"application/pdf","file_name":"2023_JourExperimentalBotany_DelBianco.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"14709","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Auxin research: Creating tools for a greener future","ddc":["580"],"status":"public","intvolume":" 74","day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","date_published":"2023-12-01T00:00:00Z","publication":"Journal of Experimental Botany","citation":{"mla":"Del Bianco, Marta, et al. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany, vol. 74, no. 22, Oxford University Press, 2023, pp. 6889–92, doi:10.1093/jxb/erad420.","short":"M. Del Bianco, J. Friml, L. Strader, S. Kepinski, Journal of Experimental Botany 74 (2023) 6889–6892.","chicago":"Del Bianco, Marta, Jiří Friml, Lucia Strader, and Stefan Kepinski. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany. Oxford University Press, 2023. https://doi.org/10.1093/jxb/erad420.","ama":"Del Bianco M, Friml J, Strader L, Kepinski S. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 2023;74(22):6889-6892. doi:10.1093/jxb/erad420","ista":"Del Bianco M, Friml J, Strader L, Kepinski S. 2023. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 74(22), 6889–6892.","ieee":"M. Del Bianco, J. Friml, L. Strader, and S. Kepinski, “Auxin research: Creating tools for a greener future,” Journal of Experimental Botany, vol. 74, no. 22. Oxford University Press, pp. 6889–6892, 2023.","apa":"Del Bianco, M., Friml, J., Strader, L., & Kepinski, S. (2023). Auxin research: Creating tools for a greener future. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erad420"},"article_type":"original","page":"6889-6892"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1903.06981"]},"oa":1,"quality_controlled":"1","doi":"10.46298/DMTCS.8383","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eissn":["1365-8050"],"issn":["1462-7264"]},"acknowledgement":"This work was begun at the University of Waterloo and was partially supported by the Natural Sciences and Engineering Council of Canada (NSERC).\r\n","year":"2023","publication_status":"published","publisher":"EPI Sciences","department":[{"_id":"KrCh"},{"_id":"HeEd"},{"_id":"UlWa"}],"author":[{"full_name":"Biniaz, Ahmad","first_name":"Ahmad","last_name":"Biniaz"},{"full_name":"Jain, Kshitij","last_name":"Jain","first_name":"Kshitij"},{"full_name":"Lubiw, Anna","last_name":"Lubiw","first_name":"Anna"},{"full_name":"Masárová, Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322","first_name":"Zuzana","last_name":"Masárová"},{"first_name":"Tillmann","last_name":"Miltzow","full_name":"Miltzow, Tillmann"},{"full_name":"Mondal, Debajyoti","first_name":"Debajyoti","last_name":"Mondal"},{"last_name":"Naredla","first_name":"Anurag Murty","full_name":"Naredla, Anurag Murty"},{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"full_name":"Turcotte, Alexi","first_name":"Alexi","last_name":"Turcotte"}],"related_material":{"record":[{"id":"7950","relation":"earlier_version","status":"public"}]},"date_updated":"2024-01-04T12:42:09Z","date_created":"2023-04-16T22:01:08Z","volume":24,"article_number":"9","file_date_updated":"2023-04-17T08:10:28Z","publication":"Discrete Mathematics and Theoretical Computer Science","citation":{"ista":"Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. 2023. Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. 24(2), 9.","ieee":"A. Biniaz et al., “Token swapping on trees,” Discrete Mathematics and Theoretical Computer Science, vol. 24, no. 2. EPI Sciences, 2023.","apa":"Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte, A. (2023). Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. EPI Sciences. https://doi.org/10.46298/DMTCS.8383","ama":"Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. 2023;24(2). doi:10.46298/DMTCS.8383","chicago":"Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” Discrete Mathematics and Theoretical Computer Science. EPI Sciences, 2023. https://doi.org/10.46298/DMTCS.8383.","mla":"Biniaz, Ahmad, et al. “Token Swapping on Trees.” Discrete Mathematics and Theoretical Computer Science, vol. 24, no. 2, 9, EPI Sciences, 2023, doi:10.46298/DMTCS.8383.","short":"A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, Discrete Mathematics and Theoretical Computer Science 24 (2023)."},"article_type":"original","date_published":"2023-01-18T00:00:00Z","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"12833","status":"public","ddc":["000"],"title":"Token swapping on trees","intvolume":" 24","file":[{"file_name":"2022_DMTCS_Biniaz.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2072197,"file_id":"12844","relation":"main_file","date_created":"2023-04-17T08:10:28Z","date_updated":"2023-04-17T08:10:28Z","success":1,"checksum":"439102ea4f6e2aeefd7107dfb9ccf532"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results: 1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan. 2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2. 3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved.","lang":"eng"}],"issue":"2"},{"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ElKo"},{"_id":"GradSch"}],"acknowledgement":"Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N.","year":"2023","date_updated":"2024-01-08T09:28:14Z","date_created":"2024-01-08T09:17:38Z","volume":13950,"author":[{"id":"a20e8902-32b0-11ee-9fa8-b23fa638b793","first_name":"Christos","last_name":"Stefo","full_name":"Stefo, Christos"},{"full_name":"Xiang, Zhuolun","first_name":"Zhuolun","last_name":"Xiang"},{"full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"}],"month":"12","publication_identifier":{"issn":["1611-3349"],"eisbn":["9783031477546"],"eissn":["0302-9743"],"isbn":["9783031477539"]},"quality_controlled":"1","project":[{"_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","grant_number":"F8512","name":"Secure Network and Hardware for Efficient Blockchains"}],"main_file_link":[{"url":"https://eprint.iacr.org/2022/1554","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"FC: Financial Cryptography and Data Security","end_date":"2023-05-05","location":"Bol, Brac, Croatia","start_date":"2023-05-01"},"doi":"10.1007/978-3-031-47754-6_1","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Scaling blockchain protocols to perform on par with the expected needs of Web3.0 has been proven to be a challenging task with almost a decade of research. In the forefront of the current solution is the idea of separating the execution of the updates encoded in a block from the ordering of blocks. In order to achieve this, a new class of protocols called rollups has emerged. Rollups have as input a total ordering of valid and invalid transactions and as output a new valid state-transition.\r\nIf we study rollups from a distributed computing perspective, we uncover that rollups take as input the output of a Byzantine Atomic Broadcast (BAB) protocol and convert it to a State Machine Replication (SMR) protocol. BAB and SMR, however, are considered equivalent as far as distributed computing is concerned and a solution to one can easily be retrofitted to solve the other simply by adding/removing an execution step before the validation of the input.\r\nThis “easy” step of retrofitting an atomic broadcast solution to implement an SMR has, however, been overlooked in practice. In this paper, we formalize the problem and show that after BAB is solved, traditional impossibility results for consensus no longer apply towards an SMR. Leveraging this we propose a distributed execution protocol that allows reduced execution and storage cost per executor (O(log2n/n)) without relaxing the network assumptions of the underlying BAB protocol and providing censorship-resistance. Finally, we propose efficient non-interactive light client constructions that leverage our efficient execution protocols and do not require any synchrony assumptions or expensive ZK-proofs."}],"title":"Executing and proving over dirty ledgers","status":"public","intvolume":" 13950","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14735","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","page":"3-20","publication":"27th International Conference on Financial Cryptography and Data Security","citation":{"ama":"Stefo C, Xiang Z, Kokoris Kogias E. Executing and proving over dirty ledgers. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:3-20. doi:10.1007/978-3-031-47754-6_1","ieee":"C. Stefo, Z. Xiang, and E. Kokoris Kogias, “Executing and proving over dirty ledgers,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 3–20.","apa":"Stefo, C., Xiang, Z., & Kokoris Kogias, E. (2023). Executing and proving over dirty ledgers. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 3–20). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_1","ista":"Stefo C, Xiang Z, Kokoris Kogias E. 2023. Executing and proving over dirty ledgers. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 3–20.","short":"C. Stefo, Z. Xiang, E. Kokoris Kogias, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 3–20.","mla":"Stefo, Christos, et al. “Executing and Proving over Dirty Ledgers.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 3–20, doi:10.1007/978-3-031-47754-6_1.","chicago":"Stefo, Christos, Zhuolun Xiang, and Eleftherios Kokoris Kogias. “Executing and Proving over Dirty Ledgers.” In 27th International Conference on Financial Cryptography and Data Security, 13950:3–20. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_1."},"date_published":"2023-12-01T00:00:00Z"},{"day":"28","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","keyword":["Electrical and Electronic Engineering","Materials Chemistry","Electrochemistry","Energy Engineering and Power Technology","Chemical Engineering (miscellaneous)"],"date_published":"2023-12-28T00:00:00Z","publication":"ACS Applied Energy Materials","citation":{"mla":"Jethwa, Rajesh B., et al. “Exploring the Landscape of Heterocyclic Quinones for Redox Flow Batteries.” ACS Applied Energy Materials, American Chemical Society, 2023, doi:10.1021/acsaem.3c02223.","short":"R.B. Jethwa, D. Hey, R.N. Kerber, A.D. Bond, D.S. Wright, C.P. Grey, ACS Applied Energy Materials (2023).","chicago":"Jethwa, Rajesh B, Dominic Hey, Rachel N. Kerber, Andrew D. Bond, Dominic S. Wright, and Clare P. Grey. “Exploring the Landscape of Heterocyclic Quinones for Redox Flow Batteries.” ACS Applied Energy Materials. American Chemical Society, 2023. https://doi.org/10.1021/acsaem.3c02223.","ama":"Jethwa RB, Hey D, Kerber RN, Bond AD, Wright DS, Grey CP. Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. 2023. doi:10.1021/acsaem.3c02223","ista":"Jethwa RB, Hey D, Kerber RN, Bond AD, Wright DS, Grey CP. 2023. Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials.","ieee":"R. B. Jethwa, D. Hey, R. N. Kerber, A. D. Bond, D. S. Wright, and C. P. Grey, “Exploring the landscape of heterocyclic quinones for redox flow batteries,” ACS Applied Energy Materials. American Chemical Society, 2023.","apa":"Jethwa, R. B., Hey, D., Kerber, R. N., Bond, A. D., Wright, D. S., & Grey, C. P. (2023). Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. American Chemical Society. https://doi.org/10.1021/acsaem.3c02223"},"article_type":"original","abstract":[{"lang":"eng","text":"Redox flow batteries (RFBs) rely on the development of cheap, highly soluble, and high-energy-density electrolytes. Several candidate quinones have already been investigated in the literature as two-electron anolytes or catholytes, benefiting from fast kinetics, high tunability, and low cost. Here, an investigation of nitrogen-rich fused heteroaromatic quinones was carried out to explore avenues for electrolyte development. These quinones were synthesized and screened by using electrochemical techniques. The most promising candidate, 4,8-dioxo-4,8-dihydrobenzo[1,2-d:4,5-d′]bis([1,2,3]triazole)-1,5-diide (−0.68 V(SHE)), was tested in both an asymmetric and symmetric full-cell setup resulting in capacity fade rates of 0.35% per cycle and 0.0124% per cycle, respectively. In situ ultraviolet-visible spectroscopy (UV–Vis), nuclear magnetic resonance (NMR), and electron paramagnetic resonance (EPR) spectroscopies were used to investigate the electrochemical stability of the charged species during operation. UV–Vis spectroscopy, supported by density functional theory (DFT) modeling, reaffirmed that the two-step charging mechanism observed during battery operation consisted of two, single-electron transfers. The radical concentration during battery operation and the degree of delocalization of the unpaired electron were quantified with NMR and EPR spectroscopy."}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14733","ddc":["540"],"status":"public","title":"Exploring the landscape of heterocyclic quinones for redox flow batteries","month":"12","publication_identifier":{"eissn":["2574-0962"]},"doi":"10.1021/acsaem.3c02223","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsaem.3c02223"}],"quality_controlled":"1","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"ec_funded":1,"author":[{"first_name":"Rajesh B","last_name":"Jethwa","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","orcid":"0000-0002-0404-4356","full_name":"Jethwa, Rajesh B"},{"last_name":"Hey","first_name":"Dominic","full_name":"Hey, Dominic"},{"full_name":"Kerber, Rachel N.","last_name":"Kerber","first_name":"Rachel N."},{"full_name":"Bond, Andrew D.","first_name":"Andrew D.","last_name":"Bond"},{"last_name":"Wright","first_name":"Dominic S.","full_name":"Wright, Dominic S."},{"last_name":"Grey","first_name":"Clare P.","full_name":"Grey, Clare P."}],"date_created":"2024-01-05T09:20:48Z","date_updated":"2024-01-08T09:03:01Z","year":"2023","publication_status":"epub_ahead","department":[{"_id":"StFr"}],"publisher":"American Chemical Society"},{"article_processing_charge":"No","publication_identifier":{"eissn":["2366-9608"]},"day":"28","month":"12","scopus_import":"1","date_published":"2023-12-28T00:00:00Z","doi":"10.1002/smtd.202301377","language":[{"iso":"eng"}],"external_id":{"pmid":["38152986"]},"citation":{"chicago":"Wan, Shanhong, Shanshan Xiao, Mingquan Li, Xin Wang, Khak Ho Lim, Min Hong, Maria Ibáñez, Andreu Cabot, and Yu Liu. “Band Engineering through Pb-Doping of Nanocrystal Building Blocks to Enhance Thermoelectric Performance in Cu3SbSe4.” Small Methods. Wiley, 2023. https://doi.org/10.1002/smtd.202301377.","short":"S. Wan, S. Xiao, M. Li, X. Wang, K.H. Lim, M. Hong, M. Ibáñez, A. Cabot, Y. Liu, Small Methods (2023).","mla":"Wan, Shanhong, et al. “Band Engineering through Pb-Doping of Nanocrystal Building Blocks to Enhance Thermoelectric Performance in Cu3SbSe4.” Small Methods, Wiley, 2023, doi:10.1002/smtd.202301377.","apa":"Wan, S., Xiao, S., Li, M., Wang, X., Lim, K. H., Hong, M., … Liu, Y. (2023). Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods. Wiley. https://doi.org/10.1002/smtd.202301377","ieee":"S. Wan et al., “Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4,” Small Methods. Wiley, 2023.","ista":"Wan S, Xiao S, Li M, Wang X, Lim KH, Hong M, Ibáñez M, Cabot A, Liu Y. 2023. Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods.","ama":"Wan S, Xiao S, Li M, et al. Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods. 2023. doi:10.1002/smtd.202301377"},"publication":"Small Methods","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"quality_controlled":"1","article_type":"original","abstract":[{"lang":"eng","text":"Developing cost-effective and high-performance thermoelectric (TE) materials to assemble efficient TE devices presents a multitude of challenges and opportunities. Cu3SbSe4 is a promising p-type TE material based on relatively earth abundant elements. However, the challenge lies in its poor electrical conductivity. Herein, an efficient and scalable solution-based approach is developed to synthesize high-quality Cu3SbSe4 nanocrystals doped with Pb at the Sb site. After ligand displacement and annealing treatments, the dried powders are consolidated into dense pellets, and their TE properties are investigated. Pb doping effectively increases the charge carrier concentration, resulting in a significant increase in electrical conductivity, while the Seebeck coefficients remain consistently high. The calculated band structure shows that Pb doping induces band convergence, thereby increasing the effective mass. Furthermore, the large ionic radius of Pb2+ results in the generation of additional point and plane defects and interphases, dramatically enhancing phonon scattering, which significantly decreases the lattice thermal conductivity at high temperatures. Overall, a maximum figure of merit (zTmax) ≈ 0.85 at 653 K is obtained in Cu3Sb0.97Pb0.03Se4. This represents a 1.6-fold increase compared to the undoped sample and exceeds most doped Cu3SbSe4-based materials produced by solid-state, demonstrating advantages of versatility and cost-effectiveness using a solution-based technology."}],"type":"journal_article","author":[{"first_name":"Shanhong","last_name":"Wan","full_name":"Wan, Shanhong"},{"last_name":"Xiao","first_name":"Shanshan","full_name":"Xiao, Shanshan"},{"full_name":"Li, Mingquan","last_name":"Li","first_name":"Mingquan"},{"full_name":"Wang, Xin","last_name":"Wang","first_name":"Xin"},{"first_name":"Khak Ho","last_name":"Lim","full_name":"Lim, Khak Ho"},{"first_name":"Min","last_name":"Hong","full_name":"Hong, Min"},{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"},{"last_name":"Liu","first_name":"Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"}],"oa_version":"None","date_updated":"2024-01-08T09:17:04Z","date_created":"2024-01-07T23:00:51Z","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14734","acknowledgement":"Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges financial support from the National Natural Science Foundation of China (NSFC) (Grant No. 22208293). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.","year":"2023","department":[{"_id":"MaIb"}],"publisher":"Wiley","status":"public","title":"Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4","publication_status":"epub_ahead"},{"year":"2023","acknowledgement":"We thank Alexander Litvak for the many discussions on Theorem 1.1. Igor Tsiutsiurupa participated in the early stage of this project. To our deep regret, Igor chose another road for his life and stopped working with us.\r\nThis work was supported by the János Bolyai Scholarship of the Hungarian Academy of Sciences [to M.N.]; the National Research, Development, and Innovation Fund (NRDI) [K119670 and K131529 to M.N.]; and the ÚNKP-22-5 New National Excellence Program of the Ministry for Innovation and Technology from the source of the NRDI [to M.N.].","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"UlWa"}],"author":[{"last_name":"Ivanov","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","full_name":"Ivanov, Grigory"},{"last_name":"Naszódi","first_name":"Márton","full_name":"Naszódi, Márton"}],"date_created":"2024-01-08T09:48:56Z","date_updated":"2024-01-08T09:57:25Z","volume":2023,"file_date_updated":"2024-01-08T09:53:09Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"arxiv":["2212.11781"]},"oa":1,"quality_controlled":"1","doi":"10.1093/imrn/rnad210","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14737","ddc":["510"],"title":"Functional John and Löwner conditions for pairs of log-concave functions","status":"public","intvolume":" 2023","file":[{"access_level":"open_access","file_name":"2023_IMRN_Ivanov.pdf","creator":"dernst","file_size":815777,"content_type":"application/pdf","file_id":"14738","relation":"main_file","success":1,"checksum":"353666cea80633beb0f1ffd342dff6d4","date_created":"2024-01-08T09:53:09Z","date_updated":"2024-01-08T09:53:09Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"John’s fundamental theorem characterizing the largest volume ellipsoid contained in a convex body $K$ in $\\mathbb{R}^{d}$ has seen several generalizations and extensions. One direction, initiated by V. Milman is to replace ellipsoids by positions (affine images) of another body $L$. Another, more recent direction is to consider logarithmically concave functions on $\\mathbb{R}^{d}$ instead of convex bodies: we designate some special, radially symmetric log-concave function $g$ as the analogue of the Euclidean ball, and want to find its largest integral position under the constraint that it is pointwise below some given log-concave function $f$. We follow both directions simultaneously: we consider the functional question, and allow essentially any meaningful function to play the role of $g$ above. Our general theorems jointly extend known results in both directions. The dual problem in the setting of convex bodies asks for the smallest volume ellipsoid, called Löwner’s ellipsoid, containing $K$. We consider the analogous problem for functions: we characterize the solutions of the optimization problem of finding a smallest integral position of some log-concave function $g$ under the constraint that it is pointwise above $f$. It turns out that in the functional setting, the relationship between the John and the Löwner problems is more intricate than it is in the setting of convex bodies.","lang":"eng"}],"issue":"23","publication":"International Mathematics Research Notices","citation":{"chicago":"Ivanov, Grigory, and Márton Naszódi. “Functional John and Löwner Conditions for Pairs of Log-Concave Functions.” International Mathematics Research Notices. Oxford University Press, 2023. https://doi.org/10.1093/imrn/rnad210.","mla":"Ivanov, Grigory, and Márton Naszódi. “Functional John and Löwner Conditions for Pairs of Log-Concave Functions.” International Mathematics Research Notices, vol. 2023, no. 23, Oxford University Press, 2023, pp. 20613–69, doi:10.1093/imrn/rnad210.","short":"G. Ivanov, M. Naszódi, International Mathematics Research Notices 2023 (2023) 20613–20669.","ista":"Ivanov G, Naszódi M. 2023. Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. 2023(23), 20613–20669.","apa":"Ivanov, G., & Naszódi, M. (2023). Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnad210","ieee":"G. Ivanov and M. Naszódi, “Functional John and Löwner conditions for pairs of log-concave functions,” International Mathematics Research Notices, vol. 2023, no. 23. Oxford University Press, pp. 20613–20669, 2023.","ama":"Ivanov G, Naszódi M. Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. 2023;2023(23):20613-20669. doi:10.1093/imrn/rnad210"},"article_type":"original","page":"20613-20669","date_published":"2023-12-01T00:00:00Z","keyword":["General Mathematics"],"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"publication":"27th International Conference on Financial Cryptography and Data Security","citation":{"chicago":"Bastankhah, Mahsa, Krishnendu Chatterjee, Mohammad Ali Maddah-Ali, Stefan Schmid, Jakub Svoboda, and Michelle X Yeo. “R2: Boosting Liquidity in Payment Channel Networks with Online Admission Control.” In 27th International Conference on Financial Cryptography and Data Security, 13950:309–25. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_18.","short":"M. Bastankhah, K. Chatterjee, M.A. Maddah-Ali, S. Schmid, J. Svoboda, M.X. Yeo, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 309–325.","mla":"Bastankhah, Mahsa, et al. “R2: Boosting Liquidity in Payment Channel Networks with Online Admission Control.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 309–25, doi:10.1007/978-3-031-47754-6_18.","apa":"Bastankhah, M., Chatterjee, K., Maddah-Ali, M. A., Schmid, S., Svoboda, J., & Yeo, M. X. (2023). R2: Boosting liquidity in payment channel networks with online admission control. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 309–325). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_18","ieee":"M. Bastankhah, K. Chatterjee, M. A. Maddah-Ali, S. Schmid, J. Svoboda, and M. X. Yeo, “R2: Boosting liquidity in payment channel networks with online admission control,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 309–325.","ista":"Bastankhah M, Chatterjee K, Maddah-Ali MA, Schmid S, Svoboda J, Yeo MX. 2023. R2: Boosting liquidity in payment channel networks with online admission control. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 309–325.","ama":"Bastankhah M, Chatterjee K, Maddah-Ali MA, Schmid S, Svoboda J, Yeo MX. R2: Boosting liquidity in payment channel networks with online admission control. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:309-325. doi:10.1007/978-3-031-47754-6_18"},"page":"309-325","date_published":"2023-12-01T00:00:00Z","day":"01","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14736","title":"R2: Boosting liquidity in payment channel networks with online admission control","status":"public","intvolume":" 13950","oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Payment channel networks (PCNs) are a promising technology to improve the scalability of cryptocurrencies. PCNs, however, face the challenge that the frequent usage of certain routes may deplete channels in one direction, and hence prevent further transactions. In order to reap the full potential of PCNs, recharging and rebalancing mechanisms are required to provision channels, as well as an admission control logic to decide which transactions to reject in case capacity is insufficient. This paper presents a formal model of this optimisation problem. In particular, we consider an online algorithms perspective, where transactions arrive over time in an unpredictable manner. Our main contributions are competitive online algorithms which come with provable guarantees over time. We empirically evaluate our algorithms on randomly generated transactions to compare the average performance of our algorithms to our theoretical bounds. We also show how this model and approach differs from related problems in classic communication networks."}],"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"conference":{"end_date":"2023-05-05","start_date":"2023-05-01","location":"Bol, Brac, Croatia","name":"FC: Financial Cryptography and Data Security"},"doi":"10.1007/978-3-031-47754-6_18","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031477546"],"isbn":["9783031477539"],"eissn":["1611-3349"]},"acknowledgement":"Supported by the German Federal Ministry of Education and Research (BMBF), grant 16KISK020K (6G-RIC), 2021–2025, and ERC CoG 863818 (ForM-SMArt).","year":"2023","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"KrPi"}],"publisher":"Springer Nature","author":[{"full_name":"Bastankhah, Mahsa","first_name":"Mahsa","last_name":"Bastankhah"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Maddah-Ali","first_name":"Mohammad Ali","full_name":"Maddah-Ali, Mohammad Ali"},{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"},{"full_name":"Svoboda, Jakub","first_name":"Jakub","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","orcid":"0000-0002-1419-3267"},{"last_name":"Yeo","first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X"}],"date_created":"2024-01-08T09:30:22Z","date_updated":"2024-01-08T09:36:36Z","volume":13950,"ec_funded":1},{"file_date_updated":"2024-01-08T10:09:14Z","publisher":"IEEE","department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"The work of Maria-Jose Jimenez, Eduardo Paluzo-Hidalgo and Manuel Soriano-Trigueros was supported in part by the Spanish grant Ministerio de Ciencia e Innovacion under Grants TED2021-129438B-I00 and PID2019-107339GB-I00, and in part by REXASI-PRO H-EU project, call HORIZON-CL4-2021-HUMAN-01-01 under Grant 101070028. The work of\r\nMaria-Jose Jimenez was supported by a grant of Convocatoria de la Universidad de Sevilla para la recualificacion del sistema universitario español, 2021-23, funded by the European Union, NextGenerationEU. The work of Vidit Nanda was supported in part by EPSRC under Grant EP/R018472/1 and in part by US AFOSR under Grant FA9550-22-1-0462. \r\nWe are grateful to the team of GUDHI and TEASPOON developers, for their work and their support. We are also grateful to Streamlit for providing extra resources to deploy the web app\r\nonline on Streamlit community cloud. We thank the anonymous referees for their helpful suggestions.","year":"2023","volume":45,"date_updated":"2024-01-08T10:11:46Z","date_created":"2024-01-08T09:59:46Z","author":[{"last_name":"Ali","first_name":"Dashti","full_name":"Ali, Dashti"},{"full_name":"Asaad, Aras","first_name":"Aras","last_name":"Asaad"},{"full_name":"Jimenez, Maria-Jose","last_name":"Jimenez","first_name":"Maria-Jose"},{"full_name":"Nanda, Vidit","first_name":"Vidit","last_name":"Nanda"},{"first_name":"Eduardo","last_name":"Paluzo-Hidalgo","full_name":"Paluzo-Hidalgo, Eduardo"},{"full_name":"Soriano Trigueros, Manuel","id":"15ebd7cf-15bf-11ee-aebd-bb4bb5121ea8","orcid":"0000-0003-2449-1433","first_name":"Manuel","last_name":"Soriano Trigueros"}],"publication_identifier":{"issn":["0162-8828"],"eissn":["1939-3539"]},"month":"12","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1109/tpami.2023.3308391","type":"journal_article","issue":"12","abstract":[{"lang":"eng","text":"Attempts to incorporate topological information in supervised learning tasks have resulted in the creation of several techniques for vectorizing persistent homology barcodes. In this paper, we study thirteen such methods. Besides describing an organizational framework for these methods, we comprehensively benchmark them against three well-known classification tasks. Surprisingly, we discover that the best-performing method is a simple vectorization, which consists only of a few elementary summary statistics. Finally, we provide a convenient web application which has been designed to facilitate exploration and experimentation with various vectorization methods."}],"intvolume":" 45","ddc":["000"],"title":"A survey of vectorization methods in topological data analysis","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14739","oa_version":"Published Version","file":[{"file_id":"14740","relation":"main_file","date_created":"2024-01-08T10:09:14Z","date_updated":"2024-01-08T10:09:14Z","success":1,"checksum":"465c28ef0b151b4b1fb47977ed5581ab","file_name":"2023_IEEEToP_Ali.pdf","access_level":"open_access","creator":"dernst","file_size":2370988,"content_type":"application/pdf"}],"keyword":["Applied Mathematics","Artificial Intelligence","Computational Theory and Mathematics","Computer Vision and Pattern Recognition","Software"],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","page":"14069-14080","article_type":"original","citation":{"ama":"Ali D, Asaad A, Jimenez M-J, Nanda V, Paluzo-Hidalgo E, Soriano Trigueros M. A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2023;45(12):14069-14080. doi:10.1109/tpami.2023.3308391","ista":"Ali D, Asaad A, Jimenez M-J, Nanda V, Paluzo-Hidalgo E, Soriano Trigueros M. 2023. A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 45(12), 14069–14080.","ieee":"D. Ali, A. Asaad, M.-J. Jimenez, V. Nanda, E. Paluzo-Hidalgo, and M. Soriano Trigueros, “A survey of vectorization methods in topological data analysis,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 45, no. 12. IEEE, pp. 14069–14080, 2023.","apa":"Ali, D., Asaad, A., Jimenez, M.-J., Nanda, V., Paluzo-Hidalgo, E., & Soriano Trigueros, M. (2023). A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/tpami.2023.3308391","mla":"Ali, Dashti, et al. “A Survey of Vectorization Methods in Topological Data Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 45, no. 12, IEEE, 2023, pp. 14069–80, doi:10.1109/tpami.2023.3308391.","short":"D. Ali, A. Asaad, M.-J. Jimenez, V. Nanda, E. Paluzo-Hidalgo, M. Soriano Trigueros, IEEE Transactions on Pattern Analysis and Machine Intelligence 45 (2023) 14069–14080.","chicago":"Ali, Dashti, Aras Asaad, Maria-Jose Jimenez, Vidit Nanda, Eduardo Paluzo-Hidalgo, and Manuel Soriano Trigueros. “A Survey of Vectorization Methods in Topological Data Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2023. https://doi.org/10.1109/tpami.2023.3308391."},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","date_published":"2023-12-01T00:00:00Z"},{"date_published":"2023-11-01T00:00:00Z","publication":"Cold Spring Harbor Perspectives in Biology","citation":{"ista":"Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447.","ieee":"K. Lucek et al., “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.","apa":"Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory. https://doi.org/10.1101/cshperspect.a041447","ama":"Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 2023;15(11). doi:10.1101/cshperspect.a041447","chicago":"Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory, 2023. https://doi.org/10.1101/cshperspect.a041447.","mla":"Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:10.1101/cshperspect.a041447.","short":"K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden, A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023)."},"article_type":"original","day":"01","article_processing_charge":"No","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology"],"oa_version":"Published Version","_id":"14742","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","status":"public","intvolume":" 15","abstract":[{"text":"Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.","lang":"eng"}],"issue":"11","type":"journal_article","doi":"10.1101/cshperspect.a041447","language":[{"iso":"eng"}],"external_id":{"pmid":["37604585"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/cshperspect.a041447","open_access":"1"}],"quality_controlled":"1","month":"11","publication_identifier":{"issn":["1943-0264"]},"author":[{"full_name":"Lucek, Kay","last_name":"Lucek","first_name":"Kay"},{"full_name":"Giménez, Mabel D.","last_name":"Giménez","first_name":"Mabel D."},{"full_name":"Joron, Mathieu","first_name":"Mathieu","last_name":"Joron"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Searle, Jeremy B.","first_name":"Jeremy B.","last_name":"Searle"},{"full_name":"Walden, Nora","last_name":"Walden","first_name":"Nora"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"}],"date_updated":"2024-01-08T12:52:29Z","date_created":"2024-01-08T12:43:48Z","volume":15,"year":"2023","acknowledgement":"K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper.","pmid":1,"publication_status":"published","publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"article_number":"a041447"},{"volume":13892,"date_created":"2024-01-08T12:56:46Z","date_updated":"2024-01-09T07:40:57Z","author":[{"full_name":"Avarikioti, Zeta","first_name":"Zeta","last_name":"Avarikioti"},{"last_name":"Desjardins","first_name":"Antoine","id":"06d0c166-aec1-11ee-a7c0-b96e840a602b","full_name":"Desjardins, Antoine"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias"},{"last_name":"Wattenhofer","first_name":"Roger","full_name":"Wattenhofer, Roger"}],"department":[{"_id":"ElKo"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"The work was partially supported by the Austrian Science Fund (FWF) through the project CoRaF (grant agreement 2020388).","publication_identifier":{"eisbn":["9783031327339"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031327322"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-32733-9_10","conference":{"end_date":"2023-06-09","location":"Alcalá de Henares, Spain","start_date":"2023-06-06","name":"SIROCCO: Structural Information and Communication Complexity"},"quality_controlled":"1","abstract":[{"text":"Sharding distributed ledgers is a promising on-chain solution for scaling blockchains but lacks formal grounds, nurturing skepticism on whether such complex systems can scale blockchains securely. We fill this gap by introducing the first formal framework as well as a roadmap to robust sharding. In particular, we first define the properties sharded distributed ledgers should fulfill. We build upon and extend the Bitcoin backbone protocol by defining consistency and scalability. Consistency encompasses the need for atomic execution of cross-shard transactions to preserve safety, whereas scalability encapsulates the speedup a sharded system can gain in comparison to a non-sharded system.\r\nUsing our model, we explore the limitations of sharding. We show that a sharded ledger with n participants cannot scale under a fully adaptive adversary, but it can scale up to m shards where n=c'm log m, under an epoch-adaptive adversary; the constant c' encompasses the trade-off between security and scalability. This is possible only if the sharded ledgers create succinct proofs of the valid state updates at every epoch. We leverage our results to identify the sufficient components for robust sharding, which we incorporate in a protocol abstraction termed Divide & Scale. To demonstrate the power of our framework, we analyze the most prominent sharded blockchains (Elastico, Monoxide, OmniLedger, RapidChain) and pinpoint where they fail to meet the desired properties.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"None","intvolume":" 13892","status":"public","title":"Divide & Scale: Formalization and roadmap to robust sharding","_id":"14744","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-06-01T00:00:00Z","page":"199-245","citation":{"ama":"Avarikioti Z, Desjardins A, Kokoris Kogias E, Wattenhofer R. Divide & Scale: Formalization and roadmap to robust sharding. In: 30th International Colloquium on Structural Information and Communication Complexity. Vol 13892. Springer Nature; 2023:199-245. doi:10.1007/978-3-031-32733-9_10","ista":"Avarikioti Z, Desjardins A, Kokoris Kogias E, Wattenhofer R. 2023. Divide & Scale: Formalization and roadmap to robust sharding. 30th International Colloquium on Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 13892, 199–245.","apa":"Avarikioti, Z., Desjardins, A., Kokoris Kogias, E., & Wattenhofer, R. (2023). Divide & Scale: Formalization and roadmap to robust sharding. In 30th International Colloquium on Structural Information and Communication Complexity (Vol. 13892, pp. 199–245). Alcalá de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_10","ieee":"Z. Avarikioti, A. Desjardins, E. Kokoris Kogias, and R. Wattenhofer, “Divide & Scale: Formalization and roadmap to robust sharding,” in 30th International Colloquium on Structural Information and Communication Complexity, Alcalá de Henares, Spain, 2023, vol. 13892, pp. 199–245.","mla":"Avarikioti, Zeta, et al. “Divide & Scale: Formalization and Roadmap to Robust Sharding.” 30th International Colloquium on Structural Information and Communication Complexity, vol. 13892, Springer Nature, 2023, pp. 199–245, doi:10.1007/978-3-031-32733-9_10.","short":"Z. Avarikioti, A. Desjardins, E. Kokoris Kogias, R. Wattenhofer, in:, 30th International Colloquium on Structural Information and Communication Complexity, Springer Nature, 2023, pp. 199–245.","chicago":"Avarikioti, Zeta, Antoine Desjardins, Eleftherios Kokoris Kogias, and Roger Wattenhofer. “Divide & Scale: Formalization and Roadmap to Robust Sharding.” In 30th International Colloquium on Structural Information and Communication Complexity, 13892:199–245. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_10."},"publication":"30th International Colloquium on Structural Information and Communication Complexity"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We unveil a powerful method for the stabilization of laser injection locking based on sensing variations in the output beam ellipticity of an optically seeded laser. The effect arises due to an interference between the seeding beam and the injected laser output. We demonstrate the method for a commercial semiconductor laser without the need for any internal changes to the readily operational injection locked laser system that was used. The method can also be used to increase the mode-hop free tuning range of lasers, and has the potential to fill a void in the low-noise laser industry."}],"issue":"15","title":"Monitoring and active stabilization of laser injection locking using beam ellipticity","status":"public","intvolume":" 48","_id":"14749","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","keyword":["Atomic and Molecular Physics","and Optics"],"scopus_import":"1","day":"21","article_processing_charge":"No","article_type":"original","page":"3973-3976","publication":"Optics Letters","citation":{"ama":"Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. 2023;48(15):3973-3976. doi:10.1364/ol.495553","ista":"Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. 2023. Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. 48(15), 3973–3976.","apa":"Mishra, U., Li, V., Wald, S., Agafonova, S., Diorico, F. R., & Hosten, O. (2023). Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/ol.495553","ieee":"U. Mishra, V. Li, S. Wald, S. Agafonova, F. R. Diorico, and O. Hosten, “Monitoring and active stabilization of laser injection locking using beam ellipticity,” Optics Letters, vol. 48, no. 15. Optica Publishing Group, pp. 3973–3976, 2023.","mla":"Mishra, Umang, et al. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” Optics Letters, vol. 48, no. 15, Optica Publishing Group, 2023, pp. 3973–76, doi:10.1364/ol.495553.","short":"U. Mishra, V. Li, S. Wald, S. Agafonova, F.R. Diorico, O. Hosten, Optics Letters 48 (2023) 3973–3976.","chicago":"Mishra, Umang, Vyacheslav Li, Sebastian Wald, Sofya Agafonova, Fritz R Diorico, and Onur Hosten. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” Optics Letters. Optica Publishing Group, 2023. https://doi.org/10.1364/ol.495553."},"date_published":"2023-07-21T00:00:00Z","publication_status":"published","department":[{"_id":"OnHo"}],"publisher":"Optica Publishing Group","year":"2023","date_updated":"2024-01-09T08:09:32Z","date_created":"2024-01-08T13:01:46Z","volume":48,"author":[{"id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","first_name":"Umang","last_name":"Mishra","full_name":"Mishra, Umang"},{"full_name":"Li, Vyacheslav","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87","first_name":"Vyacheslav","last_name":"Li"},{"last_name":"Wald","first_name":"Sebastian","id":"133F200A-B015-11E9-AD41-0EDAE5697425","full_name":"Wald, Sebastian"},{"id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","orcid":"0000-0003-0582-2946","first_name":"Sofya","last_name":"Agafonova","full_name":"Agafonova, Sofya"},{"last_name":"Diorico","first_name":"Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","full_name":"Diorico, Fritz R"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","first_name":"Onur","last_name":"Hosten","full_name":"Hosten, Onur"}],"month":"07","publication_identifier":{"eissn":["1539-4794"],"issn":["0146-9592"]},"quality_controlled":"1","external_id":{"arxiv":["2212.01266"]},"language":[{"iso":"eng"}],"doi":"10.1364/ol.495553"},{"date_created":"2024-01-08T13:07:49Z","date_updated":"2024-01-09T08:54:03Z","volume":4,"author":[{"full_name":"Fildier, B.","last_name":"Fildier","first_name":"B."},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","first_name":"Caroline J","last_name":"Muller","full_name":"Muller, Caroline J"},{"last_name":"Pincus","first_name":"R.","full_name":"Pincus, R."},{"last_name":"Fueglistaler","first_name":"S.","full_name":"Fueglistaler, S."}],"publication_status":"published","publisher":"American Geophysical Union","department":[{"_id":"CaMu"}],"acknowledgement":"The authors would like to thank two anonymous reviews and gratefully acknowledge diverse funding agencies and resources used for this work. B.F. and C.M. thank funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041), and the EUREC4A campaign organizers for giving the opportunity to take part to the campaign and use the data early on. R. P. was supported by the US National Science Foundation (award AGS 19–16908), by the National Oceanic and Atmospheric Administration (award NA200AR4310375), and the Vetlesen Foundation.","year":"2023","file_date_updated":"2024-01-09T08:51:25Z","ec_funded":1,"article_number":"e2023AV000880","language":[{"iso":"eng"}],"doi":"10.1029/2023av000880","quality_controlled":"1","project":[{"name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"month":"06","publication_identifier":{"eissn":["2576-604X"]},"file":[{"relation":"main_file","file_id":"14761","checksum":"af773220a9fa194c61a8dc2fae092c16","success":1,"date_updated":"2024-01-09T08:51:25Z","date_created":"2024-01-09T08:51:25Z","access_level":"open_access","file_name":"2023_AGUAdvances_Fildier.pdf","content_type":"application/pdf","file_size":24149551,"creator":"dernst"}],"oa_version":"Published Version","ddc":["550"],"status":"public","title":"How moisture shapes low‐level radiative cooling in subsidence regimes","intvolume":" 4","_id":"14752","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Radiative cooling of the lowest atmospheric levels is of strong importance for modulating atmospheric circulations and organizing convection, but detailed observations and a robust theoretical understanding are lacking. Here we use unprecedented observational constraints from subsidence regimes in the tropical Atlantic to develop a theory for the shape and magnitude of low‐level longwave radiative cooling in clear‐sky, showing peaks larger than 5–10 K/day at the top of the boundary layer. A suite of novel scaling approximations is first developed from simplified spectral theory, in close agreement with the measurements. The radiative cooling peak height is set by the maximum lapse rate in water vapor path, and its magnitude is mainly controlled by the ratio of column relative humidity above and below the peak. We emphasize how elevated intrusions of moist air can reduce low‐level cooling, by sporadically shading the spectral range which effectively cools to space. The efficiency of this spectral shading depends both on water content and altitude of moist intrusions; its height dependence cannot be explained by the temperature difference between the emitting and absorbing layers, but by the decrease of water vapor extinction with altitude. This analytical work can help to narrow the search for low‐level cloud patterns sensitive to radiative‐convective feedbacks: the most organized patterns with largest cloud fractions occur in atmospheres below 10% relative humidity and feel the strongest low‐level cooling. This motivates further assessment of favorable conditions for radiative‐convective feedbacks and a robust quantification of corresponding shallow cloud dynamics in current and warmer climates."}],"issue":"3","type":"journal_article","date_published":"2023-06-01T00:00:00Z","article_type":"original","publication":"AGU Advances","citation":{"ama":"Fildier B, Muller CJ, Pincus R, Fueglistaler S. How moisture shapes low‐level radiative cooling in subsidence regimes. AGU Advances. 2023;4(3). doi:10.1029/2023av000880","apa":"Fildier, B., Muller, C. J., Pincus, R., & Fueglistaler, S. (2023). How moisture shapes low‐level radiative cooling in subsidence regimes. AGU Advances. American Geophysical Union. https://doi.org/10.1029/2023av000880","ieee":"B. Fildier, C. J. Muller, R. Pincus, and S. Fueglistaler, “How moisture shapes low‐level radiative cooling in subsidence regimes,” AGU Advances, vol. 4, no. 3. American Geophysical Union, 2023.","ista":"Fildier B, Muller CJ, Pincus R, Fueglistaler S. 2023. How moisture shapes low‐level radiative cooling in subsidence regimes. AGU Advances. 4(3), e2023AV000880.","short":"B. Fildier, C.J. Muller, R. Pincus, S. Fueglistaler, AGU Advances 4 (2023).","mla":"Fildier, B., et al. “How Moisture Shapes Low‐level Radiative Cooling in Subsidence Regimes.” AGU Advances, vol. 4, no. 3, e2023AV000880, American Geophysical Union, 2023, doi:10.1029/2023av000880.","chicago":"Fildier, B., Caroline J Muller, R. Pincus, and S. Fueglistaler. “How Moisture Shapes Low‐level Radiative Cooling in Subsidence Regimes.” AGU Advances. American Geophysical Union, 2023. https://doi.org/10.1029/2023av000880."},"day":"01","article_processing_charge":"Yes","has_accepted_license":"1","keyword":["General Earth and Planetary Sciences"],"scopus_import":"1"},{"publisher":"The Royal Society","department":[{"_id":"BjHo"}],"publication_status":"published","pmid":1,"acknowledgement":"K.D.’s research was supported by Australian Research Council Discovery Early Career Researcher Award (DE170100171). B.W., R.A., F.M. and A.M. research was supported by the Spanish Ministerio de Economía y Competitividad (grant nos. FIS2016-77849-R and FIS2017-85794-P) and Ministerio de Ciencia e Innovación (grant no. PID2020-114043GB-I00) and the Generalitat de Catalunya (grant no. 2017-SGR-785). B.W.’s research was also supported by the Chinese Scholarship Council (grant CSC no. 201806440152). F.M. is a Serra-Húnter Fellow.","year":"2023","volume":381,"date_created":"2024-01-08T13:11:45Z","date_updated":"2024-01-09T09:15:29Z","author":[{"first_name":"B.","last_name":"Wang","full_name":"Wang, B."},{"last_name":"Mellibovsky","first_name":"F.","full_name":"Mellibovsky, F."},{"first_name":"Roger","last_name":"Ayats López","id":"ab77522d-073b-11ed-8aff-e71b39258362","orcid":"0000-0001-6572-0621","full_name":"Ayats López, Roger"},{"first_name":"K.","last_name":"Deguchi","full_name":"Deguchi, K."},{"first_name":"A.","last_name":"Meseguer","full_name":"Meseguer, A."}],"article_number":"0112","file_date_updated":"2024-01-09T09:13:53Z","quality_controlled":"1","external_id":{"pmid":["36907214"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rsta.2022.0112","publication_identifier":{"eissn":["1471-2962"],"issn":["1364-503X"]},"month":"05","intvolume":" 381","status":"public","title":"Mean structure of the supercritical turbulent spiral in Taylor–Couette flow","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14754","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2023_PhilTransactionsA_Wang_accepted.pdf","content_type":"application/pdf","file_size":6421086,"creator":"dernst","relation":"main_file","file_id":"14763","checksum":"1978d126c0ce2f47c22ac20107cc0106","success":1,"date_created":"2024-01-09T09:13:53Z","date_updated":"2024-01-09T09:13:53Z"}],"type":"journal_article","issue":"2246","abstract":[{"lang":"eng","text":"The large-scale laminar/turbulent spiral patterns that appear in the linearly unstable regime of counter-rotating Taylor–Couette flow are investigated from a statistical perspective by means of direct numerical simulation. Unlike the vast majority of previous numerical studies, we analyse the flow in periodic parallelogram-annular domains, following a coordinate change that aligns one of the parallelogram sides with the spiral pattern. The domain size, shape and spatial resolution have been varied and the results compared with those in a sufficiently large computational orthogonal domain with natural axial and azimuthal periodicity. We find that a minimal parallelogram of the right tilt significantly reduces the computational cost without notably compromising the statistical properties of the supercritical turbulent spiral. Its mean structure, obtained from extremely long time integrations in a co-rotating reference frame using the method of slices, bears remarkable similarity with the turbulent stripes observed in plane Couette flow, the centrifugal instability playing only a secondary role."}],"article_type":"original","citation":{"ama":"Wang B, Mellibovsky F, Ayats López R, Deguchi K, Meseguer A. Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. 2023;381(2246). doi:10.1098/rsta.2022.0112","ieee":"B. Wang, F. Mellibovsky, R. Ayats López, K. Deguchi, and A. Meseguer, “Mean structure of the supercritical turbulent spiral in Taylor–Couette flow,” Philosophical Transactions of the Royal Society A, vol. 381, no. 2246. The Royal Society, 2023.","apa":"Wang, B., Mellibovsky, F., Ayats López, R., Deguchi, K., & Meseguer, A. (2023). Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. The Royal Society. https://doi.org/10.1098/rsta.2022.0112","ista":"Wang B, Mellibovsky F, Ayats López R, Deguchi K, Meseguer A. 2023. Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. 381(2246), 0112.","short":"B. Wang, F. Mellibovsky, R. Ayats López, K. Deguchi, A. Meseguer, Philosophical Transactions of the Royal Society A 381 (2023).","mla":"Wang, B., et al. “Mean Structure of the Supercritical Turbulent Spiral in Taylor–Couette Flow.” Philosophical Transactions of the Royal Society A, vol. 381, no. 2246, 0112, The Royal Society, 2023, doi:10.1098/rsta.2022.0112.","chicago":"Wang, B., F. Mellibovsky, Roger Ayats López, K. Deguchi, and A. Meseguer. “Mean Structure of the Supercritical Turbulent Spiral in Taylor–Couette Flow.” Philosophical Transactions of the Royal Society A. The Royal Society, 2023. https://doi.org/10.1098/rsta.2022.0112."},"publication":"Philosophical Transactions of the Royal Society A","date_published":"2023-05-01T00:00:00Z","keyword":["General Physics and Astronomy","General Engineering","General Mathematics"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01"},{"abstract":[{"text":"Several fixed-target experiments reported J/ψ and ϒ polarizations, as functions of Feynman x (xF) and transverse momentum (PT), in three different frames, using different combinations of beam particles, target nuclei, and collision energies. Despite the diverse and heterogeneous picture formed by these measurements, a detailed look allows us to discern qualitative physical patterns that inspire a simple empirical model. This data-driven scenario offers a good quantitative description of the J/ψ and ϒ(1S) polarizations measured in proton- and pion-nucleus collisions, in the xF 0.5 domain: more than 80 data points (not statistically independent) are well reproduced with only one free parameter. This study sets the context for future low-PT\r\n quarkonium polarization measurements in proton- and pion-nucleus collisions, such as those to be made by the AMBER experiment, and shows that such measurements provide significant constraints on the poorly-known parton distribution functions of the pion.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2023_PhysicsLettersB_Faccioli.pdf","access_level":"open_access","content_type":"application/pdf","file_size":855494,"creator":"dernst","relation":"main_file","file_id":"14762","date_created":"2024-01-09T08:59:24Z","date_updated":"2024-01-09T08:59:24Z","checksum":"02dec160dbc81d95985e755869d8afbf","success":1}],"ddc":["530"],"title":"Low-pT quarkonium polarization measurements: Challenges and opportunities","status":"public","intvolume":" 840","_id":"14753","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"10","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","keyword":["Nuclear and High Energy Physics"],"scopus_import":"1","date_published":"2023-05-10T00:00:00Z","article_type":"original","publication":"Physics Letters B","citation":{"chicago":"Faccioli, Pietro, Ilse Krätschmer, and Carlos Lourenço. “Low-PT Quarkonium Polarization Measurements: Challenges and Opportunities.” Physics Letters B. Elsevier, 2023. https://doi.org/10.1016/j.physletb.2023.137871.","short":"P. Faccioli, I. Krätschmer, C. Lourenço, Physics Letters B 840 (2023).","mla":"Faccioli, Pietro, et al. “Low-PT Quarkonium Polarization Measurements: Challenges and Opportunities.” Physics Letters B, vol. 840, 137871, Elsevier, 2023, doi:10.1016/j.physletb.2023.137871.","ieee":"P. Faccioli, I. Krätschmer, and C. Lourenço, “Low-pT quarkonium polarization measurements: Challenges and opportunities,” Physics Letters B, vol. 840. Elsevier, 2023.","apa":"Faccioli, P., Krätschmer, I., & Lourenço, C. (2023). Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. Elsevier. https://doi.org/10.1016/j.physletb.2023.137871","ista":"Faccioli P, Krätschmer I, Lourenço C. 2023. Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. 840, 137871.","ama":"Faccioli P, Krätschmer I, Lourenço C. Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. 2023;840. doi:10.1016/j.physletb.2023.137871"},"file_date_updated":"2024-01-09T08:59:24Z","article_number":"137871","date_updated":"2024-01-09T09:02:22Z","date_created":"2024-01-08T13:09:17Z","volume":840,"author":[{"first_name":"Pietro","last_name":"Faccioli","full_name":"Faccioli, Pietro"},{"first_name":"Ilse","last_name":"Krätschmer","id":"30d4014e-7753-11eb-b44b-db6d61112e73","orcid":"0000-0002-5636-9259","full_name":"Krätschmer, Ilse"},{"full_name":"Lourenço, Carlos","last_name":"Lourenço","first_name":"Carlos"}],"publication_status":"published","department":[{"_id":"MaRo"}],"publisher":"Elsevier","acknowledgement":"P.F. and C.L. acknowledge support from Fundação para a Ciência e a Tecnologia, Portugal, under contract CERN/FIS-PAR/0010/2019.\r\nOpen Access funded by SCOAP3.","year":"2023","month":"05","publication_identifier":{"issn":["0370-2693"],"eissn":["1873-2445"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.physletb.2023.137871","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"publication_identifier":{"issn":["1050-5164"]},"month":"08","doi":"10.1214/22-aap1882","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2010.16083"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2010.16083"}],"project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"quality_controlled":"1","ec_funded":1,"author":[{"full_name":"Ding, Xiucai","last_name":"Ding","first_name":"Xiucai"},{"full_name":"Ji, Hong Chang","last_name":"Ji","first_name":"Hong Chang","id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d"}],"volume":33,"date_created":"2024-01-08T13:03:18Z","date_updated":"2024-01-09T08:16:41Z","acknowledgement":"The first author is partially supported by NSF Grant DMS-2113489 and grateful for the AMS-SIMONS travel grant (2020–2023). The second author is supported by the ERC Advanced Grant “RMTBeyond” No. 101020331.\r\nThe authors would like to thank the Editor, Associate Editor and an anonymous referee for their many critical suggestions which have significantly improved the paper. We also want to thank Zhigang Bao and Ji Oon Lee for many helpful discussions and comments.","year":"2023","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"date_published":"2023-08-01T00:00:00Z","citation":{"ieee":"X. Ding and H. C. Ji, “Local laws for multiplication of random matrices,” The Annals of Applied Probability, vol. 33, no. 4. Institute of Mathematical Statistics, pp. 2981–3009, 2023.","apa":"Ding, X., & Ji, H. C. (2023). Local laws for multiplication of random matrices. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/22-aap1882","ista":"Ding X, Ji HC. 2023. Local laws for multiplication of random matrices. The Annals of Applied Probability. 33(4), 2981–3009.","ama":"Ding X, Ji HC. Local laws for multiplication of random matrices. The Annals of Applied Probability. 2023;33(4):2981-3009. doi:10.1214/22-aap1882","chicago":"Ding, Xiucai, and Hong Chang Ji. “Local Laws for Multiplication of Random Matrices.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-aap1882.","short":"X. Ding, H.C. Ji, The Annals of Applied Probability 33 (2023) 2981–3009.","mla":"Ding, Xiucai, and Hong Chang Ji. “Local Laws for Multiplication of Random Matrices.” The Annals of Applied Probability, vol. 33, no. 4, Institute of Mathematical Statistics, 2023, pp. 2981–3009, doi:10.1214/22-aap1882."},"publication":"The Annals of Applied Probability","page":"2981-3009","article_type":"original","issue":"4","abstract":[{"lang":"eng","text":"Consider the random matrix model A1/2UBU∗A1/2, where A and B are two N × N deterministic matrices and U is either an N × N Haar unitary or orthogonal random matrix. It is well known that on the macroscopic scale (Invent. Math. 104 (1991) 201–220), the limiting empirical spectral distribution (ESD) of the above model is given by the free multiplicative convolution\r\nof the limiting ESDs of A and B, denoted as μα \u0002 μβ, where μα and μβ are the limiting ESDs of A and B, respectively. In this paper, we study the asymptotic microscopic behavior of the edge eigenvalues and eigenvectors statistics. We prove that both the density of μA \u0002μB, where μA and μB are the ESDs of A and B, respectively and the associated subordination functions\r\nhave a regular behavior near the edges. Moreover, we establish the local laws near the edges on the optimal scale. In particular, we prove that the entries of the resolvent are close to some functionals depending only on the eigenvalues of A, B and the subordination functions with optimal convergence rates. Our proofs and calculations are based on the techniques developed for the additive model A+UBU∗ in (J. Funct. Anal. 271 (2016) 672–719; Comm. Math.\r\nPhys. 349 (2017) 947–990; Adv. Math. 319 (2017) 251–291; J. Funct. Anal. 279 (2020) 108639), and our results can be regarded as the counterparts of (J. Funct. Anal. 279 (2020) 108639) for the multiplicative model. "}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14750","intvolume":" 33","title":"Local laws for multiplication of random matrices","status":"public"},{"file_date_updated":"2024-01-09T09:25:34Z","date_updated":"2024-01-09T09:27:46Z","date_created":"2024-01-08T13:14:48Z","volume":14,"author":[{"full_name":"Carqueville, Nils","first_name":"Nils","last_name":"Carqueville"},{"last_name":"Szegedy","first_name":"Lorant","orcid":"0000-0003-2834-5054","id":"7943226E-220E-11EA-94C7-D59F3DDC885E","full_name":"Szegedy, Lorant"}],"publication_status":"published","publisher":"European Mathematical Society","department":[{"_id":"MiLe"}],"acknowledgement":"N.C. is supported by the DFG Heisenberg Programme.\r\nWe are grateful to Tobias Dyckerhoff, Lukas Müller, Ingo Runkel, and Christopher Schommer-Pries for helpful discussions.","year":"2023","month":"10","publication_identifier":{"issn":["1663-487X"]},"language":[{"iso":"eng"}],"doi":"10.4171/qt/193","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"lang":"eng","text":"We prove the r-spin cobordism hypothesis in the setting of (weak) 2-categories for every positive integer r: the 2-groupoid of 2-dimensional fully extended r-spin TQFTs with given target is equivalent to the homotopy fixed points of an induced Spin 2r -action. In particular, such TQFTs are classified by fully dualisable objects together with a trivialisation of the rth power of their Serre automorphisms. For r=1, we recover the oriented case (on which our proof builds), while ordinary spin structures correspond to r=2.\r\nTo construct examples, we explicitly describe Spin 2r-homotopy fixed points in the equivariant completion of any symmetric monoidal 2-category. We also show that every object in a 2-category of Landau–Ginzburg models gives rise to fully extended spin TQFTs and that half of these do not factor through the oriented bordism 2-category."}],"issue":"3","type":"journal_article","file":[{"date_created":"2024-01-09T09:25:34Z","date_updated":"2024-01-09T09:25:34Z","checksum":"b0590aff6e7ec89cc149ba94d459d3a3","success":1,"relation":"main_file","file_id":"14764","file_size":707344,"content_type":"application/pdf","creator":"dernst","file_name":"2023_QuantumTopol_Carqueville.pdf","access_level":"open_access"}],"oa_version":"Published Version","status":"public","ddc":["530"],"title":"Fully extended r-spin TQFTs","intvolume":" 14","_id":"14756","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"16","article_processing_charge":"Yes","has_accepted_license":"1","keyword":["Geometry and Topology","Mathematical Physics"],"scopus_import":"1","date_published":"2023-10-16T00:00:00Z","article_type":"original","page":"467-532","publication":"Quantum Topology","citation":{"short":"N. Carqueville, L. Szegedy, Quantum Topology 14 (2023) 467–532.","mla":"Carqueville, Nils, and Lorant Szegedy. “Fully Extended R-Spin TQFTs.” Quantum Topology, vol. 14, no. 3, European Mathematical Society, 2023, pp. 467–532, doi:10.4171/qt/193.","chicago":"Carqueville, Nils, and Lorant Szegedy. “Fully Extended R-Spin TQFTs.” Quantum Topology. European Mathematical Society, 2023. https://doi.org/10.4171/qt/193.","ama":"Carqueville N, Szegedy L. Fully extended r-spin TQFTs. Quantum Topology. 2023;14(3):467-532. doi:10.4171/qt/193","ieee":"N. Carqueville and L. Szegedy, “Fully extended r-spin TQFTs,” Quantum Topology, vol. 14, no. 3. European Mathematical Society, pp. 467–532, 2023.","apa":"Carqueville, N., & Szegedy, L. (2023). Fully extended r-spin TQFTs. Quantum Topology. European Mathematical Society. https://doi.org/10.4171/qt/193","ista":"Carqueville N, Szegedy L. 2023. Fully extended r-spin TQFTs. Quantum Topology. 14(3), 467–532."}},{"publication_status":"published","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"MaMo"}],"year":"2023","acknowledgement":"The author would like to thank Amitalok J. Budkuley and Sidharth Jaggi for many helpful discussions at the early stage of this work. He would also like to thank Nir Ailon, Qi Cao, and Chandra Nair for discussions on a related problem regarding zero-error binary adder MACs.\r\nThe work of Yihan Zhang was supported by the European Union’s Horizon 2020 Research and Innovation Programme under Grant 682203-ERC-[Inf-Speed-Tradeoff]","date_updated":"2024-01-09T08:45:24Z","date_created":"2024-01-08T13:04:54Z","volume":69,"author":[{"id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","first_name":"Yihan","last_name":"Zhang","full_name":"Zhang, Yihan"}],"month":"07","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2101.12426","open_access":"1"}],"external_id":{"arxiv":["2101.12426"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1109/tit.2023.3257239","type":"journal_article","abstract":[{"lang":"eng","text":"We consider zero-error communication over a two-transmitter deterministic adversarial multiple access channel (MAC) governed by an adversary who has access to the transmissions of both senders (hence called omniscient ) and aims to maliciously corrupt the communication. None of the encoders, jammer and decoder is allowed to randomize using private or public randomness. This enforces a combinatorial nature of the problem. Our model covers a large family of channels studied in the literature, including all deterministic discrete memoryless noisy or noiseless MACs. In this work, given an arbitrary two-transmitter deterministic omniscient adversarial MAC, we characterize when the capacity region: 1) has nonempty interior (in particular, is two-dimensional); 2) consists of two line segments (in particular, has empty interior); 3) consists of one line segment (in particular, is one-dimensional); 4) or only contains (0,0) (in particular, is zero-dimensional). This extends a recent result by Wang et al. (201 9) from the point-to-point setting to the multiple access setting. Indeed, our converse arguments build upon their generalized Plotkin bound and involve delicate case analysis. One of the technical challenges is to take care of both “joint confusability” and “marginal confusability”. In particular, the treatment of marginal confusability does not follow from the point-to-point results by Wang et al. Our achievability results follow from random coding with expurgation."}],"issue":"7","status":"public","title":"Zero-error communication over adversarial MACs","intvolume":" 69","_id":"14751","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","keyword":["Computer Science Applications","Information Systems"],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"4093-4127","publication":"IEEE Transactions on Information Theory","citation":{"ista":"Zhang Y. 2023. Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. 69(7), 4093–4127.","ieee":"Y. Zhang, “Zero-error communication over adversarial MACs,” IEEE Transactions on Information Theory, vol. 69, no. 7. Institute of Electrical and Electronics Engineers, pp. 4093–4127, 2023.","apa":"Zhang, Y. (2023). Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/tit.2023.3257239","ama":"Zhang Y. Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. 2023;69(7):4093-4127. doi:10.1109/tit.2023.3257239","chicago":"Zhang, Yihan. “Zero-Error Communication over Adversarial MACs.” IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/tit.2023.3257239.","mla":"Zhang, Yihan. “Zero-Error Communication over Adversarial MACs.” IEEE Transactions on Information Theory, vol. 69, no. 7, Institute of Electrical and Electronics Engineers, 2023, pp. 4093–127, doi:10.1109/tit.2023.3257239.","short":"Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 4093–4127."},"date_published":"2023-07-01T00:00:00Z"},{"date_published":"2023-02-02T00:00:00Z","publication":"Asymptotic Analysis","citation":{"chicago":"Moser, Maximilian. “Convergence of the Scalar- and Vector-Valued Allen–Cahn Equation to Mean Curvature Flow with 90°-Contact Angle in Higher Dimensions, Part I: Convergence Result.” Asymptotic Analysis. IOS Press, 2023. https://doi.org/10.3233/asy-221775.","short":"M. Moser, Asymptotic Analysis 131 (2023) 297–383.","mla":"Moser, Maximilian. “Convergence of the Scalar- and Vector-Valued Allen–Cahn Equation to Mean Curvature Flow with 90°-Contact Angle in Higher Dimensions, Part I: Convergence Result.” Asymptotic Analysis, vol. 131, no. 3–4, IOS Press, 2023, pp. 297–383, doi:10.3233/asy-221775.","apa":"Moser, M. (2023). Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. IOS Press. https://doi.org/10.3233/asy-221775","ieee":"M. Moser, “Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result,” Asymptotic Analysis, vol. 131, no. 3–4. IOS Press, pp. 297–383, 2023.","ista":"Moser M. 2023. Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. 131(3–4), 297–383.","ama":"Moser M. Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. 2023;131(3-4):297-383. doi:10.3233/asy-221775"},"article_type":"original","page":"297-383","day":"02","article_processing_charge":"No","scopus_import":"1","keyword":["General Mathematics"],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14755","status":"public","title":"Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result","intvolume":" 131","abstract":[{"lang":"eng","text":"We consider the sharp interface limit for the scalar-valued and vector-valued Allen–Cahn equation with homogeneous Neumann boundary condition in a bounded smooth domain Ω of arbitrary dimension N ⩾ 2 in the situation when a two-phase diffuse interface has developed and intersects the boundary ∂ Ω. The limit problem is mean curvature flow with 90°-contact angle and we show convergence in strong norms for well-prepared initial data as long as a smooth solution to the limit problem exists. To this end we assume that the limit problem has a smooth solution on [ 0 , T ] for some time T > 0. Based on the latter we construct suitable curvilinear coordinates and set up an asymptotic expansion for the scalar-valued and the vector-valued Allen–Cahn equation. In order to estimate the difference of the exact and approximate solutions with a Gronwall-type argument, a spectral estimate for the linearized Allen–Cahn operator in both cases is required. The latter will be shown in a separate paper, cf. (Moser (2021))."}],"issue":"3-4","type":"journal_article","doi":"10.3233/asy-221775","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2105.07100","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2105.07100"]},"quality_controlled":"1","month":"02","publication_identifier":{"issn":["0921-7134"],"eissn":["1875-8576"]},"author":[{"full_name":"Moser, Maximilian","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c","first_name":"Maximilian","last_name":"Moser"}],"date_created":"2024-01-08T13:13:28Z","date_updated":"2024-01-09T09:22:16Z","volume":131,"acknowledgement":"The author gratefully acknowledges support through DFG, GRK 1692 “Curvature,\r\nCycles and Cohomology” during parts of the work.","year":"2023","publication_status":"published","publisher":"IOS Press","department":[{"_id":"JuFi"}]},{"author":[{"id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277","first_name":"Ana","last_name":"Villalba Requena","full_name":"Villalba Requena, Ana"},{"full_name":"Amberg, Nicole","last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-01-09T09:46:57Z","date_created":"2024-01-08T13:16:36Z","oa_version":"None","year":"2023","_id":"14757","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression","editor":[{"full_name":"Huttner, Wieland","last_name":"Huttner","first_name":"Wieland"}],"publisher":"Wiley","department":[{"_id":"SiHi"}],"abstract":[{"text":"The cerebral cortex is comprised of a vast cell-type diversity sequentially generated by cortical progenitor cells. Faithful progenitor lineage progression requires the tight orchestration of distinct molecular and cellular mechanisms regulating proper progenitor proliferation behavior and differentiation. Correct execution of developmental programs involves a complex interplay of cell intrinsic and tissue-wide mechanisms. Many studies over the past decades have been able to determine a plethora of genes critically involved in cortical development. However, only a few made use of genetic paradigms with sparse and global gene deletion to probe cell-autonomous vs. tissue-wide contribution. In this chapter, we will elaborate on the importance of dissecting the cell-autonomous and tissue-wide mechanisms to gain a precise understanding of gene function during radial glial progenitor lineage progression.","lang":"eng"}],"type":"book_chapter","date_published":"2023-08-08T00:00:00Z","doi":"10.1002/9781119860914.ch10","language":[{"iso":"eng"}],"publication":"Neocortical Neurogenesis in Development and Evolution","citation":{"mla":"Villalba Requena, Ana, et al. “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression.” Neocortical Neurogenesis in Development and Evolution, edited by Wieland Huttner, Wiley, 2023, pp. 169–91, doi:10.1002/9781119860914.ch10.","short":"A. Villalba Requena, N. Amberg, S. Hippenmeyer, in:, W. Huttner (Ed.), Neocortical Neurogenesis in Development and Evolution, Wiley, 2023, pp. 169–191.","chicago":"Villalba Requena, Ana, Nicole Amberg, and Simon Hippenmeyer. “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression.” In Neocortical Neurogenesis in Development and Evolution, edited by Wieland Huttner, 169–91. Wiley, 2023. https://doi.org/10.1002/9781119860914.ch10.","ama":"Villalba Requena A, Amberg N, Hippenmeyer S. Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In: Huttner W, ed. Neocortical Neurogenesis in Development and Evolution. Wiley; 2023:169-191. doi:10.1002/9781119860914.ch10","ista":"Villalba Requena A, Amberg N, Hippenmeyer S. 2023.Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In: Neocortical Neurogenesis in Development and Evolution. , 169–191.","ieee":"A. Villalba Requena, N. Amberg, and S. Hippenmeyer, “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression,” in Neocortical Neurogenesis in Development and Evolution, W. Huttner, Ed. Wiley, 2023, pp. 169–191.","apa":"Villalba Requena, A., Amberg, N., & Hippenmeyer, S. (2023). Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In W. Huttner (Ed.), Neocortical Neurogenesis in Development and Evolution (pp. 169–191). Wiley. https://doi.org/10.1002/9781119860914.ch10"},"quality_controlled":"1","page":"169-191","month":"08","day":"08","article_processing_charge":"No","publication_identifier":{"eisbn":["9781119860914"]},"scopus_import":"1"},{"type":"journal_article","issue":"1","abstract":[{"text":"Proper operation of electro-optic I/Q modulators relies on precise adjustment and control of the relative phase biases between the modulator’s internal interferometer arms. We present an all-analog phase bias locking scheme where error signals are obtained from the beat between the optical carrier and optical tones generated by an auxiliary 2 MHz 𝑅𝐹 tone to lock the phases of all three involved interferometers for operation up to 10 GHz. With the developed method, we demonstrate an I/Q modulator in carrier-suppressed single-sideband mode, where the suppressed carrier and sideband are locked at optical power levels <−27dB\r\n relative to the transmitted sideband. We describe a simple analytical model for calculating the error signals and detail the implementation of the electronic circuitry for the implementation of the method.","lang":"eng"}],"intvolume":" 62","title":"Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone","status":"public","_id":"14759","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","keyword":["Atomic and Molecular Physics","and Optics","Engineering (miscellaneous)","Electrical and Electronic Engineering"],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"1-7","article_type":"original","citation":{"chicago":"Wald, Sebastian, Fritz R Diorico, and Onur Hosten. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” Applied Optics. Optica Publishing Group, 2023. https://doi.org/10.1364/ao.474118.","short":"S. Wald, F.R. Diorico, O. Hosten, Applied Optics 62 (2023) 1–7.","mla":"Wald, Sebastian, et al. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” Applied Optics, vol. 62, no. 1, Optica Publishing Group, 2023, pp. 1–7, doi:10.1364/ao.474118.","ieee":"S. Wald, F. R. Diorico, and O. Hosten, “Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone,” Applied Optics, vol. 62, no. 1. Optica Publishing Group, pp. 1–7, 2023.","apa":"Wald, S., Diorico, F. R., & Hosten, O. (2023). Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. Optica Publishing Group. https://doi.org/10.1364/ao.474118","ista":"Wald S, Diorico FR, Hosten O. 2023. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 62(1), 1–7.","ama":"Wald S, Diorico FR, Hosten O. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. 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Danzl, (2023).","mla":"Danzl, Johann G. Research Data for the Publication “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12817.","apa":"Danzl, J. G. (2023). Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12817","ieee":"J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue.’” Institute of Science and Technology Austria, 2023.","ista":"Danzl JG. 2023. Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12817.","ama":"Danzl JG. Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” 2023. doi:10.15479/AT:ISTA:12817"},"oa":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"date_published":"2023-05-19T00:00:00Z","doi":"10.15479/AT:ISTA:12817","type":"research_data","license":"https://creativecommons.org/licenses/by-sa/4.0/","abstract":[{"text":"3D-reconstruction of living brain tissue down to individual synapse level would create opportunities for decoding the dynamics and structure-function relationships of the brain’s complex and dense information processing network. However, it has been hindered by insufficient 3D-resolution, inadequate signal-to-noise-ratio, and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine learning technology, LIONESS (Live Information-Optimized Nanoscopy Enabling Saturated Segmentation). It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D-reconstruction at synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.","lang":"eng"}],"file_date_updated":"2023-05-18T19:51:52Z","status":"public","ddc":["570"],"title":"Research data for the publication \"Dense 4D nanoscale reconstruction of living brain tissue\"","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoDa"}],"_id":"12817","acknowledgement":"We thank J. Vorlaufer, N. Agudelo, A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, and M. Šuplata for hardware control support, and Márcia Cunha dos Santos for initial exploration of software. We thank Paul Henderson for advice on deep-learning training and Michael Sixt, Scott Boyd, and Tamara Weiss for discussions and critical reading of the manuscript. Luke Lavis (Janelia Research Campus) generously provided JF585-HaloTag ligand. 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Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01936-6.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20:1256-1265. doi:10.1038/s41592-023-01936-6","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01936-6","ieee":"P. Velicky et al., “Dense 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023."},"publication":"Nature Methods","date_published":"2023-08-01T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","day":"01","intvolume":" 20","title":"Dense 4D nanoscale reconstruction of living brain tissue","status":"public","_id":"13267","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue."}],"project":[{"name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"name":"High content imaging to decode human immune cell interactions in health and allergic disease","_id":"23889792-32DE-11EA-91FC-C7463DDC885E"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020","grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9"},{"_id":"2668BFA0-B435-11E9-9278-68D0E5697425","grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["001025621500001"],"pmid":["37429995"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-023-01936-6"}],"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"doi":"10.1038/s41592-023-01936-6","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"month":"08","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","volume":20,"date_updated":"2024-01-10T08:37:48Z","date_created":"2023-07-23T22:01:13Z","related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/LIONESS"}],"record":[{"status":"public","relation":"research_data","id":"12817"},{"relation":"shorter_version","status":"public","id":"14770"}]},"author":[{"last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp"},{"full_name":"Miguel Villalba, Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5665-0430","first_name":"Eder","last_name":"Miguel Villalba"},{"first_name":"Julia M","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M"},{"full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Lyudchik"},{"full_name":"Wei, Donglai","last_name":"Wei","first_name":"Donglai"},{"last_name":"Lin","first_name":"Zudi","full_name":"Lin, Zudi"},{"full_name":"Watson, Jake","last_name":"Watson","first_name":"Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"full_name":"Troidl, Jakob","first_name":"Jakob","last_name":"Troidl"},{"last_name":"Beyer","first_name":"Johanna","full_name":"Beyer, Johanna"},{"full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav","last_name":"Ben Simon"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer","full_name":"Sommer, Christoph M"},{"full_name":"Jahr, Wiebke","last_name":"Jahr","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cenameri","first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban"},{"full_name":"Broichhagen, Johannes","last_name":"Broichhagen","first_name":"Johannes"},{"first_name":"Seth G.N.","last_name":"Grant","full_name":"Grant, Seth G.N."},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"},{"full_name":"Pfister, Hanspeter","first_name":"Hanspeter","last_name":"Pfister"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}],"ec_funded":1},{"date_updated":"2024-01-10T08:59:26Z","date_created":"2024-01-10T08:42:40Z","related_material":{"link":[{"url":"https://github.com/IST-DASLab/pruned-vision-model-bias","relation":"software"}]},"author":[{"last_name":"Iofinova","first_name":"Eugenia B","orcid":"0000-0002-7778-3221","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","full_name":"Iofinova, Eugenia B"},{"full_name":"Peste, Elena-Alexandra","last_name":"Peste","first_name":"Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"department":[{"_id":"DaAl"},{"_id":"ChLa"}],"publisher":"IEEE","publication_status":"published","year":"2023","acknowledgement":"The authors would like to sincerely thank Sara Hooker for her feedback during the development of this work. EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35. AP and DA acknowledge generous ERC support, via Starting Grant 805223 ScaleML.","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1109/cvpr52729.2023.02334","conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","location":"Vancouver, BC, Canada","start_date":"2023-06-17","end_date":"2023-06-24"},"project":[{"_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","grant_number":" W1260-N35","name":"Vienna Graduate School on Computational Optimization"},{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["001062531308068"],"arxiv":["2304.12622"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.12622"}],"oa":1,"publication_identifier":{"eissn":["2575-7075"],"eisbn":["9798350301298"]},"month":"08","oa_version":"Preprint","status":"public","title":"Bias in pruned vision models: In-depth analysis and countermeasures","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14771","abstract":[{"lang":"eng","text":"Pruning—that is, setting a significant subset of the parameters of a neural network to zero—is one of the most popular methods of model compression. Yet, several recent works have raised the issue that pruning may induce or exacerbate bias in the output of the compressed model. Despite existing evidence for this phenomenon, the relationship between neural network pruning and induced bias is not well-understood. In this work, we systematically investigate and characterize this phenomenon in Convolutional Neural Networks for computer vision. First, we show that it is in fact possible to obtain highly-sparse models, e.g. with less than 10% remaining weights, which do not decrease in accuracy nor substantially increase in bias when compared to dense models. At the same time, we also find that, at higher sparsities, pruned models exhibit higher uncertainty in their outputs, as well as increased correlations, which we directly link to increased bias. We propose easy-to-use criteria which, based only on the uncompressed model, establish whether bias will increase with pruning, and identify the samples most susceptible to biased predictions post-compression. Our code can be found at https://github.com/IST-DASLab/pruned-vision-model-bias."}],"type":"conference","date_published":"2023-08-22T00:00:00Z","page":"24364-24373","citation":{"chicago":"Iofinova, Eugenia B, Elena-Alexandra Peste, and Dan-Adrian Alistarh. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” In 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 24364–73. IEEE, 2023. https://doi.org/10.1109/cvpr52729.2023.02334.","mla":"Iofinova, Eugenia B., et al. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 24364–73, doi:10.1109/cvpr52729.2023.02334.","short":"E.B. Iofinova, E.-A. Peste, D.-A. Alistarh, in:, 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 24364–24373.","ista":"Iofinova EB, Peste E-A, Alistarh D-A. 2023. Bias in pruned vision models: In-depth analysis and countermeasures. 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 24364–24373.","ieee":"E. B. Iofinova, E.-A. Peste, and D.-A. Alistarh, “Bias in pruned vision models: In-depth analysis and countermeasures,” in 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Vancouver, BC, Canada, 2023, pp. 24364–24373.","apa":"Iofinova, E. B., Peste, E.-A., & Alistarh, D.-A. (2023). Bias in pruned vision models: In-depth analysis and countermeasures. In 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 24364–24373). Vancouver, BC, Canada: IEEE. https://doi.org/10.1109/cvpr52729.2023.02334","ama":"Iofinova EB, Peste E-A, Alistarh D-A. Bias in pruned vision models: In-depth analysis and countermeasures. In: 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2023:24364-24373. doi:10.1109/cvpr52729.2023.02334"},"publication":"2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition","article_processing_charge":"No","day":"22"},{"_id":"14770","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","intvolume":" 20","oa_version":"None","type":"journal_article","abstract":[{"text":"We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale.","lang":"eng"}],"issue":"8","publication":"Nature Methods","citation":{"ama":"Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20(8):1141-1142. doi:10.1038/s41592-023-01937-5","ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142.","ieee":"J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20, no. 8. Springer Nature, pp. 1141–1142, 2023.","apa":"Danzl, J. G., & Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01937-5","mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:10.1038/s41592-023-01937-5.","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.","chicago":"Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01937-5."},"article_type":"letter_note","page":"1141-1142","date_published":"2023-08-01T00:00:00Z","scopus_import":"1","keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"day":"01","article_processing_charge":"No","year":"2023","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JoDa"}],"author":[{"first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"full_name":"Velicky, Philipp","last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"13267","status":"public","relation":"extended_version"}]},"date_updated":"2024-01-10T08:37:48Z","date_created":"2024-01-10T08:07:15Z","volume":20,"external_id":{"isi":["001025621500002"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41592-023-01937-5","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]}},{"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1242/dev.201559","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001097449100002"],"pmid":["37665167"]},"oa":1,"file_date_updated":"2024-01-10T12:41:13Z","article_number":"dev201559","volume":150,"date_updated":"2024-01-10T12:45:25Z","date_created":"2024-01-10T09:18:54Z","author":[{"full_name":"Harish, Rohit K","first_name":"Rohit K","last_name":"Harish","id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d"},{"full_name":"Gupta, Mansi","last_name":"Gupta","first_name":"Mansi"},{"full_name":"Zöller, Daniela","last_name":"Zöller","first_name":"Daniela"},{"first_name":"Hella","last_name":"Hartmann","full_name":"Hartmann, Hella"},{"last_name":"Gheisari","first_name":"Ali","full_name":"Gheisari, Ali"},{"full_name":"Machate, Anja","last_name":"Machate","first_name":"Anja"},{"full_name":"Hans, Stefan","first_name":"Stefan","last_name":"Hans"},{"full_name":"Brand, Michael","first_name":"Michael","last_name":"Brand"}],"department":[{"_id":"AnKi"}],"publisher":"The Company of Biologists","publication_status":"published","pmid":1,"acknowledgement":"We thank members of the Brand lab, as well as Justina Stark (Ivo Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany) for project-related discussions; Darren Gilmour (University of Zurich), Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology platform, TU Dresden for imaging and image analysis-related support; and Maurizio Abbate (Technical support, Arivis) for help with image analysis. We are also grateful to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft (BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics of Life’ seed grant and by institutional funds from Technische Universitat Dresden (to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited in PMC for immediate release.","year":"2023","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","keyword":["Developmental Biology","Molecular Biology"],"date_published":"2023-10-01T00:00:00Z","article_type":"original","citation":{"chicago":"Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari, Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” Development. The Company of Biologists, 2023. https://doi.org/10.1242/dev.201559.","mla":"Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” Development, vol. 150, no. 19, dev201559, The Company of Biologists, 2023, doi:10.1242/dev.201559.","short":"R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S. Hans, M. Brand, Development 150 (2023).","ista":"Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559.","ieee":"R. K. Harish et al., “Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation,” Development, vol. 150, no. 19. The Company of Biologists, 2023.","apa":"Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate, A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. The Company of Biologists. https://doi.org/10.1242/dev.201559","ama":"Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 2023;150(19). doi:10.1242/dev.201559"},"publication":"Development","issue":"19","abstract":[{"text":"Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"2d6f52dc33260a9b2352b8f28374ba5f","success":1,"date_created":"2024-01-10T12:41:13Z","date_updated":"2024-01-10T12:41:13Z","relation":"main_file","file_id":"14790","file_size":12836306,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_Development_Harish.pdf"}],"intvolume":" 150","title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","ddc":["570"],"status":"public","_id":"14774","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_number":"16527","file_date_updated":"2024-01-10T13:39:42Z","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"MDPI","acknowledgement":"We thank C.U.T. Hellen for critically reading the manuscript. The MALDI MS facility and CLSM became available to us in the framework of Moscow State University Development Programs PNG 5.13 and PNR 5.13.\r\nThis work was funded by the Russian Science Foundation, grant numbers 19-14-00010 and 22-14-00071.","year":"2023","pmid":1,"date_updated":"2024-01-10T13:41:10Z","date_created":"2024-01-10T09:24:35Z","volume":24,"author":[{"first_name":"Anastasiia","last_name":"Teplova","id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia"},{"full_name":"Pigidanov, Artemii A.","first_name":"Artemii A.","last_name":"Pigidanov"},{"full_name":"Serebryakova, Marina V.","first_name":"Marina V.","last_name":"Serebryakova"},{"full_name":"Golyshev, Sergei A.","last_name":"Golyshev","first_name":"Sergei A."},{"last_name":"Galiullina","first_name":"Raisa A.","full_name":"Galiullina, Raisa A."},{"full_name":"Chichkova, Nina V.","first_name":"Nina V.","last_name":"Chichkova"},{"first_name":"Andrey B.","last_name":"Vartapetian","full_name":"Vartapetian, Andrey B."}],"month":"11","publication_identifier":{"issn":["1422-0067"]},"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38003717"],"isi":["001113792600001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3390/ijms242216527","type":"journal_article","abstract":[{"lang":"eng","text":"Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident."}],"issue":"22","status":"public","ddc":["580"],"title":"Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3","intvolume":" 24","_id":"14776","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"dernst","file_size":2637784,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_IJMS_Teplova.pdf","success":1,"checksum":"4df7d206ba022b7f54eff1f0aec1659a","date_created":"2024-01-10T13:39:42Z","date_updated":"2024-01-10T13:39:42Z","file_id":"14791","relation":"main_file"}],"keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"],"day":"01","has_accepted_license":"1","article_processing_charge":"Yes","article_type":"original","publication":"International Journal of Molecular Sciences","citation":{"mla":"Teplova, Anastasiia, et al. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” International Journal of Molecular Sciences, vol. 24, no. 22, 16527, MDPI, 2023, doi:10.3390/ijms242216527.","short":"A. Teplova, A.A. Pigidanov, M.V. Serebryakova, S.A. Golyshev, R.A. Galiullina, N.V. Chichkova, A.B. Vartapetian, International Journal of Molecular Sciences 24 (2023).","chicago":"Teplova, Anastasiia, Artemii A. Pigidanov, Marina V. Serebryakova, Sergei A. Golyshev, Raisa A. Galiullina, Nina V. Chichkova, and Andrey B. Vartapetian. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms242216527.","ama":"Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 2023;24(22). doi:10.3390/ijms242216527","ista":"Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 24(22), 16527.","apa":"Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina, R. A., Chichkova, N. V., & Vartapetian, A. B. (2023). Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms242216527","ieee":"A. Teplova et al., “Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3,” International Journal of Molecular Sciences, vol. 24, no. 22. MDPI, 2023."},"date_published":"2023-11-01T00:00:00Z"},{"date_created":"2024-01-10T09:23:31Z","date_updated":"2024-01-10T13:31:46Z","volume":33,"author":[{"full_name":"Schnelli, Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","first_name":"Kevin","last_name":"Schnelli"},{"full_name":"Xu, Yuanyuan","orcid":"0000-0003-1559-1205","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3","last_name":"Xu","first_name":"Yuanyuan"}],"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","year":"2023","acknowledgement":"K. Schnelli was supported by the Swedish Research Council Grants VR-2017-05195, and the Knut and Alice Wallenberg Foundation. Y. Xu was supported by the Swedish Research Council Grant VR-2017-05195 and the ERC Advanced Grant “RMTBeyond” No. 101020331.","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1214/22-aap1826","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331"}],"oa":1,"external_id":{"isi":["000946432400021"],"arxiv":["2108.02728"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2108.02728"}],"month":"02","publication_identifier":{"issn":["1050-5164"]},"oa_version":"Preprint","title":"Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices","status":"public","intvolume":" 33","_id":"14775","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We establish a quantitative version of the Tracy–Widom law for the largest eigenvalue of high-dimensional sample covariance matrices. To be precise, we show that the fluctuations of the largest eigenvalue of a sample covariance matrix X∗X converge to its Tracy–Widom limit at a rate nearly N−1/3, where X is an M×N random matrix whose entries are independent real or complex random variables, assuming that both M and N tend to infinity at a constant rate. This result improves the previous estimate N−2/9 obtained by Wang (2019). Our proof relies on a Green function comparison method (Adv. Math. 229 (2012) 1435–1515) using iterative cumulant expansions, the local laws for the Green function and asymptotic properties of the correlation kernel of the white Wishart ensemble.","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2023-02-01T00:00:00Z","article_type":"original","page":"677-725","publication":"The Annals of Applied Probability","citation":{"chicago":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Sample Covariance Matrices.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-aap1826.","mla":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Sample Covariance Matrices.” The Annals of Applied Probability, vol. 33, no. 1, Institute of Mathematical Statistics, 2023, pp. 677–725, doi:10.1214/22-aap1826.","short":"K. Schnelli, Y. Xu, The Annals of Applied Probability 33 (2023) 677–725.","ista":"Schnelli K, Xu Y. 2023. Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. The Annals of Applied Probability. 33(1), 677–725.","apa":"Schnelli, K., & Xu, Y. (2023). Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/22-aap1826","ieee":"K. Schnelli and Y. Xu, “Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices,” The Annals of Applied Probability, vol. 33, no. 1. Institute of Mathematical Statistics, pp. 677–725, 2023.","ama":"Schnelli K, Xu Y. Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. The Annals of Applied Probability. 2023;33(1):677-725. doi:10.1214/22-aap1826"},"day":"01","article_processing_charge":"No","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"scopus_import":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14773","status":"public","title":"The cloud dynamics of convective storm systems","intvolume":" 76","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Through a combination of idealized simulations and real-world data, researchers are uncovering how internal feedbacks and large-scale motions influence cloud dynamics.","lang":"eng"}],"issue":"5","publication":"Physics Today","citation":{"chicago":"Muller, Caroline J, and Sophie Abramian. “The Cloud Dynamics of Convective Storm Systems.” Physics Today. AIP Publishing, 2023. https://doi.org/10.1063/pt.3.5234.","short":"C.J. Muller, S. Abramian, Physics Today 76 (2023).","mla":"Muller, Caroline J., and Sophie Abramian. “The Cloud Dynamics of Convective Storm Systems.” Physics Today, vol. 76, no. 5, 28, AIP Publishing, 2023, doi:10.1063/pt.3.5234.","ieee":"C. J. Muller and S. Abramian, “The cloud dynamics of convective storm systems,” Physics Today, vol. 76, no. 5. AIP Publishing, 2023.","apa":"Muller, C. J., & Abramian, S. (2023). The cloud dynamics of convective storm systems. Physics Today. AIP Publishing. https://doi.org/10.1063/pt.3.5234","ista":"Muller CJ, Abramian S. 2023. The cloud dynamics of convective storm systems. Physics Today. 76(5), 28.","ama":"Muller CJ, Abramian S. The cloud dynamics of convective storm systems. Physics Today. 2023;76(5). doi:10.1063/pt.3.5234"},"article_type":"original","date_published":"2023-05-01T00:00:00Z","keyword":["General Physics and Astronomy"],"day":"01","article_processing_charge":"No","year":"2023","publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"CaMu"}],"author":[{"full_name":"Muller, Caroline J","first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350"},{"first_name":"Sophie","last_name":"Abramian","full_name":"Abramian, Sophie"}],"date_created":"2024-01-10T09:18:04Z","date_updated":"2024-01-10T12:38:02Z","volume":76,"article_number":"28","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.lmd.ens.fr/muller/Pubs/2023-MullerAbramianPhysToday.pdf"}],"external_id":{"isi":["000984516100007"]},"isi":1,"quality_controlled":"1","doi":"10.1063/pt.3.5234","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["0031-9228"],"eissn":["1945-0699"]}},{"article_type":"original","citation":{"chicago":"Sato, Kosuke, Saurabh Singh, Itsuki Yamazaki, Keisuke Hirata, Artoni Kevin R. Ang, Masaharu Matsunami, and Tsunehiro Takeuchi. “Improvement of Thermoelectric Performance of Flexible Compound Ag2S0.55Se0.45 by Means of Partial V-Substitution for Ag.” AIP Advances. AIP Publishing, 2023. https://doi.org/10.1063/5.0171888.","short":"K. Sato, S. Singh, I. Yamazaki, K. Hirata, A.K.R. Ang, M. Matsunami, T. Takeuchi, AIP Advances 13 (2023).","mla":"Sato, Kosuke, et al. “Improvement of Thermoelectric Performance of Flexible Compound Ag2S0.55Se0.45 by Means of Partial V-Substitution for Ag.” AIP Advances, vol. 13, no. 12, 125206, AIP Publishing, 2023, doi:10.1063/5.0171888.","apa":"Sato, K., Singh, S., Yamazaki, I., Hirata, K., Ang, A. K. R., Matsunami, M., & Takeuchi, T. (2023). Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. AIP Advances. AIP Publishing. https://doi.org/10.1063/5.0171888","ieee":"K. Sato et al., “Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag,” AIP Advances, vol. 13, no. 12. AIP Publishing, 2023.","ista":"Sato K, Singh S, Yamazaki I, Hirata K, Ang AKR, Matsunami M, Takeuchi T. 2023. Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. AIP Advances. 13(12), 125206.","ama":"Sato K, Singh S, Yamazaki I, et al. Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. AIP Advances. 2023;13(12). doi:10.1063/5.0171888"},"publication":"AIP Advances","date_published":"2023-12-01T00:00:00Z","keyword":["General Physics and Astronomy"],"article_processing_charge":"Yes","has_accepted_license":"1","day":"01","intvolume":" 13","title":"Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag","status":"public","ddc":["540"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14777","file":[{"file_name":"2023_AIPAdvances_Sato.pdf","access_level":"open_access","creator":"dernst","file_size":9676071,"content_type":"application/pdf","file_id":"14792","relation":"main_file","date_updated":"2024-01-10T13:47:31Z","date_created":"2024-01-10T13:47:31Z","success":1,"checksum":"a7098388b8ff822b47f5ddd37ed3bdbc"}],"oa_version":"Published Version","type":"journal_article","issue":"12","abstract":[{"text":"The effects of the partial V-substitution for Ag on the thermoelectric (TE) properties are investigated for a flexible semiconducting compound Ag2S0.55Se0.45. Density functional theory calculations predict that such a partial V-substitution constructively modifies the electronic structure near the bottom of the conduction band to improve the TE performance. The synthesized Ag1.97V0.03S0.55Se0.45 is found to possess a TE dimensionless figure-of-merit (ZT) of 0.71 at 350 K with maintaining its flexible nature. This ZT value is relatively high in comparison with those reported for flexible TE materials below 360 K. The increase in the ZT value is caused by the enhanced absolute value of the Seebeck coefficient with less significant variation in electrical resistivity. The high ZT value with the flexible nature naturally allows us to employ the Ag1.97V0.03S0.55Se0.45 as a component of flexible TE generators.","lang":"eng"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001114917200005"]},"language":[{"iso":"eng"}],"doi":"10.1063/5.0171888","publication_identifier":{"eissn":["2158-3226"]},"month":"12","publisher":"AIP Publishing","department":[{"_id":"MaIb"}],"publication_status":"published","acknowledgement":"This work received financial support partially from Japan Science and Technology Agency (JST) CREST Grant No. JPMJCR18I2, Japan. The powder-XRD experiments were conducted at BL5S2 of Aichi Synchrotron Radiation Center, Aichi Science & Technology Foundation, Aichi, Japan (Proposal No. 202301057).","year":"2023","volume":13,"date_created":"2024-01-10T09:26:08Z","date_updated":"2024-01-10T13:49:09Z","author":[{"full_name":"Sato, Kosuke","last_name":"Sato","first_name":"Kosuke"},{"last_name":"Singh","first_name":"Saurabh","orcid":"0000-0003-2209-5269","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","full_name":"Singh, Saurabh"},{"last_name":"Yamazaki","first_name":"Itsuki","full_name":"Yamazaki, Itsuki"},{"full_name":"Hirata, Keisuke","first_name":"Keisuke","last_name":"Hirata"},{"last_name":"Ang","first_name":"Artoni Kevin R.","full_name":"Ang, Artoni Kevin R."},{"first_name":"Masaharu","last_name":"Matsunami","full_name":"Matsunami, Masaharu"},{"first_name":"Tsunehiro","last_name":"Takeuchi","full_name":"Takeuchi, Tsunehiro"}],"article_number":"125206","file_date_updated":"2024-01-10T13:47:31Z"},{"abstract":[{"lang":"eng","text":"We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence."}],"type":"journal_article","oa_version":"Published Version","_id":"9651","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Divergence of separated nets with respect to displacement equivalence","article_processing_charge":"Yes (via OA deal)","day":"17","scopus_import":"1","date_published":"2023-11-17T00:00:00Z","citation":{"chicago":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata. Springer Nature, 2023. https://doi.org/10.1007/s10711-023-00862-3.","short":"M. Dymond, V. Kaluza, Geometriae Dedicata (2023).","mla":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata, 15, Springer Nature, 2023, doi:10.1007/s10711-023-00862-3.","apa":"Dymond, M., & Kaluza, V. (2023). Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. Springer Nature. https://doi.org/10.1007/s10711-023-00862-3","ieee":"M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” Geometriae Dedicata. Springer Nature, 2023.","ista":"Dymond M, Kaluza V. 2023. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata., 15.","ama":"Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 2023. doi:10.1007/s10711-023-00862-3"},"publication":"Geometriae Dedicata","article_type":"original","article_number":"15","author":[{"first_name":"Michael","last_name":"Dymond","full_name":"Dymond, Michael"},{"orcid":"0000-0002-2512-8698","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","last_name":"Kaluza","first_name":"Vojtech","full_name":"Kaluza, Vojtech"}],"date_created":"2021-07-14T07:01:27Z","date_updated":"2024-01-11T13:06:32Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was started while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35. It was continued when the first named author was employed at University of Leipzig and the second named author was employed at Institute of Science and Technology of Austria, where he was supported by an IST Fellowship.","year":"2023","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","publication_status":"epub_ahead","publication_identifier":{"issn":["0046-5755"],"eissn":["1572-9168"]},"month":"11","doi":"10.1007/s10711-023-00862-3","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s10711-023-00862-3"}],"external_id":{"isi":["001105681500001"],"arxiv":["2102.13046"]},"isi":1,"quality_controlled":"1"},{"type":"conference","abstract":[{"text":"In all state-of-the-art sketching and coreset techniques for clustering, as well as in the best known fixed-parameter tractable approximation algorithms, randomness plays a key role. For the classic k-median and k-means problems, there are no known deterministic dimensionality reduction procedure or coreset construction that avoid an exponential dependency on the input dimension d, the precision parameter $\\varepsilon^{-1}$ or k. Furthermore, there is no coreset construction that succeeds with probability $1-1/n$ and whose size does not depend on the number of input points, n. This has led researchers in the area to ask what is the power of randomness for clustering sketches [Feldman WIREs Data Mining Knowl. Discov’20].Similarly, the best approximation ratio achievable deterministically without a complexity exponential in the dimension are $1+\\sqrt{2}$ for k-median [Cohen-Addad, Esfandiari, Mirrokni, Narayanan, STOC’22] and 6.12903 for k-means [Grandoni, Ostrovsky, Rabani, Schulman, Venkat, Inf. Process. Lett.’22]. Those are the best results, even when allowing a complexity FPT in the number of clusters k: this stands in sharp contrast with the $(1+\\varepsilon)$-approximation achievable in that case, when allowing randomization.In this paper, we provide deterministic sketches constructions for clustering, whose size bounds are close to the best-known randomized ones. We show how to compute a dimension reduction onto $\\varepsilon^{-O(1)} \\log k$ dimensions in time $k^{O\\left(\\varepsilon^{-O(1)}+\\log \\log k\\right)}$ poly $(n d)$, and how to build a coreset of size $O\\left(k^{2} \\log ^{3} k \\varepsilon^{-O(1)}\\right)$ in time $2^{\\varepsilon^{O(1)} k \\log ^{3} k}+k^{O\\left(\\varepsilon^{-O(1)}+\\log \\log k\\right)}$ poly $(n d)$. In the case where k is small, this answers an open question of [Feldman WIDM’20] and [Munteanu and Schwiegelshohn, Künstliche Intell. ’18] on whether it is possible to efficiently compute coresets deterministically.We also construct a deterministic algorithm for computing $(1+$ $\\varepsilon)$-approximation to k-median and k-means in high dimensional Euclidean spaces in time $2^{k^{2} \\log ^{3} k / \\varepsilon^{O(1)}}$ poly $(n d)$, close to the best randomized complexity of $2^{(k / \\varepsilon)^{O(1)}}$ nd (see [Kumar, Sabharwal, Sen, JACM 10] and [Bhattacharya, Jaiswal, Kumar, TCS’18]).Furthermore, our new insights on sketches also yield a randomized coreset construction that uses uniform sampling, that immediately improves over the recent results of [Braverman et al. FOCS ’22] by a factor k.","lang":"eng"}],"title":"Deterministic clustering in high dimensional spaces: Sketches and approximation","status":"public","_id":"14768","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"22","page":"1105-1130","citation":{"chicago":"Cohen-Addad, Vincent, David Saulpic, and Chris Schwiegelshohn. “Deterministic Clustering in High Dimensional Spaces: Sketches and Approximation.” In 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, 1105–30. IEEE, 2023. https://doi.org/10.1109/focs57990.2023.00066.","short":"V. Cohen-Addad, D. Saulpic, C. Schwiegelshohn, in:, 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, IEEE, 2023, pp. 1105–1130.","mla":"Cohen-Addad, Vincent, et al. “Deterministic Clustering in High Dimensional Spaces: Sketches and Approximation.” 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, IEEE, 2023, pp. 1105–30, doi:10.1109/focs57990.2023.00066.","ieee":"V. Cohen-Addad, D. Saulpic, and C. Schwiegelshohn, “Deterministic clustering in high dimensional spaces: Sketches and approximation,” in 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, Santa Cruz, CA, United States, 2023, pp. 1105–1130.","apa":"Cohen-Addad, V., Saulpic, D., & Schwiegelshohn, C. (2023). Deterministic clustering in high dimensional spaces: Sketches and approximation. In 2023 IEEE 64th Annual Symposium on Foundations of Computer Science (pp. 1105–1130). Santa Cruz, CA, United States: IEEE. https://doi.org/10.1109/focs57990.2023.00066","ista":"Cohen-Addad V, Saulpic D, Schwiegelshohn C. 2023. Deterministic clustering in high dimensional spaces: Sketches and approximation. 2023 IEEE 64th Annual Symposium on Foundations of Computer Science. FOCS: Symposium on Foundations of Computer Science, 1105–1130.","ama":"Cohen-Addad V, Saulpic D, Schwiegelshohn C. Deterministic clustering in high dimensional spaces: Sketches and approximation. In: 2023 IEEE 64th Annual Symposium on Foundations of Computer Science. IEEE; 2023:1105-1130. doi:10.1109/focs57990.2023.00066"},"publication":"2023 IEEE 64th Annual Symposium on Foundations of Computer Science","date_published":"2023-12-22T00:00:00Z","ec_funded":1,"department":[{"_id":"MoHe"}],"publisher":"IEEE","publication_status":"published","year":"2023","acknowledgement":"D. Sauplic has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413, and Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)”.\r\nC. Schwiegelshohn acknowledges the support of the Independent Research Fund Denmark (DFF) under a Sapere Aude Research Leader grant No 1051-00106B.","date_updated":"2024-01-16T07:28:06Z","date_created":"2024-01-09T16:20:09Z","author":[{"full_name":"Cohen-Addad, Vincent","first_name":"Vincent","last_name":"Cohen-Addad"},{"id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","first_name":"David","last_name":"Saulpic","full_name":"Saulpic, David"},{"full_name":"Schwiegelshohn, Chris","first_name":"Chris","last_name":"Schwiegelshohn"}],"publication_identifier":{"eisbn":["9798350318944"]},"month":"12","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"},{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures"}],"quality_controlled":"1","external_id":{"arxiv":["2310.04076"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.04076","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1109/focs57990.2023.00066","conference":{"name":"FOCS: Symposium on Foundations of Computer Science","end_date":"2023-11-09","start_date":"2023-11-06","location":"Santa Cruz, CA, United States"}},{"status":"public","title":"Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells","ddc":["570"],"intvolume":" 9","_id":"14784","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","file_size":1596639,"content_type":"application/pdf","file_name":"2023_ScienceAdvances_GallardoDodd.pdf","access_level":"open_access","date_created":"2024-01-16T09:35:28Z","date_updated":"2024-01-16T09:35:28Z","success":1,"checksum":"b9072e20e2d5d9d34d2c53319bafee41","file_id":"14809","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity."}],"issue":"34","article_type":"original","publication":"Science Advances","citation":{"chicago":"Gallardo-Dodd, Carlos J., Christian Oertlin, Julien Record, Rômulo G. Galvani, Christian Sommerauer, Nikolai V. Kuznetsov, Evangelos Doukoumopoulos, et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.adg1610.","mla":"Gallardo-Dodd, Carlos J., et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” Science Advances, vol. 9, no. 34, adg1610, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.adg1610.","short":"C.J. Gallardo-Dodd, C. Oertlin, J. Record, R.G. Galvani, C. Sommerauer, N.V. Kuznetsov, E. Doukoumopoulos, L. Ali, M.M.S. Oliveira, C. Seitz, M. Percipalle, T. Nikić, A.A. Sadova, S.M. Shulgina, V.A. Shmarov, O.V. Kutko, D.D. Vlasova, K.D. Orlova, M.P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S.A. Ponomarev, L.S. Westerberg, Science Advances 9 (2023).","ista":"Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. 2023. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 9(34), adg1610.","apa":"Gallardo-Dodd, C. J., Oertlin, C., Record, J., Galvani, R. G., Sommerauer, C., Kuznetsov, N. V., … Westerberg, L. S. (2023). Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adg1610","ieee":"C. J. Gallardo-Dodd et al., “Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells,” Science Advances, vol. 9, no. 34. American Association for the Advancement of Science, 2023.","ama":"Gallardo-Dodd CJ, Oertlin C, Record J, et al. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 2023;9(34). doi:10.1126/sciadv.adg1610"},"date_published":"2023-08-25T00:00:00Z","keyword":["Multidisciplinary"],"day":"25","article_processing_charge":"Yes","has_accepted_license":"1","publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"FlSc"}],"acknowledgement":"This work was supported by a postdoctoral fellowship from the Swedish Society for Medical Research to J.R., a CAPES-STINT joint grant to R.G.G. and L.S.W., a PhD fellowship from Karolinska Institutet (KID) to E.D., a PhD fellowship from Fundação para a Ciência e a Tecnologia and European Social Fund to M.M.S.O., the program of fundamental research (theme 65.1) of the Institute for Biomedical Problems of the Russian Academy of Sciences (IBMP RAS) to A.A.S., S.M.S., V.A.S., O.V.K., D.D.V., K.D.O., M.P.R., and S.A.P., the Tamkeen under the NYU Abu Dhabi Research Institute Award to the NYUAD Center for Genomics and Systems Biology (ADHPG-CGSB) to P.P., the Knut and Alice Wallenberg foundation to C.K., the Swedish National Space Agency to N.V.K. and L.S.W., Swedish Research Council, Gösta Fraenckel Foundation, and Karolinska Institutet to L.S.W.","year":"2023","pmid":1,"date_created":"2024-01-10T09:48:01Z","date_updated":"2024-01-16T09:38:58Z","volume":9,"author":[{"full_name":"Gallardo-Dodd, Carlos J.","first_name":"Carlos J.","last_name":"Gallardo-Dodd"},{"full_name":"Oertlin, Christian","first_name":"Christian","last_name":"Oertlin"},{"full_name":"Record, Julien","first_name":"Julien","last_name":"Record"},{"full_name":"Galvani, Rômulo G.","last_name":"Galvani","first_name":"Rômulo G."},{"full_name":"Sommerauer, Christian","last_name":"Sommerauer","first_name":"Christian"},{"full_name":"Kuznetsov, Nikolai V.","first_name":"Nikolai V.","last_name":"Kuznetsov"},{"last_name":"Doukoumopoulos","first_name":"Evangelos","full_name":"Doukoumopoulos, Evangelos"},{"full_name":"Ali, Liaqat","first_name":"Liaqat","last_name":"Ali"},{"last_name":"Oliveira","first_name":"Mariana M. S.","full_name":"Oliveira, Mariana M. S."},{"first_name":"Christina","last_name":"Seitz","full_name":"Seitz, Christina"},{"full_name":"Percipalle, Mathias","id":"45adb726-eb97-11eb-a6c2-c7c3d3caabe9","first_name":"Mathias","last_name":"Percipalle"},{"full_name":"Nikić, Tijana","first_name":"Tijana","last_name":"Nikić"},{"full_name":"Sadova, Anastasia A.","first_name":"Anastasia A.","last_name":"Sadova"},{"full_name":"Shulgina, Sofia M.","first_name":"Sofia M.","last_name":"Shulgina"},{"last_name":"Shmarov","first_name":"Vjacheslav A.","full_name":"Shmarov, Vjacheslav A."},{"last_name":"Kutko","first_name":"Olga V.","full_name":"Kutko, Olga V."},{"full_name":"Vlasova, Daria D.","last_name":"Vlasova","first_name":"Daria D."},{"full_name":"Orlova, Kseniya D.","last_name":"Orlova","first_name":"Kseniya D."},{"full_name":"Rykova, Marina P.","first_name":"Marina P.","last_name":"Rykova"},{"last_name":"Andersson","first_name":"John","full_name":"Andersson, John"},{"full_name":"Percipalle, Piergiorgio","first_name":"Piergiorgio","last_name":"Percipalle"},{"first_name":"Claudia","last_name":"Kutter","full_name":"Kutter, Claudia"},{"full_name":"Ponomarev, Sergey A.","last_name":"Ponomarev","first_name":"Sergey A."},{"full_name":"Westerberg, Lisa S.","last_name":"Westerberg","first_name":"Lisa S."}],"article_number":"adg1610","file_date_updated":"2024-01-16T09:35:28Z","isi":1,"quality_controlled":"1","external_id":{"isi":["001054596800007"],"pmid":["37624890"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.adg1610","month":"08","publication_identifier":{"issn":["2375-2548"]}},{"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"06","keyword":["Biophysics"],"date_published":"2023-06-06T00:00:00Z","citation":{"mla":"Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” Biophysical Journal, vol. 122, no. 11, Elsevier, 2023, pp. 2311–24, doi:10.1016/j.bpj.2023.02.018.","short":"L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical Journal 122 (2023) 2311–2324.","chicago":"Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” Biophysical Journal. Elsevier, 2023. https://doi.org/10.1016/j.bpj.2023.02.018.","ama":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 2023;122(11):2311-2324. doi:10.1016/j.bpj.2023.02.018","ista":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. 2023. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 122(11), 2311–2324.","ieee":"L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink, “Branched actin cortices reconstituted in vesicles sense membrane curvature,” Biophysical Journal, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.","apa":"Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., & Koenderink, G. H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.02.018"},"publication":"Biophysical Journal","page":"2311-2324","article_type":"original","issue":"11","abstract":[{"lang":"eng","text":"The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks are inherently able to sense and generate membrane curvature, or whether they rely on their diverse binding partners to accomplish this. Here, we show that curvature sensing is an inherent capability of branched actin networks nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface of the GUV membrane. We show that actin forms a uniform and thin cortical layer when present at high concentration and distinct patches associated with negative membrane curvature at low concentration. Serendipitously, we find that the GUV production method also produces dumbbell-shaped GUVs, which we explain using mathematical modeling in terms of membrane hemifusion of nested GUVs. We find that branched actin networks preferentially assemble at the neck of the dumbbells, which possess a micrometer-range convex curvature comparable with the curvature of the actin patches found in spherical GUVs. Minimal branched actin networks can thus sense membrane curvature, which may help mammalian cells to robustly recruit actin to curved membranes to facilitate diverse cellular functions such as cytokinesis and migration."}],"type":"journal_article","file":[{"creator":"dernst","content_type":"application/pdf","file_size":3285810,"file_name":"2023_BiophysicalJournal_Baldauf.pdf","access_level":"open_access","date_updated":"2024-01-16T09:09:29Z","date_created":"2024-01-16T09:09:29Z","success":1,"checksum":"70566e54cd95ea6df340909ad44c5cd5","file_id":"14807","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14782","intvolume":" 122","ddc":["570"],"title":"Branched actin cortices reconstituted in vesicles sense membrane curvature","status":"public","publication_identifier":{"issn":["0006-3495"]},"month":"06","doi":"10.1016/j.bpj.2023.02.018","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["001016792600001"],"pmid":["36806830"]},"quality_controlled":"1","isi":1,"file_date_updated":"2024-01-16T09:09:29Z","related_material":{"link":[{"url":"https://github.com/BioSoftMatterGroup/actin-curvature-sensing","relation":"software"}]},"author":[{"full_name":"Baldauf, Lucia","first_name":"Lucia","last_name":"Baldauf"},{"full_name":"Frey, Felix F","first_name":"Felix F","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3"},{"full_name":"Arribas Perez, Marcos","last_name":"Arribas Perez","first_name":"Marcos"},{"last_name":"Idema","first_name":"Timon","full_name":"Idema, Timon"},{"last_name":"Koenderink","first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H."}],"volume":122,"date_updated":"2024-01-16T09:20:03Z","date_created":"2024-01-10T09:45:48Z","pmid":1,"acknowledgement":"We thank Jeffrey den Haan for protein purification, Kristina Ganzinger (AMOLF) for providing the 10xHis VCA construct, David Kovar (University of Chicago) for the CP constructs, and Michael Way (Crick Institute) for providing purified human Arp2/3 proteins. We are grateful to Iris Lambert for early actin encapsulation experiments that formed the basis for establishing the eDICE method, to Federico Fanalista for acquiring images of dumbbell-shaped GUVs in samples produced by cDICE, and to Tom Aarts for images of dumbbell-shaped GUVs produced by gel-assisted swelling. Lennard van Buren is thanked for his help with image analysis to quantify actin concentrations in GUVs. We thank Kristina Ganzinger (AMOLF) for hosting us to perform pyrene assays in her lab, and Balász Antalicz (AMOLF) for technical assistance with the spectrophotometer. The authors also thank Matthieu Piel and Daniel Fletcher for insightful and inspiring discussions. We acknowledge financial support from The Netherlands Organization of Scientific Research (NWO/OCW) Gravitation program Building a Synthetic Cell (BaSyC) (024.003.019). F.F. gratefully acknowledges funding from the Kavli Synergy program of the Kavli Institute of Nanoscience Delft.","year":"2023","department":[{"_id":"AnSa"}],"publisher":"Elsevier","publication_status":"published"},{"article_number":"1133","file_date_updated":"2024-01-16T09:26:52Z","publisher":"MDPI","department":[{"_id":"SiHi"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"This research was funded by grants from the European Research Council (Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD) to N.R., as well as from FP7-PEOPLE Marie Curie Intra-European Fellowship for career development (grant #622289) to G.C. We thank Elena Dossi, Grégory Ghézali, and Jérémie Teillon for support with setting up the MEA system for the two-photon microscope. We would also like to thank Tayfun Palaz for their technical assistance with the EM preparations.","volume":12,"date_created":"2024-01-10T09:46:35Z","date_updated":"2024-01-16T09:29:35Z","author":[{"full_name":"Cheung, Giselle T","first_name":"Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572"},{"full_name":"Chever, Oana","last_name":"Chever","first_name":"Oana"},{"full_name":"Rollenhagen, Astrid","first_name":"Astrid","last_name":"Rollenhagen"},{"first_name":"Nicole","last_name":"Quenech’du","full_name":"Quenech’du, Nicole"},{"full_name":"Ezan, Pascal","first_name":"Pascal","last_name":"Ezan"},{"first_name":"Joachim H. R.","last_name":"Lübke","full_name":"Lübke, Joachim H. R."},{"full_name":"Rouach, Nathalie","last_name":"Rouach","first_name":"Nathalie"}],"publication_identifier":{"issn":["2073-4409"]},"month":"04","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000977445700001"],"pmid":["37190042"]},"language":[{"iso":"eng"}],"doi":"10.3390/cells12081133","type":"journal_article","issue":"8","abstract":[{"text":"Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic astroglial processes and plays major roles in synaptic transmission. We have previously found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent glutamine release to sustain physiological synaptic transmissions and cognitiogns. However, whether Cx43 is important for the release of synaptic vesicles, which is a critical component of synaptic efficacy, remains unanswered. Here, using transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate whether and how astrocytes regulate the release of synaptic vesicles from hippocampal synapses. We report that CA1 pyramidal neurons and their synapses develop normally in the absence of astroglial Cx43. However, a significant impairment in synaptic vesicle distribution and release dynamics were observed. In particular, the FM1-43 assays performed using two-photon live imaging and combined with multi-electrode array stimulation in acute hippocampal slices, revealed a slower rate of synaptic vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that synaptic vesicle release probability was also reduced and is dependent on glutamine supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for Cx43 in regulating presynaptic functions by controlling the rate and probability of synaptic vesicle release. Our findings further highlight the significance of astroglial Cx43 in synaptic transmission and efficacy.","lang":"eng"}],"intvolume":" 12","ddc":["570"],"status":"public","title":"Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14783","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":7931643,"access_level":"open_access","file_name":"2023_Cells_Cheung.pdf","success":1,"checksum":"6798cd75d8857976fbc58a43fd173d68","date_created":"2024-01-16T09:26:52Z","date_updated":"2024-01-16T09:26:52Z","file_id":"14808","relation":"main_file"}],"keyword":["General Medicine"],"has_accepted_license":"1","article_processing_charge":"Yes","day":"11","article_type":"original","citation":{"ista":"Cheung GT, Chever O, Rollenhagen A, Quenech’du N, Ezan P, Lübke JHR, Rouach N. 2023. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. 12(8), 1133.","apa":"Cheung, G. T., Chever, O., Rollenhagen, A., Quenech’du, N., Ezan, P., Lübke, J. H. R., & Rouach, N. (2023). Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. MDPI. https://doi.org/10.3390/cells12081133","ieee":"G. T. Cheung et al., “Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses,” Cells, vol. 12, no. 8. MDPI, 2023.","ama":"Cheung GT, Chever O, Rollenhagen A, et al. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. 2023;12(8). doi:10.3390/cells12081133","chicago":"Cheung, Giselle T, Oana Chever, Astrid Rollenhagen, Nicole Quenech’du, Pascal Ezan, Joachim H. R. Lübke, and Nathalie Rouach. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” Cells. MDPI, 2023. https://doi.org/10.3390/cells12081133.","mla":"Cheung, Giselle T., et al. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” Cells, vol. 12, no. 8, 1133, MDPI, 2023, doi:10.3390/cells12081133.","short":"G.T. Cheung, O. Chever, A. Rollenhagen, N. Quenech’du, P. Ezan, J.H.R. Lübke, N. Rouach, Cells 12 (2023)."},"publication":"Cells","date_published":"2023-04-11T00:00:00Z"},{"file_date_updated":"2024-01-16T09:42:10Z","publication_status":"published","publisher":"Wiley","department":[{"_id":"MaLo"}],"year":"2023","acknowledgement":"We thank the lab of Francisco Javier Florencio Bel-lido, Sevilla, Spain for supplying theSynechocystislabtype Sevilla used in this work and the lab of MartinHagemann, Rostock, Germany for supplying the pIGAplasmidusedinthiswork.WethankNilsHülterforfruitful discussions. We thank Fenna Stücker forgraphical illustrations and Katrin Schumann, FennaStücker, and Lidusha Manivannan for technicalsupport.\r\nChilean National Agency for Research andDevelopment (ANID), Grant/Award Number:21191763; DeutscheForschungsgemeinschaft, Grant/AwardNumbers: 456882089, RTG2501; EuropeanResearch Council (ERC), Grant/AwardNumber: 101043835","pmid":1,"date_created":"2024-01-10T10:41:07Z","date_updated":"2024-01-16T09:46:12Z","volume":15,"author":[{"full_name":"Nies, Fabian","first_name":"Fabian","last_name":"Nies"},{"full_name":"Wein, Tanita","first_name":"Tanita","last_name":"Wein"},{"last_name":"Hanke","first_name":"Dustin M.","full_name":"Hanke, Dustin M."},{"full_name":"Springstein, Benjamin L","orcid":"0000-0002-3461-5391","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","last_name":"Springstein","first_name":"Benjamin L"},{"full_name":"Alcorta, Jaime","last_name":"Alcorta","first_name":"Jaime"},{"full_name":"Taubenheim, Claudia","last_name":"Taubenheim","first_name":"Claudia"},{"first_name":"Tal","last_name":"Dagan","full_name":"Dagan, Tal"}],"month":"12","publication_identifier":{"eissn":["1758-2229"]},"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001080203100001"],"pmid":["37794696"]},"language":[{"iso":"eng"}],"doi":"10.1111/1758-2229.13203","type":"journal_article","abstract":[{"text":"Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid‐encoded genes is similar to that of chromosome‐encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two Synechocystis sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited.","lang":"eng"}],"issue":"6","status":"public","ddc":["570"],"title":"Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803","intvolume":" 15","_id":"14785","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"14810","relation":"main_file","success":1,"checksum":"d09ebb68fee61f4e2e09ec286c9cf1d3","date_updated":"2024-01-16T09:42:10Z","date_created":"2024-01-16T09:42:10Z","access_level":"open_access","file_name":"2023_EnvirMicroBiolReports_Nies.pdf","creator":"dernst","content_type":"application/pdf","file_size":1518350}],"keyword":["Agricultural and Biological Sciences (miscellaneous)","Ecology","Evolution","Behavior and Systematics"],"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","article_type":"original","page":"656-668","publication":"Environmental Microbiology Reports","citation":{"mla":"Nies, Fabian, et al. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental Microbiology Reports, vol. 15, no. 6, Wiley, 2023, pp. 656–68, doi:10.1111/1758-2229.13203.","short":"F. Nies, T. Wein, D.M. Hanke, B.L. Springstein, J. Alcorta, C. Taubenheim, T. Dagan, Environmental Microbiology Reports 15 (2023) 656–668.","chicago":"Nies, Fabian, Tanita Wein, Dustin M. Hanke, Benjamin L Springstein, Jaime Alcorta, Claudia Taubenheim, and Tal Dagan. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental Microbiology Reports. Wiley, 2023. https://doi.org/10.1111/1758-2229.13203.","ama":"Nies F, Wein T, Hanke DM, et al. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 2023;15(6):656-668. doi:10.1111/1758-2229.13203","ista":"Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T. 2023. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 15(6), 656–668.","ieee":"F. Nies et al., “Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803,” Environmental Microbiology Reports, vol. 15, no. 6. Wiley, pp. 656–668, 2023.","apa":"Nies, F., Wein, T., Hanke, D. M., Springstein, B. L., Alcorta, J., Taubenheim, C., & Dagan, T. (2023). Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. Wiley. https://doi.org/10.1111/1758-2229.13203"},"date_published":"2023-12-01T00:00:00Z"},{"publication_identifier":{"eissn":["1879-209X"],"issn":["0304-4149"]},"month":"09","doi":"10.1016/j.spa.2023.05.009","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2302.13502"],"isi":["001113615900001"]},"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"quality_controlled":"1","isi":1,"ec_funded":1,"file_date_updated":"2024-01-16T08:47:31Z","author":[{"last_name":"Ding","first_name":"Xiucai","full_name":"Ding, Xiucai"},{"id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d","last_name":"Ji","first_name":"Hong Chang","full_name":"Ji, Hong Chang"}],"volume":163,"date_created":"2024-01-10T09:29:25Z","date_updated":"2024-01-16T08:49:51Z","acknowledgement":"The authors would like to thank the editor, the associated editor and two anonymous referees for their many critical suggestions which have significantly improved the paper. The authors are also grateful to Zhigang Bao and Ji Oon Lee for many helpful discussions. The first author also wants to thank Hari Bercovici for many useful comments. The first author is partially supported by National Science Foundation DMS-2113489 and the second author is supported by ERC Advanced Grant “RMTBeyond” No. 101020331.","year":"2023","publisher":"Elsevier","department":[{"_id":"LaEr"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","keyword":["Applied Mathematics","Modeling and Simulation","Statistics and Probability"],"date_published":"2023-09-01T00:00:00Z","citation":{"short":"X. Ding, H.C. Ji, Stochastic Processes and Their Applications 163 (2023) 25–60.","mla":"Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and Principal Components.” Stochastic Processes and Their Applications, vol. 163, Elsevier, 2023, pp. 25–60, doi:10.1016/j.spa.2023.05.009.","chicago":"Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and Principal Components.” Stochastic Processes and Their Applications. Elsevier, 2023. https://doi.org/10.1016/j.spa.2023.05.009.","ama":"Ding X, Ji HC. Spiked multiplicative random matrices and principal components. Stochastic Processes and their Applications. 2023;163:25-60. doi:10.1016/j.spa.2023.05.009","ieee":"X. Ding and H. C. Ji, “Spiked multiplicative random matrices and principal components,” Stochastic Processes and their Applications, vol. 163. Elsevier, pp. 25–60, 2023.","apa":"Ding, X., & Ji, H. C. (2023). Spiked multiplicative random matrices and principal components. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2023.05.009","ista":"Ding X, Ji HC. 2023. Spiked multiplicative random matrices and principal components. Stochastic Processes and their Applications. 163, 25–60."},"publication":"Stochastic Processes and their Applications","page":"25-60","article_type":"original","abstract":[{"lang":"eng","text":"In this paper, we study the eigenvalues and eigenvectors of the spiked invariant multiplicative models when the randomness is from Haar matrices. We establish the limits of the outlier eigenvalues λˆi and the generalized components (⟨v,uˆi⟩ for any deterministic vector v) of the outlier eigenvectors uˆi with optimal convergence rates. Moreover, we prove that the non-outlier eigenvalues stick with those of the unspiked matrices and the non-outlier eigenvectors are delocalized. The results also hold near the so-called BBP transition and for degenerate spikes. On one hand, our results can be regarded as a refinement of the counterparts of [12] under additional regularity conditions. On the other hand, they can be viewed as an analog of [34] by replacing the random matrix with i.i.d. entries with Haar random matrix."}],"type":"journal_article","file":[{"file_id":"14806","relation":"main_file","success":1,"checksum":"46a708b0cd5569a73d0f3d6c3e0a44dc","date_updated":"2024-01-16T08:47:31Z","date_created":"2024-01-16T08:47:31Z","access_level":"open_access","file_name":"2023_StochasticProcAppl_Ding.pdf","creator":"dernst","file_size":1870349,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"14780","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 163","ddc":["510"],"title":"Spiked multiplicative random matrices and principal components","status":"public"},{"oa_version":"Published Version","file":[{"creator":"dernst","file_size":2529327,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_GeophysicalResearchLetter_Shaw.pdf","success":1,"checksum":"391a3005c95340a0ae129ce4fbdf2bae","date_updated":"2024-01-16T08:35:02Z","date_created":"2024-01-16T08:35:02Z","file_id":"14805","relation":"main_file"}],"intvolume":" 50","ddc":["550"],"title":"The decaying near‐surface boundary layer of a retreating alpine glacier","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14779","issue":"11","abstract":[{"text":"The presence of a developed boundary layer decouples a glacier's response from ambient conditions, suggesting that sensitivity to climate change is increased by glacier retreat. To test this hypothesis, we explore six years of distributed meteorological data on a small Swiss glacier in the period 2001–2022. Large glacier fragmentation has occurred since 2001 (−35% area change up to 2022) coinciding with notable frontal retreat, an observed switch from down‐glacier katabatic to up‐glacier valley winds and an increased sensitivity (ratio) of on‐glacier to off‐glacier temperature. As the glacier ceases to develop density‐driven katabatic winds, sensible heat fluxes on the glacier are increasingly determined by the conditions occurring outside the boundary layer of the glacier, sealing the glacier's demise as the climate continues to warm and experience an increased frequency of extreme summers.","lang":"eng"}],"type":"journal_article","date_published":"2023-06-16T00:00:00Z","article_type":"original","citation":{"short":"T.E. Shaw, P. Buri, M. McCarthy, E.S. Miles, Á. Ayala, F. Pellicciotti, Geophysical Research Letters 50 (2023).","mla":"Shaw, Thomas E., et al. “The Decaying Near‐surface Boundary Layer of a Retreating Alpine Glacier.” Geophysical Research Letters, vol. 50, no. 11, e2023GL103043, American Geophysical Union, 2023, doi:10.1029/2023gl103043.","chicago":"Shaw, Thomas E., Pascal Buri, Michael McCarthy, Evan S. Miles, Álvaro Ayala, and Francesca Pellicciotti. “The Decaying Near‐surface Boundary Layer of a Retreating Alpine Glacier.” Geophysical Research Letters. American Geophysical Union, 2023. https://doi.org/10.1029/2023gl103043.","ama":"Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. The decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical Research Letters. 2023;50(11). doi:10.1029/2023gl103043","apa":"Shaw, T. E., Buri, P., McCarthy, M., Miles, E. S., Ayala, Á., & Pellicciotti, F. (2023). The decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2023gl103043","ieee":"T. E. Shaw, P. Buri, M. McCarthy, E. S. Miles, Á. Ayala, and F. Pellicciotti, “The decaying near‐surface boundary layer of a retreating alpine glacier,” Geophysical Research Letters, vol. 50, no. 11. American Geophysical Union, 2023.","ista":"Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. 2023. The decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical Research Letters. 50(11), e2023GL103043."},"publication":"Geophysical Research Letters","article_processing_charge":"No","has_accepted_license":"1","day":"16","keyword":["General Earth and Planetary Sciences","Geophysics"],"volume":50,"date_updated":"2024-01-16T08:42:36Z","date_created":"2024-01-10T09:28:34Z","author":[{"first_name":"Thomas E.","last_name":"Shaw","full_name":"Shaw, Thomas E."},{"full_name":"Buri, Pascal","last_name":"Buri","first_name":"Pascal"},{"last_name":"McCarthy","first_name":"Michael","full_name":"McCarthy, Michael"},{"full_name":"Miles, Evan S.","last_name":"Miles","first_name":"Evan S."},{"first_name":"Álvaro","last_name":"Ayala","full_name":"Ayala, Álvaro"},{"orcid":"0000-0002-5554-8087","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca","full_name":"Pellicciotti, Francesca"}],"publisher":"American Geophysical Union","department":[{"_id":"FrPe"}],"publication_status":"published","acknowledgement":"This work was funded by the EU Horizon 2020 Marie Skłodowska-Curie Actions Grant 101026058. The authors acknowl-edge the dedicated collection of field data by many parties since 2001, including those acknowledged for the cited works on Arolla Glacier. The authors would like to thank Fabienne Meier, Alice Zaugg, Raphael Willi, Maria Grundmann, and Marta Corrà for assistance in the field for the summers of 2021 and 2022. Off-glacier data provided by Grand Dixence SA (Arolla) and MeteoSwiss are kindly acknowledged. Simone Fatichi is thanked for the provision and support in the use of the Tethys-Chloris model. We thank Editor Mathieu Morlighem and two anonymous reviewers whose comments have helped to improve the quality of the manuscript.","year":"2023","file_date_updated":"2024-01-16T08:35:02Z","article_number":"e2023GL103043","language":[{"iso":"eng"}],"doi":"10.1029/2023gl103043","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000999436400001"]},"publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"month":"06"},{"date_published":"2023-11-15T00:00:00Z","page":"256","citation":{"ista":"Zikelic D. 2023. Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria.","apa":"Zikelic, D. (2023). Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria. https://doi.org/10.15479/14539","ieee":"D. Zikelic, “Automated verification and control of infinite state stochastic systems,” Institute of Science and Technology Austria, 2023.","ama":"Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:10.15479/14539","chicago":"Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14539.","mla":"Zikelic, Dorde. Automated Verification and Control of Infinite State Stochastic Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/14539.","short":"D. Zikelic, Automated Verification and Control of Infinite State Stochastic Systems, Institute of Science and Technology Austria, 2023."},"article_processing_charge":"No","day":"15","file":[{"file_id":"14540","relation":"main_file","date_updated":"2023-11-15T13:43:28Z","date_created":"2023-11-15T13:43:28Z","success":1,"checksum":"f23e002b0059ca78e1fbb864da52dd7e","file_name":"main.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":2116426},{"file_size":35884057,"content_type":"application/x-zip-compressed","creator":"cchlebak","file_name":"thesis_source.zip","access_level":"closed","date_created":"2023-11-15T13:44:24Z","date_updated":"2023-11-15T13:44:24Z","checksum":"80ca37618a3c7b59866875f8be9b15ed","relation":"source_file","file_id":"14541"}],"oa_version":"Published Version","title":"Automated verification and control of infinite state stochastic systems","status":"public","ddc":["000"],"_id":"14539","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal\r\nverification and control of finite state stochastic systems, a subfield of formal methods\r\nalso known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively\r\nless attention. However, infinite state stochastic systems commonly arise in practice.\r\nFor instance, probabilistic models that contain continuous probability distributions such\r\nas normal or uniform, or stochastic dynamical systems which are a classical model for\r\ncontrol under uncertainty, both give rise to infinite state systems.\r\nThe goal of this thesis is to contribute to laying theoretical and algorithmic foundations\r\nof fully automated formal verification and control of infinite state stochastic systems,\r\nwith a particular focus on systems that may be executed over a long or infinite time.\r\nWe consider formal verification of infinite state stochastic systems in the setting of\r\nstatic analysis of probabilistic programs and formal control in the setting of controller\r\nsynthesis in stochastic dynamical systems. For both problems, we present some of the\r\nfirst fully automated methods for probabilistic (a.k.a. quantitative) reachability and\r\nsafety analysis applicable to infinite time horizon systems. We also advance the state\r\nof the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems.\r\nFinally, for formal controller synthesis in stochastic dynamical systems, we present a\r\nnovel framework for learning neural network control policies in stochastic dynamical\r\nsystems with formal guarantees on correctness with respect to quantitative reachability,\r\nsafety or reach-avoid specifications.\r\n"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"doi":"10.15479/14539","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-036-7"]},"month":"11","date_updated":"2024-01-16T11:58:15Z","date_created":"2023-11-15T13:39:10Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1194"},{"status":"public","relation":"part_of_dissertation","id":"12000"},{"id":"9644","relation":"part_of_dissertation","status":"public"},{"id":"12511","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"14600"},{"id":"14601","relation":"part_of_dissertation","status":"public"},{"id":"10414","status":"public","relation":"part_of_dissertation"}]},"author":[{"first_name":"Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde"}],"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2023","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"file_date_updated":"2023-11-15T13:44:24Z"},{"oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":5678069,"access_level":"open_access","file_name":"2023_JCB_Mund.pdf","success":1,"checksum":"505d5cac36c14b073b68c7fed1a92bd3","date_created":"2024-01-16T10:15:09Z","date_updated":"2024-01-16T10:15:09Z","file_id":"14811","relation":"main_file"}],"_id":"14788","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Clathrin coats partially preassemble and subsequently bend during endocytosis","status":"public","intvolume":" 222","abstract":[{"lang":"eng","text":"Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane."}],"issue":"3","type":"journal_article","date_published":"2023-02-03T00:00:00Z","publication":"Journal of Cell Biology","citation":{"short":"M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam, U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).","mla":"Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” Journal of Cell Biology, vol. 222, no. 3, e202206038, Rockefeller University Press, 2023, doi:10.1083/jcb.202206038.","chicago":"Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” Journal of Cell Biology. Rockefeller University Press, 2023. https://doi.org/10.1083/jcb.202206038.","ama":"Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 2023;222(3). doi:10.1083/jcb.202206038","ieee":"M. Mund et al., “Clathrin coats partially preassemble and subsequently bend during endocytosis,” Journal of Cell Biology, vol. 222, no. 3. Rockefeller University Press, 2023.","apa":"Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., … Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202206038","ista":"Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 222(3), e202206038."},"article_type":"original","day":"03","article_processing_charge":"No","has_accepted_license":"1","keyword":["Cell Biology"],"author":[{"first_name":"Markus","last_name":"Mund","full_name":"Mund, Markus"},{"full_name":"Tschanz, Aline","first_name":"Aline","last_name":"Tschanz"},{"first_name":"Yu-Le","last_name":"Wu","full_name":"Wu, Yu-Le"},{"orcid":"0000-0001-8501-6017","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","last_name":"Frey","first_name":"Felix F","full_name":"Frey, Felix F"},{"first_name":"Johanna L.","last_name":"Mehl","full_name":"Mehl, Johanna L."},{"first_name":"Marko","last_name":"Kaksonen","full_name":"Kaksonen, Marko"},{"full_name":"Avinoam, Ori","first_name":"Ori","last_name":"Avinoam"},{"full_name":"Schwarz, Ulrich S.","first_name":"Ulrich S.","last_name":"Schwarz"},{"full_name":"Ries, Jonas","last_name":"Ries","first_name":"Jonas"}],"date_created":"2024-01-10T10:45:55Z","date_updated":"2024-01-16T10:17:05Z","volume":222,"year":"2023","acknowledgement":"We thank the entire Ries and Kaksonen labs for fruitful discussions and support. This work was supported by the European Research Council (ERC CoG-724489 to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND (Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund, A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant 310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent of the Miriam Berman Presidential Development Chair.","pmid":1,"publication_status":"published","department":[{"_id":"AnSa"}],"publisher":"Rockefeller University Press","file_date_updated":"2024-01-16T10:15:09Z","article_number":"e202206038","doi":"10.1083/jcb.202206038","language":[{"iso":"eng"}],"external_id":{"pmid":["36734980"],"isi":["000978065000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","month":"02","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]}},{"volume":32,"date_updated":"2024-01-16T10:10:00Z","date_created":"2024-01-10T10:44:45Z","author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Chase, Madeline A.","last_name":"Chase","first_name":"Madeline A."},{"full_name":"McIntosh, Hanna","first_name":"Hanna","last_name":"McIntosh"},{"full_name":"Streisfeld, Matthew A.","first_name":"Matthew A.","last_name":"Streisfeld"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","pmid":1,"acknowledgement":"We thank Julian Catchen for making modifications to Stacks to aid this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and Nicholas H. Barton provided advice, stimulating discussion and critical feedback. The project was supported by National Science Foundation grant DEB-1258199.","year":"2023","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1111/mec.16849","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1101/2022.01.28.478139","open_access":"1"}],"oa":1,"external_id":{"isi":["000919244600001"],"pmid":["36651268"]},"issue":"8","abstract":[{"lang":"eng","text":"Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes ofMimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 32","title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14787","article_processing_charge":"No","day":"01","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"date_published":"2023-04-01T00:00:00Z","page":"2041-2054","article_type":"original","citation":{"chicago":"Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16849.","short":"S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054.","mla":"Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:10.1111/mec.16849.","ieee":"S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone,” Molecular Ecology, vol. 32, no. 8. Wiley, pp. 2041–2054, 2023.","apa":"Stankowski, S., Chase, M. A., McIntosh, H., & Streisfeld, M. A. (2023). Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16849","ista":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.","ama":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 2023;32(8):2041-2054. doi:10.1111/mec.16849"},"publication":"Molecular Ecology"},{"month":"12","publication_identifier":{"issn":["1084-9521"]},"doi":"10.1016/j.semcdb.2022.11.005","language":[{"iso":"eng"}],"external_id":{"pmid":["36470715"],"isi":["001053522200001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"file_date_updated":"2024-01-08T10:16:04Z","ec_funded":1,"author":[{"orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"}],"date_created":"2023-01-12T12:09:47Z","date_updated":"2024-01-16T13:22:32Z","volume":"150-151","acknowledgement":"This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.).\r\nB. C-M wants to acknowledge the support of the field of excellence Complexity of Life, in Basic Research and Innovation of the University of Graz.","year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"Elsevier","day":"02","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","keyword":["Cell Biology","Developmental Biology"],"date_published":"2023-12-02T00:00:00Z","publication":"Seminars in Cell & Developmental Biology","citation":{"ista":"Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 150–151, 58–65.","ieee":"B. Corominas-Murtra and E. B. Hannezo, “Modelling the dynamics of mammalian gut homeostasis,” Seminars in Cell & Developmental Biology, vol. 150–151. Elsevier, pp. 58–65, 2023.","apa":"Corominas-Murtra, B., & Hannezo, E. B. (2023). Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. Elsevier. https://doi.org/10.1016/j.semcdb.2022.11.005","ama":"Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 2023;150-151:58-65. doi:10.1016/j.semcdb.2022.11.005","chicago":"Corominas-Murtra, Bernat, and Edouard B Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology. Elsevier, 2023. https://doi.org/10.1016/j.semcdb.2022.11.005.","mla":"Corominas-Murtra, Bernat, and Edouard B. Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology, vol. 150–151, Elsevier, 2023, pp. 58–65, doi:10.1016/j.semcdb.2022.11.005.","short":"B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell & Developmental Biology 150–151 (2023) 58–65."},"article_type":"review","page":"58-65","abstract":[{"lang":"eng","text":"Homeostatic balance in the intestinal epithelium relies on a fast cellular turnover, which is coordinated by an intricate interplay between biochemical signalling, mechanical forces and organ geometry. We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues."}],"type":"journal_article","file":[{"file_id":"14741","relation":"main_file","success":1,"checksum":"c619887cf130f4649bf3035417186004","date_created":"2024-01-08T10:16:04Z","date_updated":"2024-01-08T10:16:04Z","access_level":"open_access","file_name":"2023_SeminarsCellDevBiology_CorominasMurtra.pdf","creator":"dernst","content_type":"application/pdf","file_size":1343750}],"oa_version":"Published Version","_id":"12162","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Modelling the dynamics of mammalian gut homeostasis","ddc":["570"],"status":"public"},{"month":"06","publication_identifier":{"eissn":["1945-001X"],"issn":["1073-2780"]},"language":[{"iso":"eng"}],"doi":"10.4310/mrl.2023.v30.n1.a6","quality_controlled":"1","isi":1,"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"oa":1,"external_id":{"arxiv":["2108.01587"],"isi":["001027656000006"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2108.01587"}],"ec_funded":1,"date_updated":"2024-01-16T12:00:47Z","date_created":"2023-07-23T22:01:14Z","volume":30,"author":[{"first_name":"D.","last_name":"Huybrechts","full_name":"Huybrechts, D."},{"full_name":"Mauri, Mirko","last_name":"Mauri","first_name":"Mirko","id":"2cf70c34-09c1-11ed-bd8d-c34fac206130"}],"publication_status":"published","publisher":"International Press","department":[{"_id":"TaHa"}],"year":"2023","acknowledgement":"The first author is supported by the ERC Synergy Grant HyperK. The second author is supported by the Max Planck Institute for Mathematics and the Institute of Science and Technology Austria. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","day":"21","article_processing_charge":"No","scopus_import":"1","date_published":"2023-06-21T00:00:00Z","article_type":"original","page":"125-141","publication":"Mathematical Research Letters","citation":{"ista":"Huybrechts D, Mauri M. 2023. On type II degenerations of hyperkähler manifolds. Mathematical Research Letters. 30(1), 125–141.","ieee":"D. Huybrechts and M. Mauri, “On type II degenerations of hyperkähler manifolds,” Mathematical Research Letters, vol. 30, no. 1. International Press, pp. 125–141, 2023.","apa":"Huybrechts, D., & Mauri, M. (2023). On type II degenerations of hyperkähler manifolds. Mathematical Research Letters. International Press. https://doi.org/10.4310/mrl.2023.v30.n1.a6","ama":"Huybrechts D, Mauri M. On type II degenerations of hyperkähler manifolds. Mathematical Research Letters. 2023;30(1):125-141. doi:10.4310/mrl.2023.v30.n1.a6","chicago":"Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.” Mathematical Research Letters. International Press, 2023. https://doi.org/10.4310/mrl.2023.v30.n1.a6.","mla":"Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.” Mathematical Research Letters, vol. 30, no. 1, International Press, 2023, pp. 125–41, doi:10.4310/mrl.2023.v30.n1.a6.","short":"D. Huybrechts, M. Mauri, Mathematical Research Letters 30 (2023) 125–141."},"abstract":[{"lang":"eng","text":"We give a simple argument to prove Nagai’s conjecture for type II degenerations of compact hyperkähler manifolds and cohomology classes of middle degree. Under an additional assumption, the techniques yield the conjecture in arbitrary degree. This would complete the proof of Nagai’s conjecture in general, as it was proved already for type I degenerations by Kollár, Laza, Saccà, and Voisin [10] and independently by Soldatenkov [18], while it is immediate for type III degenerations. Our arguments are close in spirit to a recent paper by Harder [8] proving similar results for the restrictive class of good degenerations."}],"issue":"1","type":"journal_article","oa_version":"Preprint","status":"public","title":"On type II degenerations of hyperkähler manifolds","intvolume":" 30","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13268"},{"month":"01","publication_identifier":{"issn":["0944-6532"],"eissn":["2363-6394"]},"oa":1,"external_id":{"arxiv":["1811.09857"],"isi":["001115503400013"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.09857"}],"isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"year":"2023","publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"Heldermann Verlag","author":[{"full_name":"Carioni, Marcello","first_name":"Marcello","last_name":"Carioni"},{"full_name":"Fischer, Julian L","first_name":"Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X"},{"full_name":"Schlömerkemper, Anja","last_name":"Schlömerkemper","first_name":"Anja"}],"date_created":"2023-12-10T23:00:59Z","date_updated":"2024-01-16T12:03:05Z","volume":30,"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Journal of Convex Analysis","citation":{"short":"M. Carioni, J.L. Fischer, A. Schlömerkemper, Journal of Convex Analysis 30 (2023) 217–247.","mla":"Carioni, Marcello, et al. “External Forces in the Continuum Limit of Discrete Systems with Non-Convex Interaction Potentials: Compactness for a Γ-Development.” Journal of Convex Analysis, vol. 30, no. 1, Heldermann Verlag, 2023, pp. 217–47.","chicago":"Carioni, Marcello, Julian L Fischer, and Anja Schlömerkemper. “External Forces in the Continuum Limit of Discrete Systems with Non-Convex Interaction Potentials: Compactness for a Γ-Development.” Journal of Convex Analysis. Heldermann Verlag, 2023.","ama":"Carioni M, Fischer JL, Schlömerkemper A. External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development. Journal of Convex Analysis. 2023;30(1):217-247.","apa":"Carioni, M., Fischer, J. L., & Schlömerkemper, A. (2023). External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development. Journal of Convex Analysis. Heldermann Verlag.","ieee":"M. Carioni, J. L. Fischer, and A. Schlömerkemper, “External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development,” Journal of Convex Analysis, vol. 30, no. 1. Heldermann Verlag, pp. 217–247, 2023.","ista":"Carioni M, Fischer JL, Schlömerkemper A. 2023. External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development. Journal of Convex Analysis. 30(1), 217–247."},"article_type":"original","page":"217-247","date_published":"2023-01-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"This paper is concerned with equilibrium configurations of one-dimensional particle systems with non-convex nearest-neighbour and next-to-nearest-neighbour interactions and its passage to the continuum. The goal is to derive compactness results for a Γ-development of the energy with the novelty that external forces are allowed. In particular, the forces may depend on Lagrangian or Eulerian coordinates and thus may model dead as well as live loads. Our result is based on a new technique for deriving compactness results which are required for calculating the first-order Γ-limit in the presence of external forces: instead of comparing a configuration of n atoms to a global minimizer of the Γ-limit, we compare the configuration to a minimizer in some subclass of functions which in some sense are \"close to\" the configuration. The paper is complemented with the study of the minimizers of the Γ-limit."}],"issue":"1","_id":"14661","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development","status":"public","intvolume":" 30","oa_version":"Preprint"},{"type":"journal_article","issue":"2","abstract":[{"text":"We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in a LexRSM not existing even for simple terminating programs. Our contributions are twofold. First, we introduce a generalization of LexRSMs that allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs.","lang":"eng"}],"_id":"14778","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 35","title":"On lexicographic proof rules for probabilistic termination","status":"public","ddc":["000"],"oa_version":"Published Version","file":[{"success":1,"checksum":"3bb133eeb27ec01649a9a36445d952d9","date_created":"2024-01-16T08:11:24Z","date_updated":"2024-01-16T08:11:24Z","file_id":"14804","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":502522,"access_level":"open_access","file_name":"2023_FormalAspectsComputing_Chatterjee.pdf"}],"keyword":["Theoretical Computer Science","Software"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"23","citation":{"ama":"Chatterjee K, Kafshdar Goharshady E, Novotný P, Zárevúcky J, Zikelic D. On lexicographic proof rules for probabilistic termination. Formal Aspects of Computing. 2023;35(2). doi:10.1145/3585391","ista":"Chatterjee K, Kafshdar Goharshady E, Novotný P, Zárevúcky J, Zikelic D. 2023. On lexicographic proof rules for probabilistic termination. Formal Aspects of Computing. 35(2), 11.","ieee":"K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic, “On lexicographic proof rules for probabilistic termination,” Formal Aspects of Computing, vol. 35, no. 2. Association for Computing Machinery, 2023.","apa":"Chatterjee, K., Kafshdar Goharshady, E., Novotný, P., Zárevúcky, J., & Zikelic, D. (2023). On lexicographic proof rules for probabilistic termination. Formal Aspects of Computing. Association for Computing Machinery. https://doi.org/10.1145/3585391","mla":"Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic Termination.” Formal Aspects of Computing, vol. 35, no. 2, 11, Association for Computing Machinery, 2023, doi:10.1145/3585391.","short":"K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, Formal Aspects of Computing 35 (2023).","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky, and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.” Formal Aspects of Computing. Association for Computing Machinery, 2023. https://doi.org/10.1145/3585391."},"publication":"Formal Aspects of Computing","article_type":"original","date_published":"2023-06-23T00:00:00Z","article_number":"11","ec_funded":1,"file_date_updated":"2024-01-16T08:11:24Z","acknowledgement":"This research was partially supported by the ERC CoG (grant no. 863818; ForM-SMArt), the Czech Science Foundation (grant no. GA21-24711S), and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2023","department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","publication_status":"published","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10414"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Kafshdar Goharshady, Ehsan","first_name":"Ehsan","last_name":"Kafshdar Goharshady"},{"last_name":"Novotný","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr"},{"full_name":"Zárevúcky, Jiří","first_name":"Jiří","last_name":"Zárevúcky"},{"orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde","full_name":"Zikelic, Dorde"}],"volume":35,"date_created":"2024-01-10T09:27:43Z","date_updated":"2024-01-17T08:19:41Z","publication_identifier":{"eissn":["1433-299X"],"issn":["0934-5043"]},"month":"06","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2108.02188"]},"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"quality_controlled":"1","doi":"10.1145/3585391","language":[{"iso":"eng"}]},{"publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"publication_status":"published","year":"2023","acknowledgement":"This work is supported by FWF Lise Meitner (Grant M 3319), Spanish Agencia Estatal de Investigación (project PID2022-141539NBI00), European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement\r\nN◦ 725253–EyeCode), Swiss National Science Foundation (Grant no. 200502), and academic gifts from Meta. We thank Dmitry Lubyako and Ali Özgür Yöntem for building the turntable for our experiment.","date_updated":"2024-01-17T08:38:35Z","date_created":"2024-01-14T23:00:57Z","author":[{"last_name":"Chen","first_name":"Bin","full_name":"Chen, Bin"},{"last_name":"Jindal","first_name":"Akshay","full_name":"Jindal, Akshay"},{"last_name":"Piovarci","first_name":"Michael","orcid":"0000-0002-5062-4474","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael"},{"full_name":"Wang, Chao","first_name":"Chao","last_name":"Wang"},{"first_name":"Hans Peter","last_name":"Seidel","full_name":"Seidel, Hans Peter"},{"full_name":"Didyk, Piotr","last_name":"Didyk","first_name":"Piotr"},{"full_name":"Myszkowski, Karol","last_name":"Myszkowski","first_name":"Karol"},{"full_name":"Serrano, Ana","first_name":"Ana","last_name":"Serrano"},{"first_name":"Rafał K.","last_name":"Mantiuk","full_name":"Mantiuk, Rafał K."}],"article_number":"90","file_date_updated":"2024-01-17T08:33:06Z","project":[{"grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1145/3610548.3618226","conference":{"location":"Sydney, Australia","start_date":"2023-12-12","end_date":"2023-12-15","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference"},"publication_identifier":{"isbn":["9798400703157"]},"month":"12","status":"public","title":"The effect of display capabilities on the gloss consistency between real and virtual objects","ddc":["000"],"_id":"14798","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"2023_SA_Chen.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":95967451,"file_id":"14823","relation":"main_file","date_updated":"2024-01-17T08:33:06Z","date_created":"2024-01-17T08:33:06Z","success":1,"checksum":"8abe27432ed222b50d1af9b3388db1b0"}],"type":"conference","abstract":[{"text":"A faithful reproduction of gloss is inherently difficult because of the limited dynamic range, peak luminance, and 3D capabilities of display devices. This work investigates how the display capabilities affect gloss appearance with respect to a real-world reference object. To this end, we employ an accurate imaging pipeline to achieve a perceptual gloss match between a virtual and real object presented side-by-side on an augmented-reality high-dynamic-range (HDR) stereoscopic display, which has not been previously attained to this extent. Based on this precise gloss reproduction, we conduct a series of gloss matching experiments to study how gloss perception degrades based on individual factors: object albedo, display luminance, dynamic range, stereopsis, and tone mapping. We support the study with a detailed analysis of individual factors, followed by an in-depth discussion on the observed perceptual effects. Our experiments demonstrate that stereoscopic presentation has a limited effect on the gloss matching task on our HDR display. However, both reduced luminance and dynamic range of the display reduce the perceived gloss. This means that the visual system cannot compensate for the changes in gloss appearance across luminance (lack of gloss constancy), and the tone mapping operator should be carefully selected when reproducing gloss on a low dynamic range (LDR) display.","lang":"eng"}],"citation":{"short":"B. Chen, A. Jindal, M. Piovarci, C. Wang, H.P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, R.K. Mantiuk, in:, Proceedings of the SIGGRAPH Asia 2023 Conference, Association for Computing Machinery, 2023.","mla":"Chen, Bin, et al. “The Effect of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.” Proceedings of the SIGGRAPH Asia 2023 Conference, 90, Association for Computing Machinery, 2023, doi:10.1145/3610548.3618226.","chicago":"Chen, Bin, Akshay Jindal, Michael Piovarci, Chao Wang, Hans Peter Seidel, Piotr Didyk, Karol Myszkowski, Ana Serrano, and Rafał K. Mantiuk. “The Effect of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.” In Proceedings of the SIGGRAPH Asia 2023 Conference. Association for Computing Machinery, 2023. https://doi.org/10.1145/3610548.3618226.","ama":"Chen B, Jindal A, Piovarci M, et al. The effect of display capabilities on the gloss consistency between real and virtual objects. In: Proceedings of the SIGGRAPH Asia 2023 Conference. Association for Computing Machinery; 2023. doi:10.1145/3610548.3618226","apa":"Chen, B., Jindal, A., Piovarci, M., Wang, C., Seidel, H. P., Didyk, P., … Mantiuk, R. K. (2023). The effect of display capabilities on the gloss consistency between real and virtual objects. In Proceedings of the SIGGRAPH Asia 2023 Conference. Sydney, Australia: Association for Computing Machinery. https://doi.org/10.1145/3610548.3618226","ieee":"B. Chen et al., “The effect of display capabilities on the gloss consistency between real and virtual objects,” in Proceedings of the SIGGRAPH Asia 2023 Conference, Sydney, Australia, 2023.","ista":"Chen B, Jindal A, Piovarci M, Wang C, Seidel HP, Didyk P, Myszkowski K, Serrano A, Mantiuk RK. 2023. The effect of display capabilities on the gloss consistency between real and virtual objects. Proceedings of the SIGGRAPH Asia 2023 Conference. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 90."},"publication":"Proceedings of the SIGGRAPH Asia 2023 Conference","date_published":"2023-12-10T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"10"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2002.12410"],"isi":["001111578500001"]},"oa":1,"quality_controlled":"1","isi":1,"language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["1533-7928"]},"acknowledgement":"The work in Sections 1-5 was conducted while A. Beznosikov was a research intern in the Optimizationand Machine Learning Lab of Peter Richtárik at KAUST; this visit was funded by the KAUST Baseline Research Funding Scheme. The work of A. Beznosikov in Section 6 was conducted in Skoltech and was supported by Ministry of Science and Higher Education grant No. 075-10-2021-068. ","year":"2023","publication_status":"published","publisher":"Journal of Machine Learning Research","department":[{"_id":"DaAl"}],"author":[{"full_name":"Beznosikov, Aleksandr","first_name":"Aleksandr","last_name":"Beznosikov"},{"full_name":"Horvath, Samuel","first_name":"Samuel","last_name":"Horvath"},{"full_name":"Richtarik, Peter","last_name":"Richtarik","first_name":"Peter"},{"last_name":"Safaryan","first_name":"Mher","id":"dd546b39-0804-11ed-9c55-ef075c39778d","full_name":"Safaryan, Mher"}],"date_updated":"2024-01-17T09:14:13Z","date_created":"2024-01-16T12:13:36Z","volume":24,"file_date_updated":"2024-01-16T12:13:27Z","publication":"Journal of Machine Learning Research","citation":{"short":"A. Beznosikov, S. Horvath, P. Richtarik, M. Safaryan, Journal of Machine Learning Research 24 (2023) 1–50.","mla":"Beznosikov, Aleksandr, et al. “On Biased Compression for Distributed Learning.” Journal of Machine Learning Research, vol. 24, Journal of Machine Learning Research, 2023, pp. 1–50.","chicago":"Beznosikov, Aleksandr, Samuel Horvath, Peter Richtarik, and Mher Safaryan. “On Biased Compression for Distributed Learning.” Journal of Machine Learning Research. Journal of Machine Learning Research, 2023.","ama":"Beznosikov A, Horvath S, Richtarik P, Safaryan M. On biased compression for distributed learning. Journal of Machine Learning Research. 2023;24:1-50.","apa":"Beznosikov, A., Horvath, S., Richtarik, P., & Safaryan, M. (2023). On biased compression for distributed learning. Journal of Machine Learning Research. Journal of Machine Learning Research.","ieee":"A. Beznosikov, S. Horvath, P. Richtarik, and M. Safaryan, “On biased compression for distributed learning,” Journal of Machine Learning Research, vol. 24. Journal of Machine Learning Research, pp. 1–50, 2023.","ista":"Beznosikov A, Horvath S, Richtarik P, Safaryan M. 2023. On biased compression for distributed learning. Journal of Machine Learning Research. 24, 1–50."},"article_type":"original","page":"1-50","date_published":"2023-10-01T00:00:00Z","day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","_id":"14815","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On biased compression for distributed learning","status":"public","ddc":["000"],"intvolume":" 24","oa_version":"Published Version","file":[{"success":1,"checksum":"c50f2b9db53938b755e30a085f464059","date_created":"2024-01-16T12:13:27Z","date_updated":"2024-01-16T12:13:27Z","file_id":"14816","relation":"main_file","creator":"dernst","file_size":1510993,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_JMLR_Beznosikov.pdf"}],"type":"journal_article","abstract":[{"text":"In the last few years, various communication compression techniques have emerged as an indispensable tool helping to alleviate the communication bottleneck in distributed learning. However, despite the fact biased compressors often show superior performance in practice when compared to the much more studied and understood unbiased compressors, very little is known about them. In this work we study three classes of biased compression operators, two of which are new, and their performance when applied to (stochastic) gradient descent and distributed (stochastic) gradient descent. We show for the first time that biased compressors can lead to linear convergence rates both in the single node and distributed settings. We prove that distributed compressed SGD method, employed with error feedback mechanism, enjoys the ergodic rate O(δLexp[−μKδL]+(C+δD)Kμ), where δ≥1 is a compression parameter which grows when more compression is applied, L and μ are the smoothness and strong convexity constants, C captures stochastic gradient noise (C=0 if full gradients are computed on each node) and D captures the variance of the gradients at the optimum (D=0 for over-parameterized models). Further, via a theoretical study of several synthetic and empirical distributions of communicated gradients, we shed light on why and by how much biased compressors outperform their unbiased variants. Finally, we propose several new biased compressors with promising theoretical guarantees and practical performance.","lang":"eng"}]},{"intvolume":" 14292","status":"public","title":"Shortest dominating set reconfiguration under token sliding","_id":"14456","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"In this paper, we present novel algorithms that efficiently compute a shortest reconfiguration sequence between two given dominating sets in trees and interval graphs under the TOKEN SLIDING model. In this problem, a graph is provided along with its two dominating sets, which can be imagined as tokens placed on vertices. The objective is to find a shortest sequence of dominating sets that transforms one set into the other, with each set in the sequence resulting from sliding a single token in the previous set. While identifying any sequence has been well studied, our work presents the first polynomial algorithms for this optimization variant in the context of dominating sets."}],"page":"333-347","citation":{"chicago":"Křišťan, Jan Matyáš, and Jakub Svoboda. “Shortest Dominating Set Reconfiguration under Token Sliding.” In 24th International Symposium on Fundamentals of Computation Theory, 14292:333–47. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-43587-4_24.","short":"J.M. Křišťan, J. Svoboda, in:, 24th International Symposium on Fundamentals of Computation Theory, Springer Nature, 2023, pp. 333–347.","mla":"Křišťan, Jan Matyáš, and Jakub Svoboda. “Shortest Dominating Set Reconfiguration under Token Sliding.” 24th International Symposium on Fundamentals of Computation Theory, vol. 14292, Springer Nature, 2023, pp. 333–47, doi:10.1007/978-3-031-43587-4_24.","apa":"Křišťan, J. M., & Svoboda, J. (2023). Shortest dominating set reconfiguration under token sliding. In 24th International Symposium on Fundamentals of Computation Theory (Vol. 14292, pp. 333–347). Trier, Germany: Springer Nature. https://doi.org/10.1007/978-3-031-43587-4_24","ieee":"J. M. Křišťan and J. Svoboda, “Shortest dominating set reconfiguration under token sliding,” in 24th International Symposium on Fundamentals of Computation Theory, Trier, Germany, 2023, vol. 14292, pp. 333–347.","ista":"Křišťan JM, Svoboda J. 2023. Shortest dominating set reconfiguration under token sliding. 24th International Symposium on Fundamentals of Computation Theory. FCT: Fundamentals of Computation Theory, LNCS, vol. 14292, 333–347.","ama":"Křišťan JM, Svoboda J. Shortest dominating set reconfiguration under token sliding. In: 24th International Symposium on Fundamentals of Computation Theory. Vol 14292. Springer Nature; 2023:333-347. doi:10.1007/978-3-031-43587-4_24"},"publication":"24th International Symposium on Fundamentals of Computation Theory","date_published":"2023-09-21T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"21","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2023","volume":14292,"date_created":"2023-10-29T23:01:16Z","date_updated":"2024-01-22T08:10:49Z","related_material":{"link":[{"url":"https://doi.org/10.1007/978-3-031-43587-4_31","relation":"erratum"}]},"author":[{"last_name":"Křišťan","first_name":"Jan Matyáš","full_name":"Křišťan, Jan Matyáš"},{"first_name":"Jakub","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","orcid":"0000-0002-1419-3267","full_name":"Svoboda, Jakub"}],"quality_controlled":"1","external_id":{"arxiv":["2307.10847"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.10847"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-43587-4_24","conference":{"name":"FCT: Fundamentals of Computation Theory","location":"Trier, Germany","start_date":"2023-09-18","end_date":"2023-09-21"},"publication_identifier":{"isbn":["9783031435867"],"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"09"},{"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14829","title":"Proof of availability and retrieval in a modular blockchain architecture","status":"public","intvolume":" 13951","abstract":[{"text":"This paper explores a modular design architecture aimed at helping blockchains (and other SMR implementation) to scale to a very large number of processes. This comes in contrast to existing monolithic architectures that interleave transaction dissemination, ordering, and execution in a single functionality. To achieve this we first split the monolith to multiple layers which can use existing distributed computing primitives. The exact specifications of the data dissemination part are formally defined by the Proof of Availability & Retrieval (PoA &R) abstraction. Solutions to the PoA &R problem contain two related sub-protocols: one that “pushes” information into the network and another that “pulls” this information. Regarding the latter, there is a dearth of research literature which is rectified in this paper. We present a family of pulling sub-protocols and rigorously analyze them. Extensive simulations support the theoretical claims of efficiency and robustness in case of a very large number of players. Finally, actual implementation and deployment on a small number of machines (roughly the size of several industrial systems) demonstrates the viability of the architecture’s paradigm.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2023-12-01T00:00:00Z","publication":"27th International Conference on Financial Cryptography and Data Security","citation":{"ista":"Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. 2023. Proof of availability and retrieval in a modular blockchain architecture. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13951, 36–53.","ieee":"S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, and A. Spiegelman, “Proof of availability and retrieval in a modular blockchain architecture,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13951, pp. 36–53.","apa":"Cohen, S., Goren, G., Kokoris Kogias, E., Sonnino, A., & Spiegelman, A. (2023). Proof of availability and retrieval in a modular blockchain architecture. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13951, pp. 36–53). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47751-5_3","ama":"Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. Proof of availability and retrieval in a modular blockchain architecture. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13951. Springer Nature; 2023:36-53. doi:10.1007/978-3-031-47751-5_3","chicago":"Cohen, Shir, Guy Goren, Eleftherios Kokoris Kogias, Alberto Sonnino, and Alexander Spiegelman. “Proof of Availability and Retrieval in a Modular Blockchain Architecture.” In 27th International Conference on Financial Cryptography and Data Security, 13951:36–53. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47751-5_3.","mla":"Cohen, Shir, et al. “Proof of Availability and Retrieval in a Modular Blockchain Architecture.” 27th International Conference on Financial Cryptography and Data Security, vol. 13951, Springer Nature, 2023, pp. 36–53, doi:10.1007/978-3-031-47751-5_3.","short":"S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 36–53."},"page":"36-53","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"last_name":"Cohen","first_name":"Shir","full_name":"Cohen, Shir"},{"last_name":"Goren","first_name":"Guy","full_name":"Goren, Guy"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"first_name":"Alberto","last_name":"Sonnino","full_name":"Sonnino, Alberto"},{"full_name":"Spiegelman, Alexander","last_name":"Spiegelman","first_name":"Alexander"}],"date_created":"2024-01-18T07:41:12Z","date_updated":"2024-01-22T13:58:07Z","volume":13951,"acknowledgement":"This work is partially supported by Meta. Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N. Shir Cohen is supported by the Adams Fellowship Program of the Israel Academy of Sciences and Humanities.","year":"2023","publication_status":"published","department":[{"_id":"ElKo"}],"publisher":"Springer Nature","conference":{"location":"Bol, Brac, Croatia","start_date":"2023-05-01","end_date":"2023-05-05","name":"FC: Financial Cryptography and Data Security"},"doi":"10.1007/978-3-031-47751-5_3","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://fc23.ifca.ai/preproceedings/150.pdf"}],"quality_controlled":"1","project":[{"name":"Secure Network and Hardware for Efficient Blockchains","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","grant_number":"F8512"}],"month":"12","publication_identifier":{"eisbn":["9783031477515"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031477508"]}},{"oa_version":"None","intvolume":" 136","status":"public","title":"Connecting theory and experiment in cell and tissue mechanics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14827","issue":"24","abstract":[{"text":"Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems.","lang":"eng"}],"type":"journal_article","date_published":"2023-12-27T00:00:00Z","article_type":"original","citation":{"ista":"Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.","apa":"Schwayer, C., & Brückner, D. (2023). Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.261515","ieee":"C. Schwayer and D. Brückner, “Connecting theory and experiment in cell and tissue mechanics,” Journal of Cell Science, vol. 136, no. 24. The Company of Biologists, 2023.","ama":"Schwayer C, Brückner D. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 2023;136(24). doi:10.1242/jcs.261515","chicago":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” Journal of Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.261515.","mla":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” Journal of Cell Science, vol. 136, no. 24, jcs. 261515, The Company of Biologists, 2023, doi:10.1242/jcs.261515.","short":"C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023)."},"publication":"Journal of Cell Science","article_processing_charge":"No","day":"27","keyword":["Cell Biology"],"scopus_import":"1","volume":136,"date_updated":"2024-01-22T13:35:48Z","date_created":"2024-01-17T12:46:55Z","author":[{"orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwayer","first_name":"Cornelia","full_name":"Schwayer, Cornelia"},{"full_name":"Brückner, David","first_name":"David","last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975"}],"department":[{"_id":"EdHa"},{"_id":"CaHe"}],"publisher":"The Company of Biologists","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank Prisca Liberali and Edouard Hannezo for many inspiring discussions; Mehmet Can Uçar, Nicoletta I Petridou and Qiutan Yang for a critical reading of the manuscript, and Claudia Flandoli for the artwork in Figs 2 and 3. We would also like to thank The Company of Biologists for the opportunity to attend the 2023 workshop on Collective Cell Migration, and all workshop participants for discussions.\r\nC.S. was supported by a European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 660-2020) and Human Frontier Science Program (HFSP) Postdoctoral fellowship (LT000746/2021-L). D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","article_number":"jcs.261515","language":[{"iso":"eng"}],"doi":"10.1242/jcs.261515","project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"quality_controlled":"1","external_id":{"pmid":["38149871"]},"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"month":"12"},{"date_published":"2023-06-26T00:00:00Z","publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","citation":{"short":"D. Zikelic, M. Lechner, T.A. Henzinger, K. Chatterjee, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2023, pp. 11926–11935.","mla":"Zikelic, Dorde, et al. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol. 37, no. 10, Association for the Advancement of Artificial Intelligence, 2023, pp. 11926–35, doi:10.1609/aaai.v37i10.26407.","chicago":"Zikelic, Dorde, Mathias Lechner, Thomas A Henzinger, and Krishnendu Chatterjee. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” In Proceedings of the 37th AAAI Conference on Artificial Intelligence, 37:11926–35. Association for the Advancement of Artificial Intelligence, 2023. https://doi.org/10.1609/aaai.v37i10.26407.","ama":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence. Vol 37. Association for the Advancement of Artificial Intelligence; 2023:11926-11935. doi:10.1609/aaai.v37i10.26407","ieee":"D. Zikelic, M. Lechner, T. A. Henzinger, and K. Chatterjee, “Learning control policies for stochastic systems with reach-avoid guarantees,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence, Washington, DC, United States, 2023, vol. 37, no. 10, pp. 11926–11935.","apa":"Zikelic, D., Lechner, M., Henzinger, T. A., & Chatterjee, K. (2023). Learning control policies for stochastic systems with reach-avoid guarantees. In Proceedings of the 37th AAAI Conference on Artificial Intelligence (Vol. 37, pp. 11926–11935). Washington, DC, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v37i10.26407","ista":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. 2023. Learning control policies for stochastic systems with reach-avoid guarantees. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 11926–11935."},"page":"11926-11935","day":"26","article_processing_charge":"No","keyword":["General Medicine"],"oa_version":"Preprint","_id":"14830","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Learning control policies for stochastic systems with reach-avoid guarantees","intvolume":" 37","abstract":[{"text":"We study the problem of learning controllers for discrete-time non-linear stochastic dynamical systems with formal reach-avoid guarantees. This work presents the first method for providing formal reach-avoid guarantees, which combine and generalize stability and safety guarantees, with a tolerable probability threshold p in [0,1] over the infinite time horizon. Our method leverages advances in machine learning literature and it represents formal certificates as neural networks. In particular, we learn a certificate in the form of a reach-avoid supermartingale (RASM), a novel notion that we introduce in this work. Our RASMs provide reachability and avoidance guarantees by imposing constraints on what can be viewed as a stochastic extension of level sets of Lyapunov functions for deterministic systems. Our approach solves several important problems -- it can be used to learn a control policy from scratch, to verify a reach-avoid specification for a fixed control policy, or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification. We validate our approach on 3 stochastic non-linear reinforcement learning tasks.","lang":"eng"}],"issue":"10","type":"conference","conference":{"name":"AAAI: Conference on Artificial Intelligence","location":"Washington, DC, United States","start_date":"2023-02-07","end_date":"2023-02-14"},"doi":"10.1609/aaai.v37i10.26407","language":[{"iso":"eng"}],"external_id":{"arxiv":["2210.05308"]},"quality_controlled":"1","project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"month":"06","publication_identifier":{"eissn":["2374-3468"],"issn":["2159-5399"]},"author":[{"full_name":"Zikelic, Dorde","last_name":"Zikelic","first_name":"Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"14600"}]},"date_updated":"2024-01-22T14:08:29Z","date_created":"2024-01-18T07:44:31Z","volume":37,"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2023","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Association for the Advancement of Artificial Intelligence","ec_funded":1},{"oa_version":"Published Version","file":[{"file_size":3408944,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_EvolJourLinneanSociety_Stankowski.pdf","checksum":"ba6f9102d3a9fe6631c4fa398c5e4313","success":1,"date_updated":"2024-01-23T08:10:00Z","date_created":"2024-01-23T08:10:00Z","relation":"main_file","file_id":"14875"}],"intvolume":" 2","status":"public","title":"Whole-genome phylogeography of the intertidal snail Littorina saxatilis","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14833","issue":"1","abstract":[{"text":"Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies.","lang":"eng"}],"type":"journal_article","date_published":"2023-08-17T00:00:00Z","article_type":"original","citation":{"ama":"Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2023;2(1). doi:10.1093/evolinnean/kzad002","ieee":"S. Stankowski et al., “Whole-genome phylogeography of the intertidal snail Littorina saxatilis,” Evolutionary Journal of the Linnean Society, vol. 2, no. 1. Oxford University Press, 2023.","apa":"Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R., Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. Oxford University Press. https://doi.org/10.1093/evolinnean/kzad002","ista":"Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002.","short":"S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N. Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame, A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean Society 2 (2023).","mla":"Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean Society, vol. 2, no. 1, kzad002, Oxford University Press, 2023, doi:10.1093/evolinnean/kzad002.","chicago":"Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón, Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean Society. Oxford University Press, 2023. https://doi.org/10.1093/evolinnean/kzad002."},"publication":"Evolutionary Journal of the Linnean Society","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"17","volume":2,"date_created":"2024-01-18T07:54:10Z","date_updated":"2024-01-23T08:13:43Z","author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"},{"last_name":"Zagrodzka","first_name":"Zuzanna B","full_name":"Zagrodzka, Zuzanna B"},{"full_name":"Galindo, Juan","first_name":"Juan","last_name":"Galindo"},{"first_name":"Mauricio","last_name":"Montaño-Rendón","full_name":"Montaño-Rendón, Mauricio"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Mikhailova, Natalia","first_name":"Natalia","last_name":"Mikhailova"},{"full_name":"Blakeslee, April M H","first_name":"April M H","last_name":"Blakeslee"},{"full_name":"Arnason, Einar","last_name":"Arnason","first_name":"Einar"},{"first_name":"Thomas","last_name":"Broquet","full_name":"Broquet, Thomas"},{"full_name":"Morales, Hernán E","first_name":"Hernán E","last_name":"Morales"},{"last_name":"Grahame","first_name":"John W","full_name":"Grahame, John W"},{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Butlin","first_name":"Roger K","full_name":"Butlin, Roger K"}],"department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published","year":"2023","acknowledgement":"Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield high-performance computing cluster, ShARC. Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council (ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00).","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2024-01-23T08:10:00Z","article_number":"kzad002","language":[{"iso":"eng"}],"doi":"10.1093/evolinnean/kzad002","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"publication_identifier":{"eissn":["2752-938X"]},"month":"08"},{"date_created":"2024-01-18T07:47:11Z","date_updated":"2024-01-23T07:58:27Z","volume":127,"author":[{"full_name":"Sakref, Yann","first_name":"Yann","last_name":"Sakref"},{"id":"1a8a7950-82cd-11ed-bd4f-9624c913a607","orcid":"0000-0003-1483-1457","first_name":"Maitane","last_name":"Muñoz Basagoiti","full_name":"Muñoz Basagoiti, Maitane"},{"first_name":"Zorana","last_name":"Zeravcic","full_name":"Zeravcic, Zorana"},{"full_name":"Rivoire, Olivier","last_name":"Rivoire","first_name":"Olivier"}],"publication_status":"published","department":[{"_id":"AnSa"}],"publisher":"American Chemical Society","acknowledgement":"We acknowledge funding from ANR-22-CE06-0037-02. This work has received funding from the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754387.","year":"2023","month":"12","publication_identifier":{"issn":["1520-6106"],"eissn":["1520-5207"]},"language":[{"iso":"eng"}],"doi":"10.1021/acs.jpcb.3c04627","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["001134068000001"],"arxiv":["2312.15940"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.15940","open_access":"1"}],"abstract":[{"text":"Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the products. While efforts to design catalysts are often focused on accelerating the chemical reaction on the catalyst, catalysis is a global property of the catalytic cycle that involves all processes. These are controlled by both intrinsic parameters such as the composition and shape of the catalyst and extrinsic parameters such as the concentration of the chemical species at play. We examine here the conditions that catalysis imposes on the different steps of a reaction cycle and the respective role of intrinsic and extrinsic parameters of the system on the emergence of catalysis by using an approach based on first-passage times. We illustrate this approach for various decompositions of a catalytic cycle into elementary steps, including non-Markovian decompositions, which are useful when the presence and nature of intermediate states are a priori unknown. Our examples cover different types of reactions and clarify the constraints on elementary steps and the impact of species concentrations on catalysis.","lang":"eng"}],"issue":"51","type":"journal_article","oa_version":"Preprint","title":"On kinetic constraints that catalysis imposes on elementary processes","status":"public","intvolume":" 127","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14831","day":"13","article_processing_charge":"No","keyword":["Materials Chemistry","Surfaces","Coatings and Films","Physical and Theoretical Chemistry"],"date_published":"2023-12-13T00:00:00Z","article_type":"original","page":"10950-10959","publication":"The Journal of Physical Chemistry B","citation":{"mla":"Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” The Journal of Physical Chemistry B, vol. 127, no. 51, American Chemical Society, 2023, pp. 10950–59, doi:10.1021/acs.jpcb.3c04627.","short":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical Chemistry B 127 (2023) 10950–10959.","chicago":"Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” The Journal of Physical Chemistry B. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpcb.3c04627.","ama":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints that catalysis imposes on elementary processes. The Journal of Physical Chemistry B. 2023;127(51):10950-10959. doi:10.1021/acs.jpcb.3c04627","ista":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. 2023. On kinetic constraints that catalysis imposes on elementary processes. The Journal of Physical Chemistry B. 127(51), 10950–10959.","ieee":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints that catalysis imposes on elementary processes,” The Journal of Physical Chemistry B, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023.","apa":"Sakref, Y., Muñoz Basagoiti, M., Zeravcic, Z., & Rivoire, O. (2023). On kinetic constraints that catalysis imposes on elementary processes. The Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.3c04627"}},{"article_processing_charge":"No","day":"29","scopus_import":"1","date_published":"2023-12-29T00:00:00Z","citation":{"chicago":"Azadbakht, Ali, Billie Meadowcroft, Juraj Majek, Anđela Šarić, and Daniela J. Kraft. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” Biophysical Journal. Elsevier, n.d. https://doi.org/10.1016/j.bpj.2023.12.020.","short":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical Journal (n.d.).","mla":"Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” Biophysical Journal, Elsevier, doi:10.1016/j.bpj.2023.12.020.","apa":"Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., & Kraft, D. J. (n.d.). Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.12.020","ieee":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, and D. J. Kraft, “Nonadditivity in interactions between three membrane-wrapped colloidal spheres,” Biophysical Journal. Elsevier.","ista":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal.","ama":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal. doi:10.1016/j.bpj.2023.12.020"},"publication":"Biophysical Journal","article_type":"original","abstract":[{"lang":"eng","text":"Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that these proteins induce. While the pairwise interaction potential of two membrane-deforming spheres has recently been measured, membrane-deformation-induced interactions have been predicted to be nonadditive, and hence their collective behavior cannot be deduced from this measurement. We here employ a colloidal model system consisting of adhesive spheres and giant unilamellar vesicles to test these predictions by measuring the interaction potential of the simplest case of three membrane-deforming, spherical particles. We quantify their interactions and arrangements and, for the first time, experimentally confirm and quantify the nonadditive nature of membrane-deformation-induced interactions. We furthermore conclude that there exist two favorable configurations on the membrane: (1) a linear and (2) a triangular arrangement of the three spheres. Using Monte Carlo simulations, we corroborate the experimentally observed energy minima and identify a lowering of the membrane deformation as the cause for the observed configurations. The high symmetry of the preferred arrangements for three particles suggests that arrangements of many membrane-deforming objects might follow simple rules."}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14844","status":"public","ddc":["570"],"title":"Nonadditivity in interactions between three membrane-wrapped colloidal spheres","publication_identifier":{"issn":["0006-3495"],"eissn":["1542-0086"]},"month":"12","doi":"10.1016/j.bpj.2023.12.020","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.bpj.2023.12.020","open_access":"1"}],"project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"}],"quality_controlled":"1","ec_funded":1,"author":[{"last_name":"Azadbakht","first_name":"Ali","full_name":"Azadbakht, Ali"},{"full_name":"Meadowcroft, Billie","orcid":"0000-0003-3441-1337","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","last_name":"Meadowcroft","first_name":"Billie"},{"full_name":"Majek, Juraj","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","last_name":"Majek","first_name":"Juraj"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"},{"last_name":"Kraft","first_name":"Daniela J.","full_name":"Kraft, Daniela J."}],"date_created":"2024-01-21T23:00:56Z","date_updated":"2024-01-23T09:26:35Z","year":"2023","acknowledgement":"We gratefully acknowledge useful discussions with Casper van der Wel, help by Yogesh Shelke with PAA coverslip preparation, and support by Rachel Doherty with particle functionalization. A.A. and D.J.K. would like to thank Timon Idema and George Dadunashvili for initial attempts to simulate the experimental system. D.J.K. would like to thank the physics department at Leiden University for funding the PhD position of A.A. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC starting grant no. 802960).","department":[{"_id":"AnSa"}],"publisher":"Elsevier","publication_status":"inpress"},{"date_published":"2023-05-02T00:00:00Z","publication":"Angewandte Chemie International Edition","citation":{"chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues. Angewandte Chemie International Edition. Vol. 62. Wiley, 2023. https://doi.org/10.1002/anie.202304138.","mla":"Becker, Lea Marie, et al. “Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues.” Angewandte Chemie International Edition, vol. 62, no. 19, e202304138, Wiley, 2023, doi:10.1002/anie.202304138.","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues, Wiley, 2023.","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues, Wiley,p.","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues. Angewandte Chemie International Edition (Vol. 62). Wiley. https://doi.org/10.1002/anie.202304138","ieee":"L. M. Becker et al., Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues, vol. 62, no. 19. Wiley, 2023.","ama":"Becker LM, Berbon M, Vallet A, et al. Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues. Vol 62. Wiley; 2023. doi:10.1002/anie.202304138"},"day":"02","article_processing_charge":"No","keyword":["General Chemistry","Catalysis"],"oa_version":"Published Version","title":"Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues","status":"public","intvolume":" 62","_id":"14861","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Cover Page","lang":"eng"}],"issue":"19","type":"other_academic_publication","language":[{"iso":"eng"}],"doi":"10.1002/anie.202304138","oa":1,"main_file_link":[{"url":"https://doi.org/10.1002/anie.202304138","open_access":"1"}],"month":"05","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"date_created":"2024-01-22T11:54:34Z","date_updated":"2024-01-23T08:48:14Z","volume":62,"author":[{"orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker","first_name":"Lea Marie","full_name":"Becker, Lea Marie"},{"first_name":"Mélanie","last_name":"Berbon","full_name":"Berbon, Mélanie"},{"full_name":"Vallet, Alicia","first_name":"Alicia","last_name":"Vallet"},{"full_name":"Grelard, Axelle","first_name":"Axelle","last_name":"Grelard"},{"last_name":"Morvan","first_name":"Estelle","full_name":"Morvan, Estelle"},{"full_name":"Bardiaux, Benjamin","first_name":"Benjamin","last_name":"Bardiaux"},{"first_name":"Roman","last_name":"Lichtenecker","full_name":"Lichtenecker, Roman"},{"full_name":"Ernst, Matthias","first_name":"Matthias","last_name":"Ernst"},{"last_name":"Loquet","first_name":"Antoine","full_name":"Loquet, Antoine"},{"last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"related_material":{"record":[{"status":"public","relation":"other","id":"12675"}],"link":[{"url":"https://doi.org/10.1002/ange.202304138","relation":"translation"}]},"publication_status":"published","publisher":"Wiley","department":[{"_id":"PaSc"}],"year":"2023","article_number":" e202304138"},{"publication_identifier":{"issn":["0091-1798"]},"month":"11","project":[{"call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["2206.04448"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.04448","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1214/23-aop1643","ec_funded":1,"publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2023","acknowledgement":"The second and the fourth author were supported by the ERC Advanced Grant\r\n“RMTBeyond” No. 101020331. The third author was supported by Dr. Max Rössler, the\r\nWalter Haefner Foundation and the ETH Zürich Foundation.","volume":51,"date_created":"2024-01-22T08:08:41Z","date_updated":"2024-01-23T10:56:30Z","author":[{"full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio"},{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"},{"first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J"},{"full_name":"Xu, Yuanyuan","last_name":"Xu","first_name":"Yuanyuan"}],"keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"article_processing_charge":"No","day":"01","page":"2192-2242","article_type":"original","citation":{"chicago":"Cipolloni, Giorgio, László Erdös, Dominik J Schröder, and Yuanyuan Xu. “On the Rightmost Eigenvalue of Non-Hermitian Random Matrices.” The Annals of Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/23-aop1643.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Y. Xu, The Annals of Probability 51 (2023) 2192–2242.","mla":"Cipolloni, Giorgio, et al. “On the Rightmost Eigenvalue of Non-Hermitian Random Matrices.” The Annals of Probability, vol. 51, no. 6, Institute of Mathematical Statistics, 2023, pp. 2192–242, doi:10.1214/23-aop1643.","ieee":"G. Cipolloni, L. Erdös, D. J. Schröder, and Y. Xu, “On the rightmost eigenvalue of non-Hermitian random matrices,” The Annals of Probability, vol. 51, no. 6. Institute of Mathematical Statistics, pp. 2192–2242, 2023.","apa":"Cipolloni, G., Erdös, L., Schröder, D. J., & Xu, Y. (2023). On the rightmost eigenvalue of non-Hermitian random matrices. The Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-aop1643","ista":"Cipolloni G, Erdös L, Schröder DJ, Xu Y. 2023. On the rightmost eigenvalue of non-Hermitian random matrices. The Annals of Probability. 51(6), 2192–2242.","ama":"Cipolloni G, Erdös L, Schröder DJ, Xu Y. On the rightmost eigenvalue of non-Hermitian random matrices. The Annals of Probability. 2023;51(6):2192-2242. doi:10.1214/23-aop1643"},"publication":"The Annals of Probability","date_published":"2023-11-01T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"We establish a precise three-term asymptotic expansion, with an optimal estimate of the error term, for the rightmost eigenvalue of an n×n random matrix with independent identically distributed complex entries as n tends to infinity. All terms in the expansion are universal."}],"intvolume":" 51","title":"On the rightmost eigenvalue of non-Hermitian random matrices","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14849","oa_version":"Preprint"},{"date_published":"2023-05-02T00:00:00Z","publication":"Angewandte Chemie","citation":{"ama":"Becker LM, Berbon M, Vallet A, et al. Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte Chemie. 2023;135(19). doi:10.1002/ange.202219314","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte Chemie. 135(19), e202219314.","ieee":"L. M. Becker et al., “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten,” Angewandte Chemie, vol. 135, no. 19. Wiley, 2023.","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.202219314","mla":"Becker, Lea Marie, et al. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” Angewandte Chemie, vol. 135, no. 19, e202219314, Wiley, 2023, doi:10.1002/ange.202219314.","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie 135 (2023).","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” Angewandte Chemie. Wiley, 2023. https://doi.org/10.1002/ange.202219314."},"article_type":"original","day":"02","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","keyword":["General Medicine"],"oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1004676,"file_name":"2023_AngewChem_Becker.pdf","access_level":"open_access","date_updated":"2024-01-23T08:57:01Z","date_created":"2024-01-23T08:57:01Z","success":1,"checksum":"98e68d370159f7be52a3d7c8a8ee1198","file_id":"14876","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14835","ddc":["540"],"title":"Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten","status":"public","intvolume":" 135","abstract":[{"lang":"ger","text":"Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen. Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen Cross‐β‐Amyloidstruktur hervorgeht."}],"issue":"19","type":"journal_article","doi":"10.1002/ange.202219314","language":[{"iso":"ger"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","month":"05","publication_identifier":{"eissn":["1521-3757"],"issn":["0044-8249"]},"author":[{"id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151","first_name":"Lea Marie","last_name":"Becker","full_name":"Becker, Lea Marie"},{"last_name":"Berbon","first_name":"Mélanie","full_name":"Berbon, Mélanie"},{"full_name":"Vallet, Alicia","last_name":"Vallet","first_name":"Alicia"},{"full_name":"Grelard, Axelle","last_name":"Grelard","first_name":"Axelle"},{"last_name":"Morvan","first_name":"Estelle","full_name":"Morvan, Estelle"},{"full_name":"Bardiaux, Benjamin","first_name":"Benjamin","last_name":"Bardiaux"},{"last_name":"Lichtenecker","first_name":"Roman","full_name":"Lichtenecker, Roman"},{"last_name":"Ernst","first_name":"Matthias","full_name":"Ernst, Matthias"},{"full_name":"Loquet, Antoine","last_name":"Loquet","first_name":"Antoine"},{"full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}],"date_created":"2024-01-18T10:01:01Z","date_updated":"2024-01-23T12:23:35Z","volume":135,"year":"2023","acknowledgement":"Wir danken Albert A. Smith (Leipzig) für aufschlussreiche Diskussionen. Diese Arbeit wurde mit Mitteln des Europäischen Forschungsrats (StG-2012-311318 an P.S.) unterstützt und nutzte die Plattformen des Grenoble Instruct-ERIC Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) im Rahmen der Grenoble Partnership for Structural Biology (PSB) sowie die Einrichtungen und das Fachwissen der Biophysical and Structural Chemistry Platform (BPCS) am IECB, CNRS UAR3033, INSERM US001 und der Universität Bordeaux.","publication_status":"published","publisher":"Wiley","department":[{"_id":"PaSc"}],"file_date_updated":"2024-01-23T08:57:01Z","article_number":"e202219314"},{"abstract":[{"text":"Organization – or departure from a random pattern – in tropical deep convection is heavily studied due to its immediate relevance to climate sensitivity and extremes. Low-latitude convection has motivated numerical model idealizations, where the Coriolis force is removed and boundary conditions are simplified spatially and temporally. One of the most stunning aspects of such idealized simulated cloud organization is the spontaneous clumping of convection that can occur without any predetermining external perturbation, such as inhomogeneous surface boundary conditions or large-scale waves. Whereas individual convective rain cells measure only few kilometers in horizontal diameter, the clusters they form can often span hundreds or even thousands of kilometers. Hence, organization may emerge from the very small scales but can show effects at the synoptic scale. We refer to such emergent organization as convective self-organization. Convective self-organization thus features characteristics of emergence, such as non-trivial system-scale pattern formation or hysteresis. We summarize observational evidence for large-scale organization and briefly recap classical idealized modeling studies that yield convective self-aggregation – emergent organization under strongly idealized boundary conditions. We then focus on developing research, where temporal variation, such as the diurnal cycle, or two-way interactive surface properties yield distinct organizational modes. Convectively generated cold pools and mesoscale convective systems, both ubiquitous in nature, are thereby found to potentially play key roles in promoting – rather than suppressing – sustained system-scale organization.","lang":"eng"}],"type":"book_chapter","alternative_title":["Geophysical Monograph Series"],"author":[{"full_name":"Haerter, Jan O.","last_name":"Haerter","first_name":"Jan O."},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","first_name":"Caroline J","last_name":"Muller","full_name":"Muller, Caroline J"}],"date_created":"2024-01-22T08:23:16Z","date_updated":"2024-01-23T12:40:36Z","oa_version":"None","_id":"14853","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Mechanisms for the Self‐Organization of Tropical Deep Convection","editor":[{"first_name":"Sylvia","last_name":"Sullivan","full_name":"Sullivan, Sylvia"},{"last_name":"Hoose","first_name":"Corinna","full_name":"Hoose, Corinna"}],"department":[{"_id":"CaMu"}],"publisher":"Wiley","month":"12","day":"15","article_processing_charge":"No","publication_identifier":{"eisbn":["9781119700357"],"issn":["2328-8779"],"isbn":["9781119700319"]},"doi":"10.1002/9781119700357.ch8","date_published":"2023-12-15T00:00:00Z","language":[{"iso":"eng"}],"publication":"Clouds and Their Climatic Impacts","citation":{"mla":"Haerter, Jan O., and Caroline J. Muller. “Mechanisms for the Self‐Organization of Tropical Deep Convection.” Clouds and Their Climatic Impacts, edited by Sylvia Sullivan and Corinna Hoose, Wiley, 2023, pp. 179–93, doi:10.1002/9781119700357.ch8.","short":"J.O. Haerter, C.J. Muller, in:, S. Sullivan, C. Hoose (Eds.), Clouds and Their Climatic Impacts, Wiley, 2023, pp. 179–193.","chicago":"Haerter, Jan O., and Caroline J Muller. “Mechanisms for the Self‐Organization of Tropical Deep Convection.” In Clouds and Their Climatic Impacts, edited by Sylvia Sullivan and Corinna Hoose, 179–93. Wiley, 2023. https://doi.org/10.1002/9781119700357.ch8.","ama":"Haerter JO, Muller CJ. Mechanisms for the Self‐Organization of Tropical Deep Convection. In: Sullivan S, Hoose C, eds. Clouds and Their Climatic Impacts. Wiley; 2023:179-193. doi:10.1002/9781119700357.ch8","ista":"Haerter JO, Muller CJ. 2023.Mechanisms for the Self‐Organization of Tropical Deep Convection. In: Clouds and Their Climatic Impacts. Geophysical Monograph Series, , 179–193.","ieee":"J. O. Haerter and C. J. Muller, “Mechanisms for the Self‐Organization of Tropical Deep Convection,” in Clouds and Their Climatic Impacts, S. Sullivan and C. Hoose, Eds. Wiley, 2023, pp. 179–193.","apa":"Haerter, J. O., & Muller, C. J. (2023). Mechanisms for the Self‐Organization of Tropical Deep Convection. In S. Sullivan & C. Hoose (Eds.), Clouds and Their Climatic Impacts (pp. 179–193). Wiley. https://doi.org/10.1002/9781119700357.ch8"},"quality_controlled":"1","page":"179-193"},{"day":"01","article_processing_charge":"No","publication":"Biophysics of Molecular Chaperones","citation":{"chicago":"Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies.” In Biophysics of Molecular Chaperones, edited by Sebastian Hiller, Maili Liu, and Lichun He, 29:136–61. Royal Society of Chemistry, 2023. https://doi.org/10.1039/bk9781839165986-00136.","mla":"Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies.” Biophysics of Molecular Chaperones, edited by Sebastian Hiller et al., vol. 29, Royal Society of Chemistry, 2023, pp. 136–61, doi:10.1039/bk9781839165986-00136.","short":"I. Sučec, P. Schanda, in:, S. Hiller, M. Liu, L. He (Eds.), Biophysics of Molecular Chaperones, Royal Society of Chemistry, 2023, pp. 136–161.","ista":"Sučec I, Schanda P. 2023.Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In: Biophysics of Molecular Chaperones. New Developments in NMR, vol. 29, 136–161.","apa":"Sučec, I., & Schanda, P. (2023). Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In S. Hiller, M. Liu, & L. He (Eds.), Biophysics of Molecular Chaperones (Vol. 29, pp. 136–161). Royal Society of Chemistry. https://doi.org/10.1039/bk9781839165986-00136","ieee":"I. Sučec and P. Schanda, “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies,” in Biophysics of Molecular Chaperones, vol. 29, S. Hiller, M. Liu, and L. He, Eds. Royal Society of Chemistry, 2023, pp. 136–161.","ama":"Sučec I, Schanda P. Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In: Hiller S, Liu M, He L, eds. Biophysics of Molecular Chaperones. Vol 29. Royal Society of Chemistry; 2023:136-161. doi:10.1039/bk9781839165986-00136"},"page":"136-161","date_published":"2023-11-01T00:00:00Z","type":"book_chapter","alternative_title":["New Developments in NMR"],"abstract":[{"text":"Understanding the mechanisms of chaperones at the atomic level generally requires producing chaperone–client complexes in vitro. This task comes with significant challenges, because one needs to find conditions in which the client protein is presented to the chaperone in a state that binds and at the same time avoid the pitfalls of protein aggregation that are often inherent to such states. The strategy differs significantly for different client proteins and chaperones, but there are common underlying principles. Here, we discuss these principles and deduce the strategies that can be successfully applied for different chaperone–client complexes. We review successful biochemical strategies applied to making the client protein “binding competent” and illustrate the different strategies with examples of recent biophysical and biochemical studies.","lang":"eng"}],"_id":"14847","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies","status":"public","intvolume":" 29","oa_version":"Preprint","month":"11","publication_identifier":{"eisbn":["9781839165993"],"isbn":["9781839162824"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.26434/chemrxiv-2023-rpn28","open_access":"1"}],"quality_controlled":"1","doi":"10.1039/bk9781839165986-00136","language":[{"iso":"eng"}],"year":"2023","publication_status":"published","department":[{"_id":"PaSc"}],"editor":[{"full_name":"Hiller, Sebastian","first_name":"Sebastian","last_name":"Hiller"},{"last_name":"Liu","first_name":"Maili","full_name":"Liu, Maili"},{"full_name":"He, Lichun","last_name":"He","first_name":"Lichun"}],"publisher":"Royal Society of Chemistry","author":[{"last_name":"Sučec","first_name":"I.","full_name":"Sučec, I."},{"first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"date_updated":"2024-01-23T11:50:10Z","date_created":"2024-01-22T08:04:57Z","volume":29},{"page":"278-318","quality_controlled":"1","citation":{"mla":"Wruck, F., et al. “Probing Single Chaperone Substrates.” Biophysics of Molecular Chaperones, edited by Sebastian Hiller et al., vol. 29, Royal Society of Chemistry, 2023, pp. 278–318, doi:10.1039/bk9781839165986-00278.","short":"F. Wruck, M. Avellaneda Sarrió, M.M. Naqvi, E.J. Koers, K. Till, L. Gross, F. Moayed, A. Roland, L.W.H.J. Heling, A. Mashaghi, S.J. Tans, in:, S. Hiller, M. Liu, L. He (Eds.), Biophysics of Molecular Chaperones, Royal Society of Chemistry, 2023, pp. 278–318.","chicago":"Wruck, F., Mario Avellaneda Sarrió, M. M. Naqvi, E. J. Koers, K. Till, L. Gross, F. Moayed, et al. “Probing Single Chaperone Substrates.” In Biophysics of Molecular Chaperones, edited by Sebastian Hiller, Maili Liu, and Lichun He, 29:278–318. Royal Society of Chemistry, 2023. https://doi.org/10.1039/bk9781839165986-00278.","ama":"Wruck F, Avellaneda Sarrió M, Naqvi MM, et al. Probing Single Chaperone Substrates. In: Hiller S, Liu M, He L, eds. Biophysics of Molecular Chaperones. Vol 29. Royal Society of Chemistry; 2023:278-318. doi:10.1039/bk9781839165986-00278","ista":"Wruck F, Avellaneda Sarrió M, Naqvi MM, Koers EJ, Till K, Gross L, Moayed F, Roland A, Heling LWHJ, Mashaghi A, Tans SJ. 2023.Probing Single Chaperone Substrates. In: Biophysics of Molecular Chaperones. New Developments in NMR, vol. 29, 278–318.","ieee":"F. Wruck et al., “Probing Single Chaperone Substrates,” in Biophysics of Molecular Chaperones, vol. 29, S. Hiller, M. Liu, and L. He, Eds. Royal Society of Chemistry, 2023, pp. 278–318.","apa":"Wruck, F., Avellaneda Sarrió, M., Naqvi, M. M., Koers, E. J., Till, K., Gross, L., … Tans, S. J. (2023). Probing Single Chaperone Substrates. In S. Hiller, M. Liu, & L. He (Eds.), Biophysics of Molecular Chaperones (Vol. 29, pp. 278–318). Royal Society of Chemistry. https://doi.org/10.1039/bk9781839165986-00278"},"publication":"Biophysics of Molecular Chaperones","language":[{"iso":"eng"}],"doi":"10.1039/bk9781839165986-00278","date_published":"2023-11-01T00:00:00Z","publication_identifier":{"eisbn":["9781839165993"],"isbn":["9781839162824"]},"article_processing_charge":"No","month":"11","day":"01","publisher":"Royal Society of Chemistry","intvolume":" 29","department":[{"_id":"MiSi"}],"editor":[{"full_name":"Hiller, Sebastian","first_name":"Sebastian","last_name":"Hiller"},{"full_name":"Liu, Maili","first_name":"Maili","last_name":"Liu"},{"full_name":"He, Lichun","first_name":"Lichun","last_name":"He"}],"status":"public","title":"Probing Single Chaperone Substrates","publication_status":"published","year":"2023","_id":"14848","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":29,"date_created":"2024-01-22T08:07:02Z","date_updated":"2024-01-23T12:01:53Z","author":[{"first_name":"F.","last_name":"Wruck","full_name":"Wruck, F."},{"full_name":"Avellaneda Sarrió, Mario","orcid":"0000-0001-6406-524X","id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","last_name":"Avellaneda Sarrió","first_name":"Mario"},{"first_name":"M. M.","last_name":"Naqvi","full_name":"Naqvi, M. M."},{"full_name":"Koers, E. J.","first_name":"E. J.","last_name":"Koers"},{"full_name":"Till, K.","first_name":"K.","last_name":"Till"},{"full_name":"Gross, L.","last_name":"Gross","first_name":"L."},{"full_name":"Moayed, F.","last_name":"Moayed","first_name":"F."},{"last_name":"Roland","first_name":"A.","full_name":"Roland, A."},{"full_name":"Heling, L. W. H. J.","first_name":"L. W. H. J.","last_name":"Heling"},{"last_name":"Mashaghi","first_name":"A.","full_name":"Mashaghi, A."},{"full_name":"Tans, S. J.","first_name":"S. J.","last_name":"Tans"}],"alternative_title":["New Developments in NMR"],"type":"book_chapter","abstract":[{"text":"Regulating protein states is considered the core function of chaperones. However, despite their importance to all major cellular processes, the conformational changes that chaperones impart on polypeptide chains are difficult to study directly due to their heterogeneous, dynamic, and multi-step nature. Here, we review recent advances towards this aim using single-molecule manipulation methods, which are rapidly revealing new mechanisms of conformational control and helping to define a different perspective on the chaperone function.","lang":"eng"}]},{"citation":{"apa":"Mitrouskas, D. J., & Seiringer, R. (2023). Ubiquity of bound states for the strongly coupled polaron. Pure and Applied Analysis. Mathematical Sciences Publishers. https://doi.org/10.2140/paa.2023.5.973","ieee":"D. J. Mitrouskas and R. Seiringer, “Ubiquity of bound states for the strongly coupled polaron,” Pure and Applied Analysis, vol. 5, no. 4. Mathematical Sciences Publishers, pp. 973–1008, 2023.","ista":"Mitrouskas DJ, Seiringer R. 2023. Ubiquity of bound states for the strongly coupled polaron. Pure and Applied Analysis. 5(4), 973–1008.","ama":"Mitrouskas DJ, Seiringer R. Ubiquity of bound states for the strongly coupled polaron. Pure and Applied Analysis. 2023;5(4):973-1008. doi:10.2140/paa.2023.5.973","chicago":"Mitrouskas, David Johannes, and Robert Seiringer. “Ubiquity of Bound States for the Strongly Coupled Polaron.” Pure and Applied Analysis. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/paa.2023.5.973.","short":"D.J. Mitrouskas, R. Seiringer, Pure and Applied Analysis 5 (2023) 973–1008.","mla":"Mitrouskas, David Johannes, and Robert Seiringer. “Ubiquity of Bound States for the Strongly Coupled Polaron.” Pure and Applied Analysis, vol. 5, no. 4, Mathematical Sciences Publishers, 2023, pp. 973–1008, doi:10.2140/paa.2023.5.973."},"publication":"Pure and Applied Analysis","page":"973-1008","article_type":"original","quality_controlled":"1","date_published":"2023-12-15T00:00:00Z","doi":"10.2140/paa.2023.5.973","language":[{"iso":"eng"}],"keyword":["General Medicine"],"publication_identifier":{"issn":["2578-5885","2578-5893"]},"article_processing_charge":"No","day":"15","month":"12","_id":"14854","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 5","department":[{"_id":"RoSe"}],"publisher":"Mathematical Sciences Publishers","status":"public","title":"Ubiquity of bound states for the strongly coupled polaron","publication_status":"published","author":[{"full_name":"Mitrouskas, David Johannes","first_name":"David Johannes","last_name":"Mitrouskas","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"volume":5,"oa_version":"None","date_updated":"2024-01-23T12:55:12Z","date_created":"2024-01-22T08:24:23Z","type":"journal_article","issue":"4","abstract":[{"text":"\r\nAbstract\r\nWe study the spectrum of the Fröhlich Hamiltonian for the polaron at fixed total momentum. We prove the existence of excited eigenvalues between the ground state energy and the essential spectrum at strong coupling. In fact, our main result shows that the number of excited energy bands diverges in the strong coupling limit. To prove this we derive upper bounds for the min-max values of the corresponding fiber Hamiltonians and compare them with the bottom of the essential spectrum, a lower bound on which was recently obtained by Brooks and Seiringer (Comm. Math. Phys. 404:1 (2023), 287–337). The upper bounds are given in terms of the ground state energy band shifted by momentum-independent excitation energies determined by an effective Hamiltonian of Bogoliubov type.","lang":"eng"}]},{"day":"01","month":"10","publication_identifier":{"isbn":["9781957171296"]},"article_processing_charge":"No","conference":{"name":"Laser Science","start_date":"2023-10-09","location":"Tacoma, WA, United States","end_date":"2023-10-12"},"doi":"10.1364/ls.2023.lm1f.3","date_published":"2023-10-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Frontiers in Optics + Laser Science 2023","citation":{"ista":"Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling microwaves and telecom wavelength light. Frontiers in Optics + Laser Science 2023. Laser Science, LM1F.3.","apa":"Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., & Fink, J. M. (2023). Entangling microwaves and telecom wavelength light. In Frontiers in Optics + Laser Science 2023. Tacoma, WA, United States: Optica Publishing Group. https://doi.org/10.1364/ls.2023.lm1f.3","ieee":"R. Sahu et al., “Entangling microwaves and telecom wavelength light,” in Frontiers in Optics + Laser Science 2023, Tacoma, WA, United States, 2023.","ama":"Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves and telecom wavelength light. In: Frontiers in Optics + Laser Science 2023. Optica Publishing Group; 2023. doi:10.1364/ls.2023.lm1f.3","chicago":"Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Yuri Minoguchi, Peter Rabl, and Johannes M Fink. “Entangling Microwaves and Telecom Wavelength Light.” In Frontiers in Optics + Laser Science 2023. Optica Publishing Group, 2023. https://doi.org/10.1364/ls.2023.lm1f.3.","mla":"Sahu, Rishabh, et al. “Entangling Microwaves and Telecom Wavelength Light.” Frontiers in Optics + Laser Science 2023, LM1F.3, Optica Publishing Group, 2023, doi:10.1364/ls.2023.lm1f.3.","short":"R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink, in:, Frontiers in Optics + Laser Science 2023, Optica Publishing Group, 2023."},"quality_controlled":"1","abstract":[{"text":"We entangled microwave and optical photons for the first time as verified by a measured two-mode vacuum squeezing of 0.7 dB. This electro-optic entanglement is the key resource needed to connect cryogenic quantum circuits.","lang":"eng"}],"article_number":"LM1F.3","type":"conference","author":[{"last_name":"Sahu","first_name":"Rishabh","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh"},{"full_name":"Qiu, Liu","first_name":"Liu","last_name":"Qiu"},{"full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","first_name":"William J","last_name":"Hease"},{"full_name":"Arnold, Georg M","last_name":"Arnold","first_name":"Georg M","orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yuri","last_name":"Minoguchi","full_name":"Minoguchi, Yuri"},{"full_name":"Rabl, Peter","last_name":"Rabl","first_name":"Peter"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M"}],"date_created":"2024-01-22T12:29:41Z","date_updated":"2024-01-24T08:43:28Z","oa_version":"None","_id":"14872","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Entangling microwaves and telecom wavelength light","publisher":"Optica Publishing Group","department":[{"_id":"JoFi"}]},{"ec_funded":1,"file_date_updated":"2024-01-24T09:34:43Z","author":[{"full_name":"Anastos, Michael","last_name":"Anastos","first_name":"Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb"}],"date_updated":"2024-01-24T09:38:44Z","date_created":"2024-01-22T12:20:15Z","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.\r\n","year":"2023","department":[{"_id":"MaKw"}],"publisher":"Masaryk University Press","publication_status":"published","publication_identifier":{"eissn":["2788-3116"]},"month":"09","doi":"10.5817/cz.muni.eurocomb23-005","conference":{"name":"EUROCOMB: European Conference on Combinatorics, Graph Theory and Applications","end_date":"2023-09-01","location":"Prague, Czech Republic","start_date":"2023-08-28"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"arxiv":["2209.09860"]},"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"quality_controlled":"1","abstract":[{"text":"Starting with the empty graph on $[n]$, at each round, a set of $K=K(n)$ edges is presented chosen uniformly at random from the ones that have not been presented yet. We are then asked to choose at most one of the presented edges and add it to the current graph. Our goal is to construct a Hamiltonian graph with $(1+o(1))n$ edges within as few rounds as possible. We show that in this process, one can build a Hamiltonian graph of size $(1+o(1))n$ in $(1+o(1))(1+(\\log n)/2K) n$ rounds w.h.p. The case $K=1$ implies that w.h.p. one can build a Hamiltonian graph by choosing $(1+o(1))n$ edges in an online fashion as they appear along the first $(0.5+o(1))n\\log n$ rounds of the random graph process. This answers a question of Frieze, Krivelevich and Michaeli. Observe that the number of rounds is asymptotically optimal as the first $0.5n\\log n$ edges do not span a Hamilton cycle w.h.p. The case $K=\\Theta(\\log n)$ implies that the Hamiltonicity threshold of the corresponding Achlioptas process is at most $(1+o(1))(1+(\\log n)/2K) n$. This matches the $(1-o(1))(1+(\\log n)/2K) n$ lower bound due to Krivelevich, Lubetzky and Sudakov and resolves the problem of determining the Hamiltonicity threshold of the Achlioptas process with $K=\\Theta(\\log n)$. We also show that in the above process one can construct a graph $G$ that spans a matching of size $\\lfloor V(G)/2) \\rfloor$ and $(0.5+o(1))n$ edges within $(1+o(1))(0.5+(\\log n)/2K) n$ rounds w.h.p. Our proof relies on a robust Hamiltonicity property of the strong $4$-core of the binomial random graph which we use as a black-box. This property allows it to absorb paths covering vertices outside the strong $4$-core into a cycle.","lang":"eng"}],"type":"conference","file":[{"date_updated":"2024-01-24T09:34:43Z","date_created":"2024-01-24T09:34:43Z","checksum":"fb1d9a1e7389d90ec0e5e76934373cf8","success":1,"relation":"main_file","file_id":"14881","file_size":464230,"content_type":"application/pdf","creator":"dernst","file_name":"2023_Eurocomb_Anastos.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"14867","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Constructing Hamilton cycles and perfect matchings efficiently","ddc":["510"],"status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"01","date_published":"2023-09-01T00:00:00Z","citation":{"ista":"Anastos M. 2023. Constructing Hamilton cycles and perfect matchings efficiently. Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications. EUROCOMB: European Conference on Combinatorics, Graph Theory and Applications, 36–41.","apa":"Anastos, M. (2023). Constructing Hamilton cycles and perfect matchings efficiently. In Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications (pp. 36–41). Prague, Czech Republic: Masaryk University Press. https://doi.org/10.5817/cz.muni.eurocomb23-005","ieee":"M. Anastos, “Constructing Hamilton cycles and perfect matchings efficiently,” in Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications, Prague, Czech Republic, 2023, pp. 36–41.","ama":"Anastos M. Constructing Hamilton cycles and perfect matchings efficiently. In: Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications. Masaryk University Press; 2023:36-41. doi:10.5817/cz.muni.eurocomb23-005","chicago":"Anastos, Michael. “Constructing Hamilton Cycles and Perfect Matchings Efficiently.” In Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications, 36–41. Masaryk University Press, 2023. https://doi.org/10.5817/cz.muni.eurocomb23-005.","mla":"Anastos, Michael. “Constructing Hamilton Cycles and Perfect Matchings Efficiently.” Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications, Masaryk University Press, 2023, pp. 36–41, doi:10.5817/cz.muni.eurocomb23-005.","short":"M. Anastos, in:, Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications, Masaryk University Press, 2023, pp. 36–41."},"publication":"Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications","page":"36-41"},{"month":"04","doi":"10.5194/egusphere-egu23-6166","conference":{"name":"EGU General Assembly","end_date":"2023-04-28","start_date":"2023-04-23","location":"Vienna, Austria & Virtual"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120"}],"ec_funded":1,"file_date_updated":"2024-01-23T13:00:26Z","article_number":"6166","author":[{"id":"4bdcf7f6-eb97-11eb-a6c2-9981bbdc3bed","orcid":"0000-0002-0464-8440","first_name":"Andrea","last_name":"Stöllner","full_name":"Stöllner, Andrea"},{"full_name":"Lenton, Isaac C","last_name":"Lenton","first_name":"Isaac C","orcid":"0000-0002-5010-6984","id":"a550210f-223c-11ec-8182-e2d45e817efb"},{"full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J"},{"full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","first_name":"Scott R","last_name":"Waitukaitis"}],"date_updated":"2024-01-24T11:21:42Z","date_created":"2024-01-22T12:09:07Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Starting Grant (No. 949120).","year":"2023","publisher":"European Geosciences Union","department":[{"_id":"CaMu"},{"_id":"ScWa"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"23","date_published":"2023-04-23T00:00:00Z","citation":{"ista":"Stöllner A, Lenton IC, Muller CJ, Waitukaitis SR. 2023. Measuring spontaneous charging of single aerosol particles. EGU General Assembly 2023. EGU General Assembly, 6166.","ieee":"A. Stöllner, I. C. Lenton, C. J. Muller, and S. R. Waitukaitis, “Measuring spontaneous charging of single aerosol particles,” in EGU General Assembly 2023, Vienna, Austria & Virtual, 2023.","apa":"Stöllner, A., Lenton, I. C., Muller, C. J., & Waitukaitis, S. R. (2023). Measuring spontaneous charging of single aerosol particles. In EGU General Assembly 2023. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-6166","ama":"Stöllner A, Lenton IC, Muller CJ, Waitukaitis SR. Measuring spontaneous charging of single aerosol particles. In: EGU General Assembly 2023. European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-6166","chicago":"Stöllner, Andrea, Isaac C Lenton, Caroline J Muller, and Scott R Waitukaitis. “Measuring Spontaneous Charging of Single Aerosol Particles.” In EGU General Assembly 2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-6166.","mla":"Stöllner, Andrea, et al. “Measuring Spontaneous Charging of Single Aerosol Particles.” EGU General Assembly 2023, 6166, European Geosciences Union, 2023, doi:10.5194/egusphere-egu23-6166.","short":"A. Stöllner, I.C. Lenton, C.J. Muller, S.R. 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Intensification mechanisms of tropical cyclones. In: EGU General Assembly 2023. European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-6157","apa":"Polesello, A., Muller, C. J., Pasquero, C., & Meroni, A. N. (2023). Intensification mechanisms of tropical cyclones. In EGU General Assembly 2023. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-6157","ieee":"A. Polesello, C. J. Muller, C. Pasquero, and A. N. Meroni, “Intensification mechanisms of tropical cyclones,” in EGU General Assembly 2023, Vienna, Austria & Virtual, 2023.","ista":"Polesello A, Muller CJ, Pasquero C, Meroni AN. 2023. Intensification mechanisms of tropical cyclones. EGU General Assembly 2023. EGU General Assembly, EGU23-6157.","short":"A. Polesello, C.J. Muller, C. Pasquero, A.N. Meroni, in:, EGU General Assembly 2023, European Geosciences Union, 2023.","mla":"Polesello, Andrea, et al. “Intensification Mechanisms of Tropical Cyclones.” EGU General Assembly 2023, EGU23-6157, European Geosciences Union, 2023, doi:10.5194/egusphere-egu23-6157.","chicago":"Polesello, Andrea, Caroline J Muller, Claudia Pasquero, and Agostino N. Meroni. “Intensification Mechanisms of Tropical Cyclones.” In EGU General Assembly 2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-6157."},"publication":"EGU General Assembly 2023","language":[{"iso":"eng"}],"date_published":"2023-04-13T00:00:00Z","doi":"10.5194/egusphere-egu23-6157","conference":{"start_date":"2023-04-23","location":"Vienna, Austria & Virtual","end_date":"2023-04-28","name":"EGU General Assembly"}},{"type":"preprint","abstract":[{"lang":"eng","text":"Fragmented landscapes pose a significant threat to the persistence of species as they are highly susceptible to heightened risk of extinction due to the combined effects of genetic and demographic factors such as genetic drift and demographic stochasticity. This paper explores the intricate interplay between genetic load and extinction risk within metapopulations with a focus on understanding the impact of eco-evolutionary feedback mechanisms. We distinguish between two models of selection: soft selection, characterised by subpopulations maintaining carrying capacity despite load, and hard selection, where load can significantly affect population size. Within the soft selection framework, we investigate the impact of gene flow on genetic load at a single locus, while also considering the effect of selection strength and dominance coefficient. We subsequently build on this to examine how gene flow influences both population size and load under hard selection as well as identify critical thresholds for metapopulation persistence. Our analysis employs the diffusion, semi-deterministic and effective migration approximations. Our findings reveal that under soft selection, even modest levels of migration can significantly alleviate the burden of load. In sharp contrast, with hard selection, a much higher degree of gene flow is required to mitigate load and prevent the collapse of the metapopulation. Overall, this study sheds light into the crucial role migration plays in shaping the dynamics of genetic load and extinction risk in fragmented landscapes, offering valuable insights for conservation strategies and the preservation of diversity in a changing world."}],"_id":"14732","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2023","department":[{"_id":"NiBa"},{"_id":"JaMa"}],"publication_status":"submitted","title":"Genetic load, eco-evolutionary feedback and extinction in a metapopulation","status":"public","related_material":{"record":[{"id":"14711","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Olusanya, Oluwafunmilola O","first_name":"Oluwafunmilola O","last_name":"Olusanya","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1971-8314"},{"full_name":"Khudiakova, Kseniia","last_name":"Khudiakova","first_name":"Kseniia","orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"},{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani"}],"oa_version":"Preprint","date_created":"2024-01-04T09:35:54Z","date_updated":"2024-01-26T12:00:53Z","article_processing_charge":"No","month":"12","day":"04","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.12.02.569702v1","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"citation":{"chicago":"Olusanya, Oluwafunmilola O, Kseniia Khudiakova, and Himani Sachdeva. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, n.d. https://doi.org/10.1101/2023.12.02.569702.","short":"O.O. Olusanya, K. Khudiakova, H. Sachdeva, BioRxiv (n.d.).","mla":"Olusanya, Oluwafunmilola O., et al. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, doi:10.1101/2023.12.02.569702.","ieee":"O. O. Olusanya, K. Khudiakova, and H. Sachdeva, “Genetic load, eco-evolutionary feedback and extinction in a metapopulation,” bioRxiv. .","apa":"Olusanya, O. O., Khudiakova, K., & Sachdeva, H. (n.d.). Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv. https://doi.org/10.1101/2023.12.02.569702","ista":"Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv, 10.1101/2023.12.02.569702.","ama":"Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv. doi:10.1101/2023.12.02.569702"},"oa":1,"publication":"bioRxiv","project":[{"grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation"},{"name":"The impact of deleterious mutations on small populations","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8","grant_number":"26293"},{"name":"Polygenic Adaptation in a Metapopulation","grant_number":"26380","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6"}],"doi":"10.1101/2023.12.02.569702","date_published":"2023-12-04T00:00:00Z","language":[{"iso":"eng"}]},{"title":"PCBend: Light up your 3D shapes with foldable circuit boards","ddc":["006"],"status":"public","intvolume":" 42","_id":"13049","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"checksum":"a0b0ba3b36f43a94388e8824613d812a","success":1,"date_updated":"2023-06-19T11:02:23Z","date_created":"2023-06-19T11:02:23Z","relation":"main_file","file_id":"13156","file_size":78940724,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_ACMToG_Freire.pdf"},{"file_size":34345905,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_ACMToG_SuppMaterial_Freire.pdf","checksum":"b9206bbb67af82df49b7e7cdbde3410c","success":1,"date_updated":"2023-06-20T12:20:51Z","date_created":"2023-06-20T12:20:51Z","relation":"main_file","file_id":"13157"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We propose a computational design approach for covering a surface with individually addressable RGB LEDs, effectively forming a low-resolution surface screen. To achieve a low-cost and scalable approach, we propose creating designs from flat PCB panels bent in-place along the surface of a 3D printed core. Working with standard rigid PCBs enables the use of\r\nestablished PCB manufacturing services, allowing the fabrication of designs with several hundred LEDs. \r\nOur approach optimizes the PCB geometry for folding, and then jointly optimizes the LED packing, circuit and routing, solving a challenging layout problem under strict manufacturing requirements. Unlike paper, PCBs cannot bend beyond a certain point without breaking. Therefore, we introduce parametric cut patterns acting as hinges, designed to allow bending while remaining compact. To tackle the joint optimization of placement, circuit and routing, we propose a specialized algorithm that splits the global problem into one sub-problem per triangle, which is then individually solved.\r\nOur technique generates PCB blueprints in a completely automated way. After being fabricated by a PCB manufacturing service, the boards are bent and glued by the user onto the 3D printed support. We demonstrate our technique on a range of physical models and virtual examples, creating intricate surface light patterns from hundreds of LEDs."}],"issue":"4","article_type":"original","publication":"Transactions on Graphics","citation":{"chicago":"Freire, Marco, Manas Bhargava, Camille Schreck, Pierre-Alexandre Hugron, Bernd Bickel, and Sylvain Lefebvre. “PCBend: Light up Your 3D Shapes with Foldable Circuit Boards.” Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3592411.","mla":"Freire, Marco, et al. “PCBend: Light up Your 3D Shapes with Foldable Circuit Boards.” Transactions on Graphics, vol. 42, no. 4, 142, Association for Computing Machinery, 2023, doi:10.1145/3592411.","short":"M. Freire, M. Bhargava, C. Schreck, P.-A. Hugron, B. Bickel, S. Lefebvre, Transactions on Graphics 42 (2023).","ista":"Freire M, Bhargava M, Schreck C, Hugron P-A, Bickel B, Lefebvre S. 2023. PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. 42(4), 142.","ieee":"M. Freire, M. Bhargava, C. Schreck, P.-A. Hugron, B. Bickel, and S. Lefebvre, “PCBend: Light up your 3D shapes with foldable circuit boards,” Transactions on Graphics, vol. 42, no. 4. Association for Computing Machinery, 2023.","apa":"Freire, M., Bhargava, M., Schreck, C., Hugron, P.-A., Bickel, B., & Lefebvre, S. (2023). PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3592411","ama":"Freire M, Bhargava M, Schreck C, Hugron P-A, Bickel B, Lefebvre S. PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. 2023;42(4). doi:10.1145/3592411"},"date_published":"2023-07-26T00:00:00Z","keyword":["PCB design and layout","Mesh geometry models"],"day":"26","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","acknowledgement":"We thank the reviewers for the valuable feedback. We also thank the Miba Machine Shop at ISTA, PCBWay, and PragoBoard for helping us with fabrication and assembly. This project was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 715767 – MATERIALIZABLE).","year":"2023","date_updated":"2024-01-29T10:30:49Z","date_created":"2023-05-22T08:37:04Z","volume":42,"author":[{"full_name":"Freire, Marco","last_name":"Freire","first_name":"Marco"},{"full_name":"Bhargava, Manas","orcid":"0009-0007-6138-6890","id":"FF8FA64C-AA6A-11E9-99AD-50D4E5697425","last_name":"Bhargava","first_name":"Manas"},{"last_name":"Schreck","first_name":"Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","full_name":"Schreck, Camille"},{"full_name":"Hugron, Pierre-Alexandre","last_name":"Hugron","first_name":"Pierre-Alexandre"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"last_name":"Lefebvre","first_name":"Sylvain","full_name":"Lefebvre, Sylvain"}],"article_number":"142","file_date_updated":"2023-06-20T12:20:51Z","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["001044671300108"]},"acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"conference":{"name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","location":"Los Angeles, CA, United States","start_date":"2023-08-06","end_date":"2023-08-10"},"doi":"10.1145/3592411","month":"07","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]}},{"date_published":"2023-07-01T00:00:00Z","citation":{"mla":"Chen, Huihuang, et al. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant, vol. 16, no. 7, Elsevier , 2023, pp. 1117–19, doi:10.1016/j.molp.2023.06.007.","short":"H. Chen, L. Li, M. Zou, L. Qi, J. Friml, Molecular Plant 16 (2023) 1117–1119.","chicago":"Chen, Huihuang, Lanxin Li, Minxia Zou, Linlin Qi, and Jiří Friml. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant. Elsevier , 2023. https://doi.org/10.1016/j.molp.2023.06.007.","ama":"Chen H, Li L, Zou M, Qi L, Friml J. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 2023;16(7):1117-1119. doi:10.1016/j.molp.2023.06.007","ista":"Chen H, Li L, Zou M, Qi L, Friml J. 2023. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 16(7), 1117–1119.","apa":"Chen, H., Li, L., Zou, M., Qi, L., & Friml, J. (2023). Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. Elsevier . https://doi.org/10.1016/j.molp.2023.06.007","ieee":"H. Chen, L. Li, M. Zou, L. Qi, and J. Friml, “Distinct functions of TIR1 and AFB1 receptors in auxin signalling.,” Molecular Plant, vol. 16, no. 7. Elsevier , pp. 1117–1119, 2023."},"publication":"Molecular Plant","page":"1117-1119","article_type":"letter_note","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","file_size":1000871,"content_type":"application/pdf","file_name":"2023_MolecularPlant_Chen.pdf","access_level":"open_access","date_created":"2024-01-29T10:37:05Z","date_updated":"2024-01-29T10:37:05Z","success":1,"checksum":"6012b7e4a2f680ee6c1f84001e2b945f","file_id":"14894","relation":"main_file"}],"_id":"13212","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 16","ddc":["580"],"status":"public","title":"Distinct functions of TIR1 and AFB1 receptors in auxin signalling.","issue":"7","abstract":[{"text":"Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast.","lang":"eng"}],"type":"journal_article","doi":"10.1016/j.molp.2023.06.007","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["37393433"],"isi":["001044410900001"]},"oa":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1674-2052"],"issn":["1752-9867"]},"month":"07","author":[{"full_name":"Chen, Huihuang","first_name":"Huihuang","last_name":"Chen","id":"83c96512-15b2-11ec-abd3-b7eede36184f"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin"},{"full_name":"Zou, Minxia","last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"full_name":"Qi, Linlin","last_name":"Qi","first_name":"Linlin","orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"volume":16,"date_updated":"2024-01-29T10:38:57Z","date_created":"2023-07-12T07:32:46Z","pmid":1,"year":"2023","acknowledgement":"We thank all the authors for sharing the published materials. This research was supported by the Lab Support Facility and the Imaging and Optics Facility of ISTA. We thank Lukáš Fiedler (ISTA) for critical reading of the manuscript. This project was funded by the European Research Council Advanced Grant (ETAP-742985).","publisher":"Elsevier ","department":[{"_id":"JiFr"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2024-01-29T10:37:05Z"},{"type":"journal_article","issue":"4","abstract":[{"text":"Tattoos are a highly popular medium, with both artistic and medical applications. Although the mechanical process of tattoo application has evolved historically, the results are reliant on the artisanal skill of the artist. This can be especially challenging for some skin tones, or in cases where artists lack experience. We provide the first systematic overview of tattooing as a computational fabrication technique. We built an automated tattooing rig and a recipe for the creation of silicone sheets mimicking realistic skin tones, which allowed us to create an accurate model predicting tattoo appearance. This enables several exciting applications including tattoo previewing, color retargeting, novel ink spectra optimization, color-accurate prosthetics, and more.","lang":"eng"}],"intvolume":" 42","status":"public","ddc":["004"],"title":"Skin-Screen: A computational fabrication framework for color tattoos","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12984","file":[{"creator":"mpiovarc","content_type":"application/pdf","file_size":30817343,"access_level":"open_access","file_name":"Piovarci2023.pdf","success":1,"checksum":"5f0a6867689e025a661bd0b4fd90b821","date_updated":"2023-05-16T09:38:25Z","date_created":"2023-05-16T09:38:25Z","file_id":"12985","relation":"main_file"}],"oa_version":"Submitted Version","keyword":["appearance","modeling","reproduction","tattoo","skin color","gamut mapping","ink-optimization","prosthetic"],"has_accepted_license":"1","article_processing_charge":"No","day":"26","article_type":"original","citation":{"mla":"Piovarci, Michael, et al. “Skin-Screen: A Computational Fabrication Framework for Color Tattoos.” Transactions on Graphics, vol. 42, no. 4, 67, Association for Computing Machinery, 2023, doi:10.1145/3592432.","short":"M. Piovarci, A. Chapiro, B. Bickel, Transactions on Graphics 42 (2023).","chicago":"Piovarci, Michael, Alexandre Chapiro, and Bernd Bickel. “Skin-Screen: A Computational Fabrication Framework for Color Tattoos.” Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3592432.","ama":"Piovarci M, Chapiro A, Bickel B. Skin-Screen: A computational fabrication framework for color tattoos. Transactions on Graphics. 2023;42(4). doi:10.1145/3592432","ista":"Piovarci M, Chapiro A, Bickel B. 2023. Skin-Screen: A computational fabrication framework for color tattoos. Transactions on Graphics. 42(4), 67.","apa":"Piovarci, M., Chapiro, A., & Bickel, B. (2023). Skin-Screen: A computational fabrication framework for color tattoos. Transactions on Graphics. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3592432","ieee":"M. Piovarci, A. Chapiro, and B. Bickel, “Skin-Screen: A computational fabrication framework for color tattoos,” Transactions on Graphics, vol. 42, no. 4. Association for Computing Machinery, 2023."},"publication":"Transactions on Graphics","date_published":"2023-07-26T00:00:00Z","article_number":"67","file_date_updated":"2023-05-16T09:38:25Z","department":[{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","publication_status":"published","year":"2023","acknowledgement":"We thank Todor Asenov and the Miba Machine Shop for their help in assembling the tattoo machine and manufacturing the substrates. We thank Geysler Rodrigues for the insightful discussions on tattooing practices from a professional artist's perspective. We thank Maria Fernanda Portugal for sharing a doctor's perspective on medical applications of tattoos. This work is graciously supported by the FWF Lise Meitner (Grant M 3319).","volume":42,"date_created":"2023-05-16T09:39:14Z","date_updated":"2024-01-29T10:27:23Z","author":[{"id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","orcid":"0000-0002-5062-4474","first_name":"Michael","last_name":"Piovarci","full_name":"Piovarci, Michael"},{"first_name":"Alexandre","last_name":"Chapiro","full_name":"Chapiro, Alexandre"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"month":"07","project":[{"grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["001044671300033"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"doi":"10.1145/3592432","conference":{"end_date":"2023-08-10","location":"Los Angeles, CA, United States","start_date":"2023-08-06","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference"}},{"doi":"10.5281/ZENODO.10251087","date_published":"2023-12-02T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.10251087"}],"citation":{"ama":"Feitosa Tomé D. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation. 2023. doi:10.5281/ZENODO.10251087","ieee":"D. Feitosa Tomé, “douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation.” Zenodo, 2023.","apa":"Feitosa Tomé, D. (2023). douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation. Zenodo. https://doi.org/10.5281/ZENODO.10251087","ista":"Feitosa Tomé D. 2023. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation, Zenodo, 10.5281/ZENODO.10251087.","short":"D. Feitosa Tomé, (2023).","mla":"Feitosa Tomé, Douglas. Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation. Zenodo, 2023, doi:10.5281/ZENODO.10251087.","chicago":"Feitosa Tomé, Douglas. “Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.10251087."},"oa":1,"day":"02","month":"12","article_processing_charge":"No","has_accepted_license":"1","author":[{"id":"0eed2d40-3d48-11ec-8d38-f789cc2e40b2","first_name":"Douglas","last_name":"Feitosa Tomé","full_name":"Feitosa Tomé, Douglas"}],"related_material":{"record":[{"id":"14887","relation":"used_in_publication","status":"public"}]},"date_created":"2024-01-29T09:06:43Z","date_updated":"2024-01-29T09:22:01Z","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14892","year":"2023","status":"public","title":"douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation","ddc":["570"],"department":[{"_id":"TiVo"}],"publisher":"Zenodo","abstract":[{"text":"Code and data necessary to reproduce the simulations and data analyses reported in our manuscript: Tomé, D.F., Zhang, Y., Aida, T., Mosto, O., Lu, Y., Chen, M., Sadeh, S., Roy, D. S., Clopath, C. Dynamic and selective engrams emerge with memory consolidation. 2023.","lang":"eng"}],"type":"research_data_reference"},{"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"month":"11","project":[{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"},{"name":"Protected states of quantum matter","_id":"bd5b4ec5-d553-11ed-ba76-a6eedb083344"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001054563800006"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"doi":"10.1038/s41567-023-02161-w","ec_funded":1,"file_date_updated":"2024-01-29T11:25:38Z","publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"publication_status":"published","acknowledgement":"We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman for helpful feedback on the paper. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and a NOMIS foundation research grant (J.M.F. and A.P.H.).","year":"2023","volume":19,"date_updated":"2024-01-29T11:27:49Z","date_created":"2023-08-11T07:41:17Z","author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","last_name":"Mukhopadhyay","first_name":"Soham","full_name":"Mukhopadhyay, Soham"},{"orcid":"0000-0002-0672-9295","id":"5479D234-2D30-11EA-89CC-40953DDC885E","last_name":"Senior","first_name":"Jorden L","full_name":"Senior, Jorden L"},{"full_name":"Saez Mollejo, Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime","last_name":"Saez Mollejo"},{"full_name":"Puglia, Denise","first_name":"Denise","last_name":"Puglia","id":"4D495994-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0003-1144-2763"},{"full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"},{"last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"}],"keyword":["General Physics and Astronomy"],"scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","page":"1630-1635","article_type":"original","citation":{"chicago":"Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia, Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02161-w.","short":"S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M. Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635.","mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:10.1038/s41567-023-02161-w.","ieee":"S. Mukhopadhyay et al., “Superconductivity from a melted insulator in Josephson junction arrays,” Nature Physics, vol. 19. Springer Nature, pp. 1630–1635, 2023.","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., & Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02161-w","ista":"Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM, Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 19, 1630–1635.","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 2023;19:1630-1635. doi:10.1038/s41567-023-02161-w"},"publication":"Nature Physics","date_published":"2023-11-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator.","lang":"eng"}],"intvolume":" 19","title":"Superconductivity from a melted insulator in Josephson junction arrays","status":"public","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14032","oa_version":"Published Version","file":[{"file_id":"14899","relation":"main_file","success":1,"checksum":"1fc86d71bfbf836e221c1e925343adc5","date_updated":"2024-01-29T11:25:38Z","date_created":"2024-01-29T11:25:38Z","access_level":"open_access","file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","creator":"dernst","file_size":1977706,"content_type":"application/pdf"}]},{"author":[{"last_name":"Qi","first_name":"Linlin","orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","full_name":"Qi, Linlin"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-07-23T22:01:13Z","date_updated":"2024-01-29T11:21:55Z","volume":240,"year":"2023","acknowledgement":"We gratefully acknowledge our brave colleagues, whose excellent efforts kept the plant cAMP research going in the last two decades. The authors were financially supported by the Austrian Science Fund (FWF): I 6123 and P 37051-B.","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"JiFr"}],"file_date_updated":"2024-01-29T11:21:43Z","doi":"10.1111/nph.19123","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001026321500001"],"pmid":["37434303"]},"quality_controlled":"1","isi":1,"project":[{"_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123","name":"Peptide receptor complexes for auxin canalization and regeneration in Arabidopsis"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"}],"month":"10","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"file":[{"file_id":"14898","relation":"main_file","date_created":"2024-01-29T11:21:43Z","date_updated":"2024-01-29T11:21:43Z","success":1,"checksum":"6d9bbd45b8e7bb3ceee2586d447bacb2","file_name":"2023_NewPhytologist_Qi.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":974464}],"oa_version":"Published Version","_id":"13266","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Tale of cAMP as a second messenger in auxin signaling and beyond","ddc":["580"],"status":"public","intvolume":" 240","abstract":[{"text":"The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general.","lang":"eng"}],"issue":"2","type":"journal_article","date_published":"2023-10-01T00:00:00Z","publication":"New Phytologist","citation":{"ama":"Qi L, Friml J. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 2023;240(2):489-495. doi:10.1111/nph.19123","ieee":"L. Qi and J. Friml, “Tale of cAMP as a second messenger in auxin signaling and beyond,” New Phytologist, vol. 240, no. 2. Wiley, pp. 489–495, 2023.","apa":"Qi, L., & Friml, J. (2023). Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. Wiley. https://doi.org/10.1111/nph.19123","ista":"Qi L, Friml J. 2023. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 240(2), 489–495.","short":"L. Qi, J. Friml, New Phytologist 240 (2023) 489–495.","mla":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” New Phytologist, vol. 240, no. 2, Wiley, 2023, pp. 489–95, doi:10.1111/nph.19123.","chicago":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” New Phytologist. Wiley, 2023. https://doi.org/10.1111/nph.19123."},"article_type":"original","page":"489-495","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1"},{"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","citation":{"ista":"Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.","ieee":"T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the developing neural tube and somites,” Current Opinion in Systems Biology, vol. 35. Elsevier, 2023.","apa":"Minchington, T., Rus, S., & Kicheva, A. (2023). Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. Elsevier. https://doi.org/10.1016/j.coisb.2023.100459","ama":"Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 2023;35. doi:10.1016/j.coisb.2023.100459","chicago":"Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems Biology. Elsevier, 2023. https://doi.org/10.1016/j.coisb.2023.100459.","mla":"Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems Biology, vol. 35, 100459, Elsevier, 2023, doi:10.1016/j.coisb.2023.100459.","short":"T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35 (2023)."},"publication":"Current Opinion in Systems Biology","article_type":"original","date_published":"2023-09-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question.","lang":"eng"}],"_id":"13136","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 35","ddc":["570"],"title":"Control of tissue dimensions in the developing neural tube and somites","status":"public","file":[{"checksum":"8a75c4e29fd9b62e3c50663c2265b173","success":1,"date_created":"2024-01-29T11:06:45Z","date_updated":"2024-01-29T11:06:45Z","relation":"main_file","file_id":"14896","content_type":"application/pdf","file_size":598842,"creator":"dernst","access_level":"open_access","file_name":"2023_CurrOpSystBioloy_Minchington.pdf"}],"oa_version":"Published Version","publication_identifier":{"eissn":["2452-3100"]},"month":"09","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"project":[{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development"},{"_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F07802","name":"Morphogen control of growth and pattern in the spinal cord"},{"grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"quality_controlled":"1","doi":"10.1016/j.coisb.2023.100459","language":[{"iso":"eng"}],"article_number":"100459","file_date_updated":"2024-01-29T11:06:45Z","acknowledgement":"We thank J. Briscoe for comments on the manuscript. Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","year":"2023","department":[{"_id":"AnKi"}],"publisher":"Elsevier","publication_status":"published","author":[{"first_name":"Thomas","last_name":"Minchington","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas"},{"full_name":"Rus, Stefanie","orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","last_name":"Rus","first_name":"Stefanie"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna"}],"volume":35,"date_updated":"2024-01-29T11:07:47Z","date_created":"2023-06-18T22:00:46Z"},{"date_published":"2023-09-25T00:00:00Z","page":"247-300","article_type":"original","citation":{"short":"A. Agresti, M. Veraar, Journal of Differential Equations 368 (2023) 247–300.","mla":"Agresti, Antonio, and Mark Veraar. “Reaction-Diffusion Equations with Transport Noise and Critical Superlinear Diffusion: Local Well-Posedness and Positivity.” Journal of Differential Equations, vol. 368, no. 9, Elsevier, 2023, pp. 247–300, doi:10.1016/j.jde.2023.05.038.","chicago":"Agresti, Antonio, and Mark Veraar. “Reaction-Diffusion Equations with Transport Noise and Critical Superlinear Diffusion: Local Well-Posedness and Positivity.” Journal of Differential Equations. Elsevier, 2023. https://doi.org/10.1016/j.jde.2023.05.038.","ama":"Agresti A, Veraar M. Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. Journal of Differential Equations. 2023;368(9):247-300. doi:10.1016/j.jde.2023.05.038","ieee":"A. Agresti and M. Veraar, “Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity,” Journal of Differential Equations, vol. 368, no. 9. Elsevier, pp. 247–300, 2023.","apa":"Agresti, A., & Veraar, M. (2023). Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2023.05.038","ista":"Agresti A, Veraar M. 2023. Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. Journal of Differential Equations. 368(9), 247–300."},"publication":"Journal of Differential Equations","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"25","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2023_JourDifferentialEquations_Agresti.pdf","access_level":"open_access","creator":"dernst","file_size":834638,"content_type":"application/pdf","file_id":"14895","relation":"main_file","date_created":"2024-01-29T11:03:09Z","date_updated":"2024-01-29T11:03:09Z","success":1,"checksum":"246b703b091dfe047bfc79abf0891a63"}],"intvolume":" 368","title":"Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity","ddc":["510"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13135","issue":"9","abstract":[{"text":"In this paper we consider a class of stochastic reaction-diffusion equations. We provide local well-posedness, regularity, blow-up criteria and positivity of solutions. The key novelties of this work are related to the use transport noise, critical spaces and the proof of higher order regularity of solutions – even in case of non-smooth initial data. Crucial tools are Lp(Lp)-theory, maximal regularity estimates and sharp blow-up criteria. We view the results of this paper as a general toolbox for establishing global well-posedness for a large class of reaction-diffusion systems of practical interest, of which many are completely open. In our follow-up work [8], the results of this paper are applied in the specific cases of the Lotka-Volterra equations and the Brusselator model.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.jde.2023.05.038","project":[{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001019018700001"]},"publication_identifier":{"eissn":["1090-2732"],"issn":["0022-0396"]},"month":"09","volume":368,"date_created":"2023-06-18T22:00:45Z","date_updated":"2024-01-29T11:04:41Z","author":[{"full_name":"Agresti, Antonio","first_name":"Antonio","last_name":"Agresti","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962"},{"last_name":"Veraar","first_name":"Mark","full_name":"Veraar, Mark"}],"publisher":"Elsevier","department":[{"_id":"JuFi"}],"publication_status":"published","acknowledgement":"The first author has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 948819) Image 1. The second author is supported by the VICI subsidy VI.C.212.027 of the Netherlands Organisation for Scientific Research (NWO).","year":"2023","ec_funded":1,"file_date_updated":"2024-01-29T11:03:09Z"},{"month":"07","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2107.04112"],"isi":["001023742800003"]},"isi":1,"quality_controlled":"1","doi":"10.1007/s00454-023-00500-5","language":[{"iso":"eng"}],"file_date_updated":"2024-01-29T11:15:22Z","acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria).","year":"2023","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"author":[{"first_name":"Florestan R","last_name":"Brunck","id":"6ab6e556-f394-11eb-9cf6-9dfb78f00d8d","full_name":"Brunck, Florestan R"}],"date_created":"2023-07-23T22:01:14Z","date_updated":"2024-01-29T11:16:16Z","volume":70,"scopus_import":"1","day":"05","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Discrete and Computational Geometry","citation":{"ama":"Brunck FR. Iterated medial triangle subdivision in surfaces of constant curvature. Discrete and Computational Geometry. 2023;70(3):1059-1089. doi:10.1007/s00454-023-00500-5","ista":"Brunck FR. 2023. Iterated medial triangle subdivision in surfaces of constant curvature. Discrete and Computational Geometry. 70(3), 1059–1089.","apa":"Brunck, F. R. (2023). Iterated medial triangle subdivision in surfaces of constant curvature. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-023-00500-5","ieee":"F. R. Brunck, “Iterated medial triangle subdivision in surfaces of constant curvature,” Discrete and Computational Geometry, vol. 70, no. 3. Springer Nature, pp. 1059–1089, 2023.","mla":"Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant Curvature.” Discrete and Computational Geometry, vol. 70, no. 3, Springer Nature, 2023, pp. 1059–89, doi:10.1007/s00454-023-00500-5.","short":"F.R. Brunck, Discrete and Computational Geometry 70 (2023) 1059–1089.","chicago":"Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant Curvature.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-023-00500-5."},"article_type":"original","page":"1059-1089","date_published":"2023-07-05T00:00:00Z","type":"journal_article","abstract":[{"text":"Consider a geodesic triangle on a surface of constant curvature and subdivide it recursively into four triangles by joining the midpoints of its edges. We show the existence of a uniform δ>0\r\n such that, at any step of the subdivision, all the triangle angles lie in the interval (δ,π−δ)\r\n. Additionally, we exhibit stabilising behaviours for both angles and lengths as this subdivision progresses.","lang":"eng"}],"issue":"3","_id":"13270","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["510"],"title":"Iterated medial triangle subdivision in surfaces of constant curvature","intvolume":" 70","file":[{"creator":"dernst","file_size":1466020,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_DiscreteComputGeometry_Brunck.pdf","success":1,"checksum":"865e68daafdd4edcfc280172ec50f5ea","date_created":"2024-01-29T11:15:22Z","date_updated":"2024-01-29T11:15:22Z","file_id":"14897","relation":"main_file"}],"oa_version":"Published Version"},{"date_created":"2023-07-23T22:01:14Z","date_updated":"2024-01-29T11:10:54Z","volume":69,"author":[{"last_name":"Polyanskii","first_name":"Nikita","full_name":"Polyanskii, Nikita"},{"full_name":"Zhang, Yihan","first_name":"Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258"}],"publication_status":"published","department":[{"_id":"MaMo"}],"publisher":"Institute of Electrical and Electronics Engineers","year":"2023","acknowledgement":"Nikita Polyanskii’s research was conducted in part during October 2020 - December 2021 with the Technical University of Munich and the Skolkovo Institute of Science and Technology. His work was supported by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) under Grant No. WA3907/1-1 and the Russian Foundation for Basic Research (RFBR)\r\nunder Grant No. 20-01-00559.\r\nYihan Zhang is supported by funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff].","month":"07","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"language":[{"iso":"eng"}],"doi":"10.1109/TIT.2023.3292219","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2105.01427","open_access":"1"}],"external_id":{"arxiv":["2105.01427"],"isi":["001069680100011"]},"oa":1,"abstract":[{"lang":"eng","text":"This paper is a collection of results on combinatorial properties of codes for the Z-channel . A Z-channel with error fraction τ takes as input a length- n binary codeword and injects in an adversarial manner up to n τ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest ( L - 1)-list-decodable code for the Z-channel with error fraction τ has exponential size (in n ) if τ is less than a critical value that we call the ( L - 1)- list-decoding Plotkin point and has constant size if τ is larger than the threshold. The ( L -1)-list-decoding Plotkin point is known to be L -1/L-1 – L -L/ L-1 , which equals 1/4 for unique-decoding with L -1 = 1. In this paper, we derive various results for the size of the largest codes above and below the list-decoding Plotkin point. In particular, we show that the largest ( L -1)-list-decodable code ε-above the Plotkin point, for any given sufficiently small positive constant ε > 0, has size Θ L (ε -3/2 ) for any L - 1 ≥ 1. We also devise upper and lower bounds on the exponential size of codes below the list-decoding Plotkin point."}],"issue":"10","type":"journal_article","oa_version":"Preprint","title":"Codes for the Z-channel","status":"public","intvolume":" 69","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13269","day":"04","article_processing_charge":"No","scopus_import":"1","date_published":"2023-07-04T00:00:00Z","article_type":"original","page":"6340-6357","publication":"IEEE Transactions on Information Theory","citation":{"chicago":"Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/TIT.2023.3292219.","short":"N. Polyanskii, Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 6340–6357.","mla":"Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” IEEE Transactions on Information Theory, vol. 69, no. 10, Institute of Electrical and Electronics Engineers, 2023, pp. 6340–57, doi:10.1109/TIT.2023.3292219.","apa":"Polyanskii, N., & Zhang, Y. (2023). Codes for the Z-channel. IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TIT.2023.3292219","ieee":"N. Polyanskii and Y. Zhang, “Codes for the Z-channel,” IEEE Transactions on Information Theory, vol. 69, no. 10. Institute of Electrical and Electronics Engineers, pp. 6340–6357, 2023.","ista":"Polyanskii N, Zhang Y. 2023. Codes for the Z-channel. IEEE Transactions on Information Theory. 69(10), 6340–6357.","ama":"Polyanskii N, Zhang Y. Codes for the Z-channel. IEEE Transactions on Information Theory. 2023;69(10):6340-6357. doi:10.1109/TIT.2023.3292219"}},{"day":"13","article_processing_charge":"Yes","has_accepted_license":"1","date_published":"2023-11-13T00:00:00Z","article_type":"original","publication":"Plant Communications","citation":{"apa":"Xia, J., Kong, M., Yang, Z., Sun, L., Peng, Y., Mao, Y., … Tan, S. (2023). Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. Elsevier . https://doi.org/10.1016/j.xplc.2023.100632","ieee":"J. Xia et al., “Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen,” Plant Communications, vol. 4, no. 6. Elsevier , 2023.","ista":"Xia J, Kong M, Yang Z, Sun L, Peng Y, Mao Y, Wei H, Ying W, Gao Y, Friml J, Weng J, Liu X, Sun L, Tan S. 2023. Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. 4(6), 100632.","ama":"Xia J, Kong M, Yang Z, et al. Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. 2023;4(6). doi:10.1016/j.xplc.2023.100632","chicago":"Xia, Jing, Mengjuan Kong, Zhisen Yang, Lianghanxiao Sun, Yakun Peng, Yanbo Mao, Hong Wei, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters by the Anti-Inflammatory Drug Naproxen.” Plant Communications. Elsevier , 2023. https://doi.org/10.1016/j.xplc.2023.100632.","short":"J. Xia, M. Kong, Z. Yang, L. Sun, Y. Peng, Y. Mao, H. Wei, W. Ying, Y. Gao, J. Friml, J. Weng, X. Liu, L. Sun, S. Tan, Plant Communications 4 (2023).","mla":"Xia, Jing, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters by the Anti-Inflammatory Drug Naproxen.” Plant Communications, vol. 4, no. 6, 100632, Elsevier , 2023, doi:10.1016/j.xplc.2023.100632."},"abstract":[{"lang":"eng","text":"The phytohormone auxin plays central roles in many growth and developmental processes in plants. Development of chemical tools targeting the auxin pathway is useful for both plant biology and agriculture. Here we reveal that naproxen, a synthetic compound with anti-inflammatory activity in humans, acts as an auxin transport inhibitor targeting PIN-FORMED (PIN) transporters in plants. Physiological experiments indicate that exogenous naproxen treatment affects pleiotropic auxin-regulated developmental processes. Additional cellular and biochemical evidence indicates that naproxen suppresses auxin transport, specifically PIN-mediated auxin efflux. Moreover, biochemical and structural analyses confirm that naproxen binds directly to PIN1 protein via the same binding cavity as the indole-3-acetic acid substrate. Thus, by combining cellular, biochemical, and structural approaches, this study clearly establishes that naproxen is a PIN inhibitor and elucidates the underlying mechanisms. Further use of this compound may advance our understanding of the molecular mechanisms of PIN-mediated auxin transport and expand our toolkit in auxin biology and agriculture."}],"issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_PlantCommunications_Xia.pdf","creator":"dernst","content_type":"application/pdf","file_size":1434862,"file_id":"14900","relation":"main_file","success":1,"checksum":"f8ef92af6096834f91ce38587fb1db9f","date_updated":"2024-01-30T10:54:40Z","date_created":"2024-01-30T10:54:40Z"}],"title":"Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen","status":"public","ddc":["580"],"intvolume":" 4","_id":"13209","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","publication_identifier":{"eissn":["2590-3462"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.xplc.2023.100632","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["001113003000001"],"pmid":["37254481"]},"file_date_updated":"2024-01-30T10:54:40Z","article_number":"100632","date_created":"2023-07-12T07:32:00Z","date_updated":"2024-01-30T10:55:34Z","volume":4,"author":[{"first_name":"Jing","last_name":"Xia","full_name":"Xia, Jing"},{"last_name":"Kong","first_name":"Mengjuan","full_name":"Kong, Mengjuan"},{"full_name":"Yang, Zhisen","last_name":"Yang","first_name":"Zhisen"},{"last_name":"Sun","first_name":"Lianghanxiao","full_name":"Sun, Lianghanxiao"},{"full_name":"Peng, Yakun","last_name":"Peng","first_name":"Yakun"},{"first_name":"Yanbo","last_name":"Mao","full_name":"Mao, Yanbo"},{"first_name":"Hong","last_name":"Wei","full_name":"Wei, Hong"},{"full_name":"Ying, Wei","first_name":"Wei","last_name":"Ying"},{"full_name":"Gao, Yongxiao","last_name":"Gao","first_name":"Yongxiao"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jianping","last_name":"Weng","full_name":"Weng, Jianping"},{"first_name":"Xin","last_name":"Liu","full_name":"Liu, Xin"},{"full_name":"Sun, Linfeng","first_name":"Linfeng","last_name":"Sun"},{"last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Elsevier ","acknowledgement":"This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB37020103 to Linfeng Sun); research funds from the Center for Advanced Interdisciplinary Science\r\nand Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China (QYPY20220012 to S.T.); start-up funding from the University of Science and Technology of China and the\r\nChinese Academy of Sciences (GG9100007007, KY9100000026,KY9100000051, and KJ2070000079 to S.T.); the National Natural Science Foundation of China (31900885 to X.L. and 31870732 to Linfeng Sun); the Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun); the Fundamental Research Funds for the Central Universities (WK9100000021 to S.T. and WK9100000031 to Linfeng Sun); and the USTC Research Funds of the Double First-Class Initiative (YD9100002016 to S.T. and YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation.We thank Dr. Yang Zhao for sharing published materials (Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences) and the Cryo-EM Center of the University of Science and Technology of China for the EM facility support. We are grateful to Y. Gao and all other staff members for their technical support on cryo-EM data collection. ","year":"2023","pmid":1},{"type":"journal_article","abstract":[{"text":"When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases.","lang":"eng"}],"intvolume":" 19","ddc":["530"],"title":"Unconventional colloidal aggregation in chiral bacterial baths","status":"public","_id":"13971","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14906","date_updated":"2024-01-30T12:26:08Z","date_created":"2024-01-30T12:26:08Z","checksum":"7e282c2ebc0ac82125a04f6b4742d4c1","success":1,"file_name":"2023_NaturePhysics_Grober.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6365607,"creator":"dernst"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","page":"1680-1688","article_type":"original","citation":{"ama":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. 2023;19:1680-1688. doi:10.1038/s41567-023-02136-x","ieee":"D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci, “Unconventional colloidal aggregation in chiral bacterial baths,” Nature Physics, vol. 19. Springer Nature, pp. 1680–1688, 2023.","apa":"Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., & Palacci, J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02136-x","ista":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688.","short":"D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature Physics 19 (2023) 1680–1688.","mla":"Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:10.1038/s41567-023-02136-x.","chicago":"Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić, and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02136-x."},"publication":"Nature Physics","date_published":"2023-11-01T00:00:00Z","ec_funded":1,"file_date_updated":"2024-01-30T12:26:08Z","department":[{"_id":"EdHa"},{"_id":"AnSa"},{"_id":"JePa"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa for providing the E. coli strains. This material is based upon work supported by the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 754411.","volume":19,"date_updated":"2024-01-30T12:26:55Z","date_created":"2023-08-06T22:01:11Z","author":[{"full_name":"Grober, Daniel","first_name":"Daniel","last_name":"Grober","id":"abdfc56f-34fb-11ee-bd33-fd766fce5a99"},{"full_name":"Palaia, Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan","last_name":"Palaia"},{"first_name":"Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","last_name":"Palacci","full_name":"Palacci, Jérémie A"}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"month":"11","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["001037346400005"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41567-023-02136-x"},{"intvolume":" 247","status":"public","title":"The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10551","file":[{"file_name":"2023_ArchiveRationalMech_Cornalba.pdf","access_level":"open_access","file_size":1851185,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14904","date_updated":"2024-01-30T12:09:34Z","date_created":"2024-01-30T12:09:34Z","checksum":"4529eeff170b6745a461d397ee611b5a","success":1}],"oa_version":"Published Version","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"The Dean–Kawasaki equation—a strongly singular SPDE—is a basic equation of fluctuating hydrodynamics; it has been proposed in the physics literature to describe the fluctuations of the density of N independent diffusing particles in the regime of large particle numbers N≫1. The singular nature of the Dean–Kawasaki equation presents a substantial challenge for both its analysis and its rigorous mathematical justification. Besides being non-renormalisable by the theory of regularity structures by Hairer et al., it has recently been shown to not even admit nontrivial martingale solutions. In the present work, we give a rigorous and fully quantitative justification of the Dean–Kawasaki equation by considering the natural regularisation provided by standard numerical discretisations: We show that structure-preserving discretisations of the Dean–Kawasaki equation may approximate the density fluctuations of N non-interacting diffusing particles to arbitrary order in N−1 (in suitable weak metrics). In other words, the Dean–Kawasaki equation may be interpreted as a “recipe” for accurate and efficient numerical simulations of the density fluctuations of independent diffusing particles."}],"article_type":"original","citation":{"mla":"Cornalba, Federico, and Julian L. Fischer. “The Dean-Kawasaki Equation and the Structure of Density Fluctuations in Systems of Diffusing Particles.” Archive for Rational Mechanics and Analysis, vol. 247, no. 5, 76, Springer Nature, 2023, doi:10.1007/s00205-023-01903-7.","short":"F. Cornalba, J.L. Fischer, Archive for Rational Mechanics and Analysis 247 (2023).","chicago":"Cornalba, Federico, and Julian L Fischer. “The Dean-Kawasaki Equation and the Structure of Density Fluctuations in Systems of Diffusing Particles.” Archive for Rational Mechanics and Analysis. Springer Nature, 2023. https://doi.org/10.1007/s00205-023-01903-7.","ama":"Cornalba F, Fischer JL. The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. 2023;247(5). doi:10.1007/s00205-023-01903-7","ista":"Cornalba F, Fischer JL. 2023. The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. 247(5), 76.","apa":"Cornalba, F., & Fischer, J. L. (2023). The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-023-01903-7","ieee":"F. Cornalba and J. L. Fischer, “The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles,” Archive for Rational Mechanics and Analysis, vol. 247, no. 5. Springer Nature, 2023."},"publication":"Archive for Rational Mechanics and Analysis","date_published":"2023-08-04T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"04","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"We thank the anonymous referee for his/her careful reading of the manuscript and valuable suggestions. FC gratefully acknowledges funding from the Austrian Science Fund (FWF) through the project F65, and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.\r\nOpen access funding provided by Austrian Science Fund (FWF).","volume":247,"date_updated":"2024-01-30T12:10:10Z","date_created":"2021-12-16T12:16:03Z","author":[{"full_name":"Cornalba, Federico","id":"2CEB641C-A400-11E9-A717-D712E6697425","orcid":"0000-0002-6269-5149","first_name":"Federico","last_name":"Cornalba"},{"first_name":"Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L"}],"article_number":"76","ec_funded":1,"file_date_updated":"2024-01-30T12:09:34Z","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["2109.06500"],"isi":["001043086800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00205-023-01903-7","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"month":"08"}]