--- _id: '12486' abstract: - lang: eng 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. 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. " article_processing_charge: No article_type: original author: - first_name: Antonio full_name: Agresti, Antonio id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72 last_name: Agresti orcid: 0000-0002-9573-2962 citation: 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' 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' 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.' 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.' 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.' 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.' short: 'A. Agresti, Stochastics and Partial Differential Equations: Analysis and Computations (2023).' date_created: 2023-02-02T10:45:47Z date_published: 2023-11-28T00:00:00Z date_updated: 2023-12-18T07:53:45Z day: '28' ddc: - '510' department: - _id: JuFi doi: 10.1007/s40072-023-00319-4 ec_funded: 1 external_id: arxiv: - '2207.08293' has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1007/s40072-023-00319-4 month: '11' oa: 1 oa_version: Submitted Version project: - _id: 0aa76401-070f-11eb-9043-b5bb049fa26d call_identifier: H2020 grant_number: '948819' name: Bridging Scales in Random Materials publication: 'Stochastics and Partial Differential Equations: Analysis and Computations' publication_identifier: eissn: - 2194-041X issn: - 2194-0401 publication_status: epub_ahead publisher: Springer Nature scopus_import: '1' status: public title: Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14665' 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. article_processing_charge: No article_type: original author: - first_name: Yihan full_name: Zhang, Yihan id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c last_name: Zhang orcid: 0000-0002-6465-6258 - first_name: Shashank full_name: Vatedka, Shashank last_name: Vatedka citation: ama: 'Zhang Y, Vatedka S. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. 2023. doi:10.1109/TIT.2023.3334032' 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' 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.' ieee: 'Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via error exponents,” IEEE Transactions on Information Theory. IEEE, 2023.' ista: 'Zhang Y, Vatedka S. 2023. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory.' 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.' short: Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory (2023). date_created: 2023-12-10T23:01:00Z date_published: 2023-11-16T00:00:00Z date_updated: 2023-12-18T07:46:45Z day: '16' department: - _id: MaMo doi: 10.1109/TIT.2023.3334032 external_id: arxiv: - '2211.04408' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2211.04408 month: '11' oa: 1 oa_version: Preprint publication: IEEE Transactions on Information Theory publication_identifier: eissn: - 1557-9654 issn: - 0018-9448 publication_status: epub_ahead publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: 'Multiple packing: Lower bounds via error exponents' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14693' abstract: - lang: eng 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." 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." alternative_title: - LNCS article_processing_charge: No author: - first_name: Charlotte full_name: Hoffmann, Charlotte id: 0f78d746-dc7d-11ea-9b2f-83f92091afe7 last_name: Hoffmann orcid: 0000-0003-2027-5549 - first_name: Pavel full_name: Hubáček, Pavel last_name: Hubáček - first_name: Chethan full_name: Kamath, Chethan last_name: Kamath - first_name: Tomáš full_name: Krňák, Tomáš last_name: Krňák citation: 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' 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' 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. 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. 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.' 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. conference: end_date: 2023-12-02 location: Taipei, Taiwan name: 'TCC: Theory of Cryptography' start_date: 2023-11-29 date_created: 2023-12-17T23:00:54Z date_published: 2023-11-27T00:00:00Z date_updated: 2023-12-18T09:00:00Z day: '27' department: - _id: KrPi doi: 10.1007/978-3-031-48624-1_13 intvolume: ' 14372' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2023/1404 month: '11' oa: 1 oa_version: Preprint page: 336-362 publication: 21st International Conference on Theory of Cryptography publication_identifier: eissn: - 1611-3349 isbn: - '9783031486234' issn: - 0302-9743 publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: (Verifiable) delay functions from Lucas sequences type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14372 year: '2023' ... --- _id: '14691' abstract: - lang: eng 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." alternative_title: - LNCS article_processing_charge: No author: - first_name: Benedikt full_name: Auerbach, Benedikt id: D33D2B18-E445-11E9-ABB7-15F4E5697425 last_name: Auerbach orcid: 0000-0002-7553-6606 - first_name: Miguel full_name: Cueto Noval, Miguel id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc last_name: Cueto Noval - first_name: Guillermo full_name: Pascual Perez, Guillermo id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87 last_name: Pascual Perez orcid: 0000-0001-8630-415X - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: 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' 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' 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. 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. 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.' 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. conference: end_date: 2023-12-02 location: Taipei, Taiwan name: 'TCC: Theory of Cryptography' start_date: 2023-11-29 date_created: 2023-12-17T23:00:53Z date_published: 2023-11-27T00:00:00Z date_updated: 2023-12-18T08:36:51Z day: '27' department: - _id: KrPi doi: 10.1007/978-3-031-48621-0_10 intvolume: ' 14371' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2023/1123 month: '11' oa: 1 oa_version: Preprint page: 271-300 publication: 21st International Conference on Theory of Cryptography publication_identifier: eissn: - 1611-3349 isbn: - '9783031486203' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: On the cost of post-compromise security in concurrent Continuous Group-Key Agreement type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14371 year: '2023' ... --- _id: '14692' abstract: - lang: eng 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." alternative_title: - LNCS article_processing_charge: No author: - first_name: Benedikt full_name: Auerbach, Benedikt id: D33D2B18-E445-11E9-ABB7-15F4E5697425 last_name: Auerbach orcid: 0000-0002-7553-6606 - first_name: Charlotte full_name: Hoffmann, Charlotte id: 0f78d746-dc7d-11ea-9b2f-83f92091afe7 last_name: Hoffmann orcid: 0000-0003-2027-5549 - first_name: Guillermo full_name: Pascual Perez, Guillermo id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87 last_name: Pascual Perez orcid: 0000-0001-8630-415X citation: 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' 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' 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.' 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.' 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.' 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.' short: B. Auerbach, C. Hoffmann, G. Pascual Perez, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 301–330. date_created: 2023-12-17T23:00:54Z date_published: 2023-11-27T00:00:00Z date_updated: 2023-12-18T09:17:03Z day: '27' department: - _id: KrPi doi: 10.1007/978-3-031-48621-0_11 intvolume: ' 14371' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2023/808 month: '11' oa: 1 oa_version: Preprint page: 301-330 publication: 21st International Conference on Theory of Cryptography publication_identifier: eissn: - 1611-3349 isbn: - '9783031486203' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14371 year: '2023' ... --- _id: '14690' 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. 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). article_number: '205429' article_processing_charge: No article_type: original author: - first_name: Serafim full_name: Babkin, Serafim id: 41e64307-6672-11ee-b9ad-cc7a0075a479 last_name: Babkin orcid: 0009-0003-7382-8036 - first_name: I full_name: Burmistrov, I last_name: Burmistrov citation: 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 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 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. 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. ista: Babkin S, Burmistrov I. 2023. Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. 108(20), 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). date_created: 2023-12-17T23:00:53Z date_published: 2023-11-15T00:00:00Z date_updated: 2023-12-18T08:45:28Z day: '15' department: - _id: MaSe doi: 10.1103/PhysRevB.108.205429 external_id: arxiv: - '2308.16852' intvolume: ' 108' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2308.16852' month: '11' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Boundary multifractality in the spin quantum Hall symmetry class with interaction type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2023' ... --- _id: '14689' article_processing_charge: No article_type: letter_note author: - first_name: Elizabeth full_name: Ing-Simmons, Elizabeth last_name: Ing-Simmons - first_name: Nick N full_name: Machnik, Nick N id: 3591A0AA-F248-11E8-B48F-1D18A9856A87 last_name: Machnik orcid: 0000-0001-6617-9742 - first_name: Juan M. full_name: Vaquerizas, Juan M. last_name: Vaquerizas 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' 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' 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.' 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.' 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.' 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. date_created: 2023-12-17T23:00:53Z date_published: 2023-12-01T00:00:00Z date_updated: 2023-12-18T08:51:38Z day: '01' department: - _id: MaRo doi: 10.1038/s41588-023-01595-5 external_id: pmid: - '38052961' intvolume: ' 55' issue: '12' language: - iso: eng month: '12' oa_version: None page: 2053-2055 pmid: 1 publication: Nature Genetics publication_identifier: eissn: - 1546-1718 issn: - 1061-4036 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Reply to: Revisiting the use of structural similarity index in Hi-C' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2023' ... --- _id: '14701' article_processing_charge: No article_type: review author: - first_name: Lynden A. full_name: Archer, Lynden A. last_name: Archer - first_name: Peter G. full_name: Bruce, Peter G. last_name: Bruce - first_name: Ernesto J. full_name: Calvo, Ernesto J. last_name: Calvo - first_name: Daniel full_name: Dewar, Daniel last_name: Dewar - first_name: James H. J. full_name: Ellison, James H. J. last_name: Ellison - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Xiangwen full_name: Gao, Xiangwen last_name: Gao - first_name: Laurence J. full_name: Hardwick, Laurence J. last_name: Hardwick - first_name: Gabriela full_name: Horwitz, Gabriela last_name: Horwitz - first_name: Jürgen full_name: Janek, Jürgen last_name: Janek - first_name: Lee R. full_name: Johnson, Lee R. last_name: Johnson - first_name: Jack W. full_name: Jordan, Jack W. last_name: Jordan - first_name: Shoichi full_name: Matsuda, Shoichi last_name: Matsuda - first_name: Svetlana full_name: Menkin, Svetlana last_name: Menkin - first_name: Soumyadip full_name: Mondal, Soumyadip id: d25d21ef-dc8d-11ea-abe3-ec4576307f48 last_name: Mondal - first_name: Qianyuan full_name: Qiu, Qianyuan last_name: Qiu - first_name: Thukshan full_name: Samarakoon, Thukshan last_name: Samarakoon - first_name: Israel full_name: Temprano, Israel last_name: Temprano - first_name: Kohei full_name: Uosaki, Kohei last_name: Uosaki - first_name: Ganesh full_name: Vailaya, Ganesh last_name: Vailaya - first_name: Eric D. full_name: Wachsman, Eric D. last_name: Wachsman - first_name: Yiying full_name: Wu, Yiying last_name: Wu - first_name: Shen full_name: Ye, Shen last_name: Ye citation: ama: 'Archer LA, Bruce PG, Calvo EJ, et al. Towards practical metal–oxygen batteries: General discussion. Faraday Discussions. 2023. doi:10.1039/d3fd90062b' 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' 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.' ieee: 'L. A. Archer et al., “Towards practical metal–oxygen batteries: General discussion,” Faraday Discussions. Royal Society of Chemistry, 2023.' 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.' mla: 'Archer, Lynden A., et al. “Towards Practical Metal–Oxygen Batteries: General Discussion.” Faraday Discussions, Royal Society of Chemistry, 2023, doi:10.1039/d3fd90062b.' 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). date_created: 2023-12-20T10:48:09Z date_published: 2023-12-19T00:00:00Z date_updated: 2023-12-20T11:54:06Z day: '19' department: - _id: StFr doi: 10.1039/d3fd90062b keyword: - Physical and Theoretical Chemistry language: - iso: eng month: '12' oa_version: None publication: Faraday Discussions publication_identifier: eissn: - 1364-5498 issn: - 1359-6640 publication_status: epub_ahead publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Towards practical metal–oxygen batteries: General discussion' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14702' article_processing_charge: No article_type: review author: - first_name: Gary A. full_name: Attard, Gary A. last_name: Attard - first_name: Ernesto J. full_name: Calvo, Ernesto J. last_name: Calvo - first_name: Larry A. full_name: Curtiss, Larry A. last_name: Curtiss - first_name: Daniel full_name: Dewar, Daniel last_name: Dewar - first_name: James H. J. full_name: Ellison, James H. J. last_name: Ellison - first_name: Xiangwen full_name: Gao, Xiangwen last_name: Gao - first_name: Clare P. full_name: Grey, Clare P. last_name: Grey - first_name: Laurence J. full_name: Hardwick, Laurence J. last_name: Hardwick - first_name: Gabriela full_name: Horwitz, Gabriela last_name: Horwitz - first_name: Juergen full_name: Janek, Juergen last_name: Janek - first_name: Lee R. full_name: Johnson, Lee R. last_name: Johnson - first_name: Jack W. full_name: Jordan, Jack W. last_name: Jordan - first_name: Shoichi full_name: Matsuda, Shoichi last_name: Matsuda - first_name: Soumyadip full_name: Mondal, Soumyadip id: d25d21ef-dc8d-11ea-abe3-ec4576307f48 last_name: Mondal - first_name: Alex R. full_name: Neale, Alex R. last_name: Neale - first_name: Nagore full_name: Ortiz-Vitoriano, Nagore last_name: Ortiz-Vitoriano - first_name: Israel full_name: Temprano, Israel last_name: Temprano - first_name: Ganesh full_name: Vailaya, Ganesh last_name: Vailaya - first_name: Eric D. full_name: Wachsman, Eric D. last_name: Wachsman - first_name: Hsien-Hau full_name: Wang, Hsien-Hau last_name: Wang - first_name: Yiying full_name: Wu, Yiying last_name: Wu - first_name: Shen full_name: Ye, Shen last_name: Ye citation: 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' 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' 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.' ieee: 'G. A. Attard et al., “Materials for stable metal–oxygen battery cathodes: general discussion,” Faraday Discussions. Royal Society of Chemistry, 2023.' 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.' 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). date_created: 2023-12-20T10:49:43Z date_published: 2023-12-18T00:00:00Z date_updated: 2023-12-20T11:58:12Z day: '18' department: - _id: StFr doi: 10.1039/d3fd90059b keyword: - Physical and Theoretical Chemistry language: - iso: eng month: '12' oa_version: None publication: Faraday Discussions publication_identifier: eissn: - 1364-5498 issn: - 1359-6640 publication_status: epub_ahead publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: 'Materials for stable metal–oxygen battery cathodes: general discussion' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14360' 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. 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." article_number: '5644' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Ewa full_name: Sitarska, Ewa last_name: Sitarska - first_name: Silvia Dias full_name: Almeida, Silvia Dias last_name: Almeida - first_name: Marianne Sandvold full_name: Beckwith, Marianne Sandvold last_name: Beckwith - first_name: Julian A full_name: Stopp, Julian A id: 489E3F00-F248-11E8-B48F-1D18A9856A87 last_name: Stopp - first_name: Jakub full_name: Czuchnowski, Jakub last_name: Czuchnowski - first_name: Marc full_name: Siggel, Marc last_name: Siggel - first_name: Rita full_name: Roessner, Rita last_name: Roessner - first_name: Aline full_name: Tschanz, Aline last_name: Tschanz - first_name: Christer full_name: Ejsing, Christer last_name: Ejsing - first_name: Yannick full_name: Schwab, Yannick last_name: Schwab - first_name: Jan full_name: Kosinski, Jan last_name: Kosinski - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Anna full_name: Kreshuk, Anna last_name: Kreshuk - first_name: Anna full_name: Erzberger, Anna last_name: Erzberger - first_name: Alba full_name: Diz-Muñoz, Alba last_name: Diz-Muñoz citation: 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 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 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. 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. 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. 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). date_created: 2023-09-24T22:01:10Z date_published: 2023-09-13T00:00:00Z date_updated: 2023-12-21T14:30:01Z day: '13' ddc: - '570' department: - _id: MiSi doi: 10.1038/s41467-023-41173-1 external_id: isi: - '001087583700008' pmid: - '37704612' file: - access_level: open_access checksum: ad670e3b3c64fc585675948370f6b149 content_type: application/pdf creator: dernst date_created: 2023-09-25T08:22:58Z date_updated: 2023-09-25T08:22:58Z file_id: '14365' file_name: 2023_NatureComm_Sitarska.pdf file_size: 2725421 relation: main_file success: 1 file_date_updated: 2023-09-25T08:22:58Z has_accepted_license: '1' intvolume: ' 14' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '14697' relation: dissertation_contains status: public scopus_import: '1' status: public title: Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '14274' abstract: - lang: eng 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. 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." article_number: adc9584 article_processing_charge: No article_type: original author: - first_name: Jonna H full_name: Alanko, Jonna H id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87 last_name: Alanko orcid: 0000-0002-7698-3061 - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Nikola full_name: Canigova, Nikola id: 3795523E-F248-11E8-B48F-1D18A9856A87 last_name: Canigova orcid: 0000-0002-8518-5926 - first_name: Julian A full_name: Stopp, Julian A id: 489E3F00-F248-11E8-B48F-1D18A9856A87 last_name: Stopp - first_name: Jan full_name: Schwarz, Jan id: 346C1EC6-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: 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 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 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. 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. 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. 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). date_created: 2023-09-06T08:07:51Z date_published: 2023-09-01T00:00:00Z date_updated: 2023-12-21T14:30:01Z day: '01' department: - _id: MiSi - _id: EdHa - _id: NanoFab doi: 10.1126/sciimmunol.adc9584 ec_funded: 1 external_id: isi: - '001062110600003' pmid: - '37656776' intvolume: ' 8' isi: 1 issue: '87' keyword: - General Medicine - Immunology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1126/sciimmunol.adc9584 month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis - _id: 265E2996-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W01250-B20 name: Nano-Analytics of Cellular Systems - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Science Immunology publication_identifier: issn: - 2470-9468 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: record: - id: '14279' relation: research_data status: public - id: '14697' relation: dissertation_contains status: public scopus_import: '1' status: public title: CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2023' ... --- _id: '14697' acknowledged_ssus: - _id: LifeSc - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Julian A full_name: Stopp, Julian A id: 489E3F00-F248-11E8-B48F-1D18A9856A87 last_name: Stopp citation: ama: 'Stopp JA. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:10.15479/at:ista:14697' 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' 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.' 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.' 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.' 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.' date_created: 2023-12-18T19:14:28Z date_published: 2023-12-20T00:00:00Z date_updated: 2023-12-21T14:30:02Z day: '20' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: MiSi doi: 10.15479/at:ista:14697 ec_funded: 1 file: - access_level: closed checksum: 457927165d5d556305d3086f6b83e5c7 content_type: application/pdf creator: jstopp date_created: 2023-12-20T09:35:34Z date_updated: 2023-12-20T09:35:34Z embargo: 2024-12-20 embargo_to: open_access file_id: '14699' file_name: Thesis.pdf file_size: 51585778 relation: main_file - access_level: closed checksum: e8d26449ac461f5e8478a62c9507506f content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jstopp date_created: 2023-12-20T09:35:35Z date_updated: 2023-12-20T10:41:42Z file_id: '14700' file_name: Thesis.docx file_size: 69625950 relation: source_file file_date_updated: 2023-12-20T10:41:42Z has_accepted_license: '1' language: - iso: eng month: '12' oa_version: Published Version page: '226' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-038-1 issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6328' relation: part_of_dissertation status: public - id: '7885' relation: part_of_dissertation status: public - id: '12272' relation: part_of_dissertation status: public - id: '14274' relation: part_of_dissertation status: public - id: '14360' relation: part_of_dissertation status: public status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 title: 'Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14651' 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.' acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X citation: ama: Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651 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 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. ieee: L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023. ista: Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. 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. short: L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023. date_created: 2023-12-11T19:30:37Z date_published: 2023-12-12T00:00:00Z date_updated: 2023-12-22T11:04:45Z day: '12' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:14651 ec_funded: 1 file: - access_level: open_access checksum: 520bdb61e95e66070e02824947d2c5fa content_type: application/pdf creator: larathoo date_created: 2023-12-13T15:37:55Z date_updated: 2023-12-13T15:37:55Z file_id: '14684' file_name: Phd_Thesis_LA.pdf file_size: 34101468 relation: main_file success: 1 - access_level: closed checksum: d8e59afd0817c98fba2564a264508e5c content_type: application/zip creator: larathoo date_created: 2023-12-13T15:42:23Z date_updated: 2023-12-14T08:58:18Z file_id: '14685' file_name: Phd_Thesis_LA.zip file_size: 31052872 relation: source_file - access_level: closed checksum: 9a778c949932286f4519e1f1fca2820d content_type: application/zip creator: larathoo date_created: 2023-12-11T19:24:59Z date_updated: 2023-12-14T08:58:18Z file_id: '14681' file_name: Supplementary_Materials.zip file_size: 10713896 relation: supplementary_material file_date_updated: 2023-12-14T08:58:18Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '96' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11411' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14703' 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. 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." article_number: '2312.12213' article_processing_charge: No author: - first_name: Sadashige full_name: Ishida, Sadashige id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425 last_name: Ishida - first_name: Hugo full_name: Lavenant, Hugo last_name: Lavenant citation: 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 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 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. ieee: S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” arXiv. . ista: Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. 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.). date_created: 2023-12-21T10:14:37Z date_published: 2023-12-19T00:00:00Z date_updated: 2023-12-27T13:44:33Z day: '19' department: - _id: GradSch - _id: ChWo doi: 10.48550/arXiv.2312.12213 external_id: arxiv: - '2312.12213' keyword: - Optimal transport - Hamilton-Jacobi equation - convex optimization language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2312.12213 month: '12' oa: 1 oa_version: Preprint project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: arXiv publication_status: submitted status: public title: Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation type: preprint user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14716' 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." 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. article_number: '404' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Alper full_name: Yurtseven, Alper last_name: Yurtseven - first_name: Sofia full_name: Buyanova, Sofia id: 2F54A7BC-3902-11EA-AC87-BC9F3DDC885E last_name: Buyanova - first_name: Amay Ajaykumar A. full_name: Agrawal, Amay Ajaykumar A. last_name: Agrawal - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Olga V V. full_name: Kalinina, Olga V V. last_name: Kalinina citation: 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 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. 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. 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. short: A. Yurtseven, S. Buyanova, A.A.A. Agrawal, O. Bochkareva, O.V.V. Kalinina, BMC Microbiology 23 (2023). date_created: 2023-12-31T23:01:02Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T09:20:57Z day: '01' ddc: - '570' department: - _id: FyKo doi: 10.1186/s12866-023-03147-7 external_id: pmid: - '38124060' file: - access_level: open_access checksum: 7ff5e95f3496ff663301eb4a13a316d5 content_type: application/pdf creator: dernst date_created: 2024-01-02T09:09:32Z date_updated: 2024-01-02T09:09:32Z file_id: '14723' file_name: 2023_BMCMicrobiology_Yurtseven.pdf file_size: 1979922 relation: main_file success: 1 file_date_updated: 2024-01-02T09:09:32Z has_accepted_license: '1' intvolume: ' 23' issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: BMC Microbiology publication_identifier: eissn: - 1471-2180 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2023' ... --- _id: '14718' 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. ' 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." article_processing_charge: No author: - first_name: Samuel full_name: Pastva, Samuel id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b last_name: Pastva orcid: 0000-0003-1993-0331 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: 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' 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' 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. 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. 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.' 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. conference: end_date: 2023-10-27 location: Ames, IA, United States name: 'FMCAD: Conference on Formal Methods in Computer-aided design' start_date: 2023-10-25 date_created: 2023-12-31T23:01:03Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-02T08:16:28Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.34727/2023/isbn.978-3-85448-060-0_20 ec_funded: 1 file: - access_level: open_access checksum: 818d6e13dd508f3a04f0941081022e5d content_type: application/pdf creator: dernst date_created: 2024-01-02T08:14:23Z date_updated: 2024-01-02T08:14:23Z file_id: '14721' file_name: 2023_FMCAD_Pastva.pdf file_size: 524321 relation: main_file success: 1 file_date_updated: 2024-01-02T08:14:23Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 122-131 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design publication_identifier: isbn: - '9783854480600' publication_status: published publisher: TU Vienna Academic Press quality_controlled: '1' scopus_import: '1' status: public title: Binary decision diagrams on modern hardware tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14717' 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. 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Tal full_name: Horesh, Tal id: C8B7BF48-8D81-11E9-BCA9-F536E6697425 last_name: Horesh - first_name: Yakov full_name: Karasik, Yakov last_name: Karasik citation: 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 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. 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. 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. short: T. Horesh, Y. Karasik, Quarterly Journal of Mathematics 74 (2023) 1253–1294. date_created: 2023-12-31T23:01:03Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T07:39:55Z day: '01' ddc: - '510' department: - _id: TiBr doi: 10.1093/qmath/haad008 external_id: arxiv: - '2012.04508' file: - access_level: open_access checksum: bf29baa9eae8500f3374dbcb80712687 content_type: application/pdf creator: dernst date_created: 2024-01-02T07:37:09Z date_updated: 2024-01-02T07:37:09Z file_id: '14720' file_name: 2023_QuarterlyJourMath_Horesh.pdf file_size: 724748 relation: main_file success: 1 file_date_updated: 2024-01-02T07:37:09Z has_accepted_license: '1' intvolume: ' 74' issue: '4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 1253-1294 project: - _id: 26A8D266-B435-11E9-9278-68D0E5697425 grant_number: EP-P026710-2 name: Between rational and integral points publication: Quarterly Journal of Mathematics publication_identifier: eissn: - 1464-3847 issn: - 0033-5606 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Equidistribution of primitive lattices in ℝn tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 74 year: '2023' ... --- _id: '14719' 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. acknowledged_ssus: - _id: EM-Fac - _id: NanoFab 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). article_processing_charge: No article_type: original author: - first_name: Hamid full_name: Mollania, Hamid last_name: Mollania - first_name: Chaoqi full_name: Zhang, Chaoqi last_name: Zhang - first_name: Ruifeng full_name: Du, Ruifeng last_name: Du - first_name: Xueqiang full_name: Qi, Xueqiang last_name: Qi - first_name: Junshan full_name: Li, Junshan last_name: Li - first_name: Sharona full_name: Horta, Sharona id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc last_name: Horta - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Caroline full_name: Keller, Caroline last_name: Keller - first_name: Pascale full_name: Chenevier, Pascale last_name: Chenevier - first_name: Majid full_name: Oloomi-Buygi, Majid last_name: Oloomi-Buygi - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: 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 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 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. 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. 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. 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. 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. date_created: 2023-12-31T23:01:03Z date_published: 2023-12-05T00:00:00Z date_updated: 2024-01-02T08:35:06Z day: '05' department: - _id: MaIb doi: 10.1021/acsami.3c14072 intvolume: ' 15' issue: '50' language: - iso: eng month: '12' oa_version: None page: 58462–58475 publication: ACS Applied Materials and Interfaces publication_identifier: eissn: - 1944-8252 issn: - 1944-8244 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Nanostructured Li₂S cathodes for silicon-sulfur batteries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2023' ... --- _id: '14715' abstract: - lang: eng 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. 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.” article_number: '121901' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas - first_name: Peter full_name: Pickl, Peter last_name: Pickl 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 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 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. 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. 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. 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). date_created: 2023-12-31T23:01:02Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T08:51:28Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1063/5.0172199 external_id: arxiv: - '2307.11062' file: - access_level: open_access checksum: 66572f718a36465576cf0d6b3f7e01fc content_type: application/pdf creator: dernst date_created: 2024-01-02T08:45:07Z date_updated: 2024-01-02T08:45:07Z file_id: '14722' file_name: 2023_JourMathPhysics_Mitrouskas.pdf file_size: 4346922 relation: main_file success: 1 file_date_updated: 2024-01-02T08:45:07Z has_accepted_license: '1' intvolume: ' 64' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Journal of Mathematical Physics publication_identifier: eissn: - 1089-7658 issn: - 0022-2488 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Exponential decay of the number of excitations in the weakly interacting Bose gas tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 64 year: '2023' ... --- _id: '14240' abstract: - lang: eng 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. acknowledged_ssus: - _id: ScienComp 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." article_number: '83' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Jeschke S, Wojtan C. Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. 2023;42(4). 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 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. 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. 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. short: S. Jeschke, C. Wojtan, ACM Transactions on Graphics 42 (2023). date_created: 2023-08-27T22:01:17Z date_published: 2023-08-01T00:00:00Z date_updated: 2024-01-02T09:35:55Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/3592098 external_id: isi: - '001044671300049' file: - access_level: open_access checksum: 1d178bb2f8011d9f5aedda6427e18c7a content_type: video/mp4 creator: sjeschke date_created: 2023-12-21T12:26:40Z date_updated: 2023-12-21T12:26:40Z file_id: '14704' file_name: PaperVideo_final.mp4 file_size: 511572575 relation: main_file success: 1 - access_level: open_access checksum: a49b2e744d5cd1276bb8b2e0ce6dc638 content_type: application/pdf creator: dernst date_created: 2024-01-02T09:34:27Z date_updated: 2024-01-02T09:34:27Z file_id: '14725' file_name: 2023_ACMToG_Jeschke.pdf file_size: 7469177 relation: main_file success: 1 file_date_updated: 2024-01-02T09:34:27Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: ACM Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Generalizing shallow water simulations with dispersive surface waves tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2023' ... --- _id: '14710' 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. 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).' article_number: '8328' article_processing_charge: Yes article_type: original author: - first_name: Agnese I. full_name: Curatolo, Agnese I. last_name: Curatolo - first_name: Ofer full_name: Kimchi, Ofer last_name: Kimchi - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Ryan K. full_name: Krueger, Ryan K. last_name: Krueger - first_name: Michael P. full_name: Brenner, Michael P. last_name: Brenner 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 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 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. 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. 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. 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). date_created: 2023-12-24T23:00:53Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T11:36:46Z day: '01' ddc: - '530' department: - _id: CaGo doi: 10.1038/s41467-023-43168-4 file: - access_level: open_access checksum: fd9e9d527c2691f03fbc24031a75a3b3 content_type: application/pdf creator: kschuh date_created: 2023-12-27T08:40:43Z date_updated: 2023-12-27T08:40:43Z file_id: '14714' file_name: 2023_NatureComm_Curatolo.pdf file_size: 1342319 relation: main_file success: 1 file_date_updated: 2023-12-27T08:40:43Z has_accepted_license: '1' intvolume: ' 14' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A computational toolbox for the assembly yield of complex and heterogeneous structures tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '14709' abstract: - lang: eng 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Marta full_name: Del Bianco, Marta last_name: Del Bianco - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Lucia full_name: Strader, Lucia last_name: Strader - first_name: Stefan full_name: Kepinski, Stefan last_name: Kepinski citation: 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' 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' 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.' 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.' 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.' 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. date_created: 2023-12-24T23:00:53Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-02T09:29:24Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1093/jxb/erad420 external_id: pmid: - '38038239' file: - access_level: open_access checksum: f66fb960fd791dea53fd0e087f2fbbe8 content_type: application/pdf creator: dernst date_created: 2024-01-02T09:23:57Z date_updated: 2024-01-02T09:23:57Z file_id: '14724' file_name: 2023_JourExperimentalBotany_DelBianco.pdf file_size: 425194 relation: main_file success: 1 file_date_updated: 2024-01-02T09:23:57Z has_accepted_license: '1' intvolume: ' 74' issue: '22' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 6889-6892 pmid: 1 publication: Journal of Experimental Botany publication_identifier: eissn: - 1460-2431 issn: - 0022-0957 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Auxin research: Creating tools for a greener future' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 74 year: '2023' ... --- _id: '12833' abstract: - lang: eng 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.' 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" article_number: '9' article_processing_charge: No article_type: original author: - first_name: Ahmad full_name: Biniaz, Ahmad last_name: Biniaz - first_name: Kshitij full_name: Jain, Kshitij last_name: Jain - first_name: Anna full_name: Lubiw, Anna last_name: Lubiw - first_name: Zuzana full_name: Masárová, Zuzana id: 45CFE238-F248-11E8-B48F-1D18A9856A87 last_name: Masárová orcid: 0000-0002-6660-1322 - first_name: Tillmann full_name: Miltzow, Tillmann last_name: Miltzow - first_name: Debajyoti full_name: Mondal, Debajyoti last_name: Mondal - first_name: Anurag Murty full_name: Naredla, Anurag Murty last_name: Naredla - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Alexi full_name: Turcotte, Alexi last_name: Turcotte citation: 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 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 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. ieee: A. Biniaz et al., “Token swapping on trees,” Discrete Mathematics and Theoretical Computer Science, vol. 24, no. 2. EPI Sciences, 2023. 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. 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). date_created: 2023-04-16T22:01:08Z date_published: 2023-01-18T00:00:00Z date_updated: 2024-01-04T12:42:09Z day: '18' ddc: - '000' department: - _id: KrCh - _id: HeEd - _id: UlWa doi: 10.46298/DMTCS.8383 external_id: arxiv: - '1903.06981' file: - access_level: open_access checksum: 439102ea4f6e2aeefd7107dfb9ccf532 content_type: application/pdf creator: dernst date_created: 2023-04-17T08:10:28Z date_updated: 2023-04-17T08:10:28Z file_id: '12844' file_name: 2022_DMTCS_Biniaz.pdf file_size: 2072197 relation: main_file success: 1 file_date_updated: 2023-04-17T08:10:28Z has_accepted_license: '1' intvolume: ' 24' issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Discrete Mathematics and Theoretical Computer Science publication_identifier: eissn: - 1365-8050 issn: - 1462-7264 publication_status: published publisher: EPI Sciences quality_controlled: '1' related_material: record: - id: '7950' relation: earlier_version status: public scopus_import: '1' status: public title: Token swapping on trees tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2023' ... --- _id: '14735' 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." acknowledgement: 'Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Christos full_name: Stefo, Christos id: a20e8902-32b0-11ee-9fa8-b23fa638b793 last_name: Stefo - first_name: Zhuolun full_name: Xiang, Zhuolun last_name: Xiang - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias 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' 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' 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. 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. 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.' 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. short: C. Stefo, Z. Xiang, E. Kokoris Kogias, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 3–20. conference: end_date: 2023-05-05 location: Bol, Brac, Croatia name: 'FC: Financial Cryptography and Data Security' start_date: 2023-05-01 date_created: 2024-01-08T09:17:38Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T09:28:14Z day: '01' department: - _id: ElKo - _id: GradSch doi: 10.1007/978-3-031-47754-6_1 intvolume: ' 13950' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2022/1554 month: '12' oa: 1 oa_version: Preprint page: 3-20 project: - _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f grant_number: F8512 name: Secure Network and Hardware for Efficient Blockchains publication: 27th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - '9783031477546' eissn: - 0302-9743 isbn: - '9783031477539' issn: - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Executing and proving over dirty ledgers type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13950 year: '2023' ... --- _id: '14733' 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Rajesh B full_name: Jethwa, Rajesh B id: 4cc538d5-803f-11ed-ab7e-8139573aad8f last_name: Jethwa orcid: 0000-0002-0404-4356 - first_name: Dominic full_name: Hey, Dominic last_name: Hey - first_name: Rachel N. full_name: Kerber, Rachel N. last_name: Kerber - first_name: Andrew D. full_name: Bond, Andrew D. last_name: Bond - first_name: Dominic S. full_name: Wright, Dominic S. last_name: Wright - first_name: Clare P. full_name: Grey, Clare P. last_name: Grey citation: 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 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 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. 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. 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. 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). date_created: 2024-01-05T09:20:48Z date_published: 2023-12-28T00:00:00Z date_updated: 2024-01-08T09:03:01Z day: '28' ddc: - '540' department: - _id: StFr doi: 10.1021/acsaem.3c02223 ec_funded: 1 has_accepted_license: '1' keyword: - Electrical and Electronic Engineering - Materials Chemistry - Electrochemistry - Energy Engineering and Power Technology - Chemical Engineering (miscellaneous) language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/acsaem.3c02223 month: '12' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: ACS Applied Energy Materials publication_identifier: eissn: - 2574-0962 publication_status: epub_ahead publisher: American Chemical Society quality_controlled: '1' status: public title: Exploring the landscape of heterocyclic quinones for redox flow batteries tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14734' 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. 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. article_processing_charge: No article_type: original author: - first_name: Shanhong full_name: Wan, Shanhong last_name: Wan - first_name: Shanshan full_name: Xiao, Shanshan last_name: Xiao - first_name: Mingquan full_name: Li, Mingquan last_name: Li - first_name: Xin full_name: Wang, Xin last_name: Wang - first_name: Khak Ho full_name: Lim, Khak Ho last_name: Lim - first_name: Min full_name: Hong, Min last_name: Hong - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 citation: 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 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 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. 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. 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. short: S. Wan, S. Xiao, M. Li, X. Wang, K.H. Lim, M. Hong, M. Ibáñez, A. Cabot, Y. Liu, Small Methods (2023). date_created: 2024-01-07T23:00:51Z date_published: 2023-12-28T00:00:00Z date_updated: 2024-01-08T09:17:04Z day: '28' department: - _id: MaIb doi: 10.1002/smtd.202301377 external_id: pmid: - '38152986' language: - iso: eng month: '12' oa_version: None pmid: 1 project: - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication: Small Methods publication_identifier: eissn: - 2366-9608 publication_status: epub_ahead publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14737' abstract: - lang: eng 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.' 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.]." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Grigory full_name: Ivanov, Grigory id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E last_name: Ivanov - first_name: Márton full_name: Naszódi, Márton last_name: Naszódi citation: 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 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 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. 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. 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. 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. date_created: 2024-01-08T09:48:56Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T09:57:25Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.1093/imrn/rnad210 external_id: arxiv: - '2212.11781' file: - access_level: open_access checksum: 353666cea80633beb0f1ffd342dff6d4 content_type: application/pdf creator: dernst date_created: 2024-01-08T09:53:09Z date_updated: 2024-01-08T09:53:09Z file_id: '14738' file_name: 2023_IMRN_Ivanov.pdf file_size: 815777 relation: main_file success: 1 file_date_updated: 2024-01-08T09:53:09Z has_accepted_license: '1' intvolume: ' 2023' issue: '23' keyword: - General Mathematics language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '12' oa: 1 oa_version: Published Version page: 20613-20669 publication: International Mathematics Research Notices publication_identifier: eissn: - 1687-0247 issn: - 1073-7928 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Functional John and Löwner conditions for pairs of log-concave functions tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2023 year: '2023' ... --- _id: '14736' 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. acknowledgement: Supported by the German Federal Ministry of Education and Research (BMBF), grant 16KISK020K (6G-RIC), 2021–2025, and ERC CoG 863818 (ForM-SMArt). alternative_title: - LNCS article_processing_charge: No author: - first_name: Mahsa full_name: Bastankhah, Mahsa last_name: Bastankhah - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Mohammad Ali full_name: Maddah-Ali, Mohammad Ali last_name: Maddah-Ali - first_name: Stefan full_name: Schmid, Stefan last_name: Schmid - first_name: Jakub full_name: Svoboda, Jakub id: 130759D2-D7DD-11E9-87D2-DE0DE6697425 last_name: Svoboda orcid: 0000-0002-1419-3267 - first_name: Michelle X full_name: Yeo, Michelle X id: 2D82B818-F248-11E8-B48F-1D18A9856A87 last_name: Yeo citation: 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' 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' 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.' 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.' 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.' 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. conference: end_date: 2023-05-05 location: Bol, Brac, Croatia name: 'FC: Financial Cryptography and Data Security' start_date: 2023-05-01 date_created: 2024-01-08T09:30:22Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T09:36:36Z day: '01' department: - _id: KrCh - _id: KrPi doi: 10.1007/978-3-031-47754-6_18 ec_funded: 1 intvolume: ' 13950' language: - iso: eng month: '12' oa_version: None page: 309-325 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: 27th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - '9783031477546' eissn: - 1611-3349 isbn: - '9783031477539' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'R2: Boosting liquidity in payment channel networks with online admission control' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13950 year: '2023' ... --- _id: '14739' 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. 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." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Dashti full_name: Ali, Dashti last_name: Ali - first_name: Aras full_name: Asaad, Aras last_name: Asaad - first_name: Maria-Jose full_name: Jimenez, Maria-Jose last_name: Jimenez - first_name: Vidit full_name: Nanda, Vidit last_name: Nanda - first_name: Eduardo full_name: Paluzo-Hidalgo, Eduardo last_name: Paluzo-Hidalgo - first_name: Manuel full_name: Soriano Trigueros, Manuel id: 15ebd7cf-15bf-11ee-aebd-bb4bb5121ea8 last_name: Soriano Trigueros orcid: 0000-0003-2449-1433 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 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 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. 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. 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. 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. date_created: 2024-01-08T09:59:46Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T10:11:46Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1109/tpami.2023.3308391 file: - access_level: open_access checksum: 465c28ef0b151b4b1fb47977ed5581ab content_type: application/pdf creator: dernst date_created: 2024-01-08T10:09:14Z date_updated: 2024-01-08T10:09:14Z file_id: '14740' file_name: 2023_IEEEToP_Ali.pdf file_size: 2370988 relation: main_file success: 1 file_date_updated: 2024-01-08T10:09:14Z has_accepted_license: '1' intvolume: ' 45' issue: '12' keyword: - Applied Mathematics - Artificial Intelligence - Computational Theory and Mathematics - Computer Vision and Pattern Recognition - Software language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 14069-14080 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_identifier: eissn: - 1939-3539 issn: - 0162-8828 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: A survey of vectorization methods in topological data analysis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2023' ... --- _id: '14742' abstract: - lang: eng 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." 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." article_number: a041447 article_processing_charge: No article_type: original author: - first_name: Kay full_name: Lucek, Kay last_name: Lucek - first_name: Mabel D. full_name: Giménez, Mabel D. last_name: Giménez - first_name: Mathieu full_name: Joron, Mathieu last_name: Joron - first_name: Marina full_name: Rafajlović, Marina last_name: Rafajlović - first_name: Jeremy B. full_name: Searle, Jeremy B. last_name: Searle - first_name: Nora full_name: Walden, Nora last_name: Walden - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria citation: 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' 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' 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.' 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.' 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.' 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). date_created: 2024-01-08T12:43:48Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-08T12:52:29Z day: '01' department: - _id: NiBa - _id: BeVi doi: 10.1101/cshperspect.a041447 external_id: pmid: - '37604585' intvolume: ' 15' issue: '11' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/cshperspect.a041447 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Cold Spring Harbor Perspectives in Biology publication_identifier: issn: - 1943-0264 publication_status: published publisher: Cold Spring Harbor Laboratory quality_controlled: '1' scopus_import: '1' status: public title: 'The impact of chromosomal rearrangements in speciation: From micro- to macroevolution' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2023' ... --- _id: '14744' abstract: - lang: eng 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." acknowledgement: The work was partially supported by the Austrian Science Fund (FWF) through the project CoRaF (grant agreement 2020388). alternative_title: - LNCS article_processing_charge: No author: - first_name: Zeta full_name: Avarikioti, Zeta last_name: Avarikioti - first_name: Antoine full_name: Desjardins, Antoine id: 06d0c166-aec1-11ee-a7c0-b96e840a602b last_name: Desjardins - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Roger full_name: Wattenhofer, Roger last_name: Wattenhofer 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' 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' 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.' 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.' 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.' 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. conference: end_date: 2023-06-09 location: Alcalá de Henares, Spain name: 'SIROCCO: Structural Information and Communication Complexity' start_date: 2023-06-06 date_created: 2024-01-08T12:56:46Z date_published: 2023-06-01T00:00:00Z date_updated: 2024-01-09T07:40:57Z day: '01' department: - _id: ElKo doi: 10.1007/978-3-031-32733-9_10 intvolume: ' 13892' language: - iso: eng month: '06' oa_version: None page: 199-245 publication: 30th International Colloquium on Structural Information and Communication Complexity publication_identifier: eisbn: - '9783031327339' eissn: - 1611-3349 isbn: - '9783031327322' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Divide & Scale: Formalization and roadmap to robust sharding' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13892 year: '2023' ... --- _id: '14749' 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. article_processing_charge: No article_type: original author: - first_name: Umang full_name: Mishra, Umang id: 4328fa4c-f128-11eb-9611-c107b0fe4d51 last_name: Mishra - first_name: Vyacheslav full_name: Li, Vyacheslav id: 3A4FAA92-F248-11E8-B48F-1D18A9856A87 last_name: Li - first_name: Sebastian full_name: Wald, Sebastian id: 133F200A-B015-11E9-AD41-0EDAE5697425 last_name: Wald - first_name: Sofya full_name: Agafonova, Sofya id: 09501ff6-dca7-11ea-a8ae-b3e0b9166e80 last_name: Agafonova orcid: 0000-0003-0582-2946 - first_name: Fritz R full_name: Diorico, Fritz R id: 2E054C4C-F248-11E8-B48F-1D18A9856A87 last_name: Diorico - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X 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 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 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. 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. 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. 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. date_created: 2024-01-08T13:01:46Z date_published: 2023-07-21T00:00:00Z date_updated: 2024-01-09T08:09:32Z day: '21' department: - _id: OnHo doi: 10.1364/ol.495553 external_id: arxiv: - '2212.01266' intvolume: ' 48' issue: '15' keyword: - Atomic and Molecular Physics - and Optics language: - iso: eng month: '07' oa_version: Preprint page: 3973-3976 publication: Optics Letters publication_identifier: eissn: - 1539-4794 issn: - 0146-9592 publication_status: published publisher: Optica Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Monitoring and active stabilization of laser injection locking using beam ellipticity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2023' ... --- _id: '14752' 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.' 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. article_number: e2023AV000880 article_processing_charge: Yes article_type: original author: - first_name: B. full_name: Fildier, B. last_name: Fildier - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: R. full_name: Pincus, R. last_name: Pincus - first_name: S. full_name: Fueglistaler, S. last_name: Fueglistaler 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 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. 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. 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. short: B. Fildier, C.J. Muller, R. Pincus, S. Fueglistaler, AGU Advances 4 (2023). date_created: 2024-01-08T13:07:49Z date_published: 2023-06-01T00:00:00Z date_updated: 2024-01-09T08:54:03Z day: '01' ddc: - '550' department: - _id: CaMu doi: 10.1029/2023av000880 ec_funded: 1 file: - access_level: open_access checksum: af773220a9fa194c61a8dc2fae092c16 content_type: application/pdf creator: dernst date_created: 2024-01-09T08:51:25Z date_updated: 2024-01-09T08:51:25Z file_id: '14761' file_name: 2023_AGUAdvances_Fildier.pdf file_size: 24149551 relation: main_file success: 1 file_date_updated: 2024-01-09T08:51:25Z has_accepted_license: '1' intvolume: ' 4' issue: '3' keyword: - General Earth and Planetary Sciences language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 629205d8-2b32-11ec-9570-e1356ff73576 call_identifier: H2020 grant_number: '805041' name: organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate publication: AGU Advances publication_identifier: eissn: - 2576-604X publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: How moisture shapes low‐level radiative cooling in subsidence regimes tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2023' ... --- _id: '14754' 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. 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. article_number: '0112' article_processing_charge: No article_type: original author: - first_name: B. full_name: Wang, B. last_name: Wang - first_name: F. full_name: Mellibovsky, F. last_name: Mellibovsky - first_name: Roger full_name: Ayats López, Roger id: ab77522d-073b-11ed-8aff-e71b39258362 last_name: Ayats López orcid: 0000-0001-6572-0621 - first_name: K. full_name: Deguchi, K. last_name: Deguchi - first_name: A. full_name: Meseguer, A. last_name: Meseguer 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 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 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. 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. 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. 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. short: B. Wang, F. Mellibovsky, R. Ayats López, K. Deguchi, A. Meseguer, Philosophical Transactions of the Royal Society A 381 (2023). date_created: 2024-01-08T13:11:45Z date_published: 2023-05-01T00:00:00Z date_updated: 2024-01-09T09:15:29Z day: '01' ddc: - '530' department: - _id: BjHo doi: 10.1098/rsta.2022.0112 external_id: pmid: - '36907214' file: - access_level: open_access checksum: 1978d126c0ce2f47c22ac20107cc0106 content_type: application/pdf creator: dernst date_created: 2024-01-09T09:13:53Z date_updated: 2024-01-09T09:13:53Z file_id: '14763' file_name: 2023_PhilTransactionsA_Wang_accepted.pdf file_size: 6421086 relation: main_file success: 1 file_date_updated: 2024-01-09T09:13:53Z has_accepted_license: '1' intvolume: ' 381' issue: '2246' keyword: - General Physics and Astronomy - General Engineering - General Mathematics language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version pmid: 1 publication: Philosophical Transactions of the Royal Society A publication_identifier: eissn: - 1471-2962 issn: - 1364-503X publication_status: published publisher: The Royal Society quality_controlled: '1' scopus_import: '1' status: public title: Mean structure of the supercritical turbulent spiral in Taylor–Couette flow tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 381 year: '2023' ... --- _id: '14753' abstract: - lang: eng 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." 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." article_number: '137871' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Pietro full_name: Faccioli, Pietro last_name: Faccioli - first_name: Ilse full_name: Krätschmer, Ilse id: 30d4014e-7753-11eb-b44b-db6d61112e73 last_name: Krätschmer orcid: 0000-0002-5636-9259 - first_name: Carlos full_name: Lourenço, Carlos last_name: Lourenço citation: 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' 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' 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.' ieee: 'P. Faccioli, I. Krätschmer, and C. Lourenço, “Low-pT quarkonium polarization measurements: Challenges and opportunities,” Physics Letters B, vol. 840. Elsevier, 2023.' ista: 'Faccioli P, Krätschmer I, Lourenço C. 2023. Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. 840, 137871.' 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.' short: P. Faccioli, I. Krätschmer, C. Lourenço, Physics Letters B 840 (2023). date_created: 2024-01-08T13:09:17Z date_published: 2023-05-10T00:00:00Z date_updated: 2024-01-09T09:02:22Z day: '10' ddc: - '530' department: - _id: MaRo doi: 10.1016/j.physletb.2023.137871 file: - access_level: open_access checksum: 02dec160dbc81d95985e755869d8afbf content_type: application/pdf creator: dernst date_created: 2024-01-09T08:59:24Z date_updated: 2024-01-09T08:59:24Z file_id: '14762' file_name: 2023_PhysicsLettersB_Faccioli.pdf file_size: 855494 relation: main_file success: 1 file_date_updated: 2024-01-09T08:59:24Z has_accepted_license: '1' intvolume: ' 840' keyword: - Nuclear and High Energy Physics language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Physics Letters B publication_identifier: eissn: - 1873-2445 issn: - 0370-2693 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Low-pT quarkonium polarization measurements: Challenges and opportunities' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 840 year: '2023' ... --- _id: '14750' 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 \x02 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 \x02μB, 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. " 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." article_processing_charge: No article_type: original author: - first_name: Xiucai full_name: Ding, Xiucai last_name: Ding - first_name: Hong Chang full_name: Ji, Hong Chang id: dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d last_name: Ji citation: 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 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 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. 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. ista: Ding X, Ji HC. 2023. Local laws for multiplication of random matrices. The Annals of Applied Probability. 33(4), 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. short: X. Ding, H.C. Ji, The Annals of Applied Probability 33 (2023) 2981–3009. date_created: 2024-01-08T13:03:18Z date_published: 2023-08-01T00:00:00Z date_updated: 2024-01-09T08:16:41Z day: '01' department: - _id: LaEr doi: 10.1214/22-aap1882 ec_funded: 1 external_id: arxiv: - '2010.16083' intvolume: ' 33' issue: '4' keyword: - Statistics - Probability and Uncertainty - Statistics and Probability language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2010.16083 month: '08' oa: 1 oa_version: Preprint page: 2981-3009 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: The Annals of Applied Probability publication_identifier: issn: - 1050-5164 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: Local laws for multiplication of random matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2023' ... --- _id: '14756' 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." 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." article_processing_charge: Yes article_type: original author: - first_name: Nils full_name: Carqueville, Nils last_name: Carqueville - first_name: Lorant full_name: Szegedy, Lorant id: 7943226E-220E-11EA-94C7-D59F3DDC885E last_name: Szegedy orcid: 0000-0003-2834-5054 citation: ama: Carqueville N, Szegedy L. Fully extended r-spin TQFTs. Quantum Topology. 2023;14(3):467-532. doi:10.4171/qt/193 apa: Carqueville, N., & Szegedy, L. (2023). Fully extended r-spin TQFTs. Quantum Topology. European Mathematical Society. https://doi.org/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. ieee: N. Carqueville and L. Szegedy, “Fully extended r-spin TQFTs,” Quantum Topology, vol. 14, no. 3. European Mathematical Society, pp. 467–532, 2023. ista: Carqueville N, Szegedy L. 2023. Fully extended r-spin TQFTs. Quantum Topology. 14(3), 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. short: N. Carqueville, L. Szegedy, Quantum Topology 14 (2023) 467–532. date_created: 2024-01-08T13:14:48Z date_published: 2023-10-16T00:00:00Z date_updated: 2024-01-09T09:27:46Z day: '16' ddc: - '530' department: - _id: MiLe doi: 10.4171/qt/193 file: - access_level: open_access checksum: b0590aff6e7ec89cc149ba94d459d3a3 content_type: application/pdf creator: dernst date_created: 2024-01-09T09:25:34Z date_updated: 2024-01-09T09:25:34Z file_id: '14764' file_name: 2023_QuantumTopol_Carqueville.pdf file_size: 707344 relation: main_file success: 1 file_date_updated: 2024-01-09T09:25:34Z has_accepted_license: '1' intvolume: ' 14' issue: '3' keyword: - Geometry and Topology - Mathematical Physics language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 467-532 publication: Quantum Topology publication_identifier: issn: - 1663-487X publication_status: published publisher: European Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: Fully extended r-spin TQFTs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2023' ... --- _id: '14751' 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.' 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]" article_processing_charge: No article_type: original author: - first_name: Yihan full_name: Zhang, Yihan id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c last_name: Zhang orcid: 0000-0002-6465-6258 citation: 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 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 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. 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. ista: Zhang Y. 2023. Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. 69(7), 4093–4127. 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_created: 2024-01-08T13:04:54Z date_published: 2023-07-01T00:00:00Z date_updated: 2024-01-09T08:45:24Z day: '01' department: - _id: MaMo doi: 10.1109/tit.2023.3257239 external_id: arxiv: - '2101.12426' intvolume: ' 69' issue: '7' keyword: - Computer Science Applications - Information Systems language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2101.12426 month: '07' oa: 1 oa_version: Preprint page: 4093-4127 publication: IEEE Transactions on Information Theory publication_identifier: eissn: - 1557-9654 issn: - 0018-9448 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Zero-error communication over adversarial MACs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 69 year: '2023' ... --- _id: '14755' 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)). acknowledgement: "The author gratefully acknowledges support through DFG, GRK 1692 “Curvature,\r\nCycles and Cohomology” during parts of the work." article_processing_charge: No article_type: original author: - first_name: Maximilian full_name: Moser, Maximilian id: a60047a9-da77-11eb-85b4-c4dc385ebb8c last_name: Moser citation: 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' 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' 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.' 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.' 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.' short: M. Moser, Asymptotic Analysis 131 (2023) 297–383. date_created: 2024-01-08T13:13:28Z date_published: 2023-02-02T00:00:00Z date_updated: 2024-01-09T09:22:16Z day: '02' department: - _id: JuFi doi: 10.3233/asy-221775 external_id: arxiv: - '2105.07100' intvolume: ' 131' issue: 3-4 keyword: - General Mathematics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2105.07100 month: '02' oa: 1 oa_version: Preprint page: 297-383 publication: Asymptotic Analysis publication_identifier: eissn: - 1875-8576 issn: - 0921-7134 publication_status: published publisher: IOS Press quality_controlled: '1' scopus_import: '1' 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' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 131 year: '2023' ... --- _id: '14757' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Ana full_name: Villalba Requena, Ana id: 68cb85a0-39f7-11eb-9559-9aaab4f6a247 last_name: Villalba Requena orcid: 0000-0002-5615-5277 - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: 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' 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 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. 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. 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.' 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. date_created: 2024-01-08T13:16:36Z date_published: 2023-08-08T00:00:00Z date_updated: 2024-01-09T09:46:57Z day: '08' department: - _id: SiHi doi: 10.1002/9781119860914.ch10 editor: - first_name: Wieland full_name: Huttner, Wieland last_name: Huttner language: - iso: eng month: '08' oa_version: None page: 169-191 publication: Neocortical Neurogenesis in Development and Evolution publication_identifier: eisbn: - '9781119860914' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14759' abstract: - lang: eng 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 \U0001D445\U0001D439 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." acknowledgement: We thank Jakob Vorlaufer for technical contributions and Vyacheslav Li and Sofia Agafonova for comments on the manuscript. article_processing_charge: No article_type: original author: - first_name: Sebastian full_name: Wald, Sebastian id: 133F200A-B015-11E9-AD41-0EDAE5697425 last_name: Wald orcid: 0000-0002-5869-1604 - first_name: Fritz R full_name: Diorico, Fritz R id: 2E054C4C-F248-11E8-B48F-1D18A9856A87 last_name: Diorico orcid: 0000-0002-4947-8924 - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X citation: ama: Wald S, Diorico FR, Hosten O. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 2023;62(1):1-7. doi:10.1364/ao.474118 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 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. 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. 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. 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. short: S. Wald, F.R. Diorico, O. Hosten, Applied Optics 62 (2023) 1–7. date_created: 2024-01-08T13:19:14Z date_published: 2023-01-01T00:00:00Z date_updated: 2024-01-09T10:10:34Z day: '01' department: - _id: OnHo doi: 10.1364/ao.474118 external_id: arxiv: - '2208.11591' intvolume: ' 62' issue: '1' keyword: - Atomic and Molecular Physics - and Optics - Engineering (miscellaneous) - Electrical and Electronic Engineering language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2208.11591 month: '01' oa: 1 oa_version: Preprint page: 1-7 publication: Applied Optics publication_identifier: eissn: - 2155-3165 issn: - 1559-128X publication_status: published publisher: Optica Publishing Group quality_controlled: '1' scopus_import: '1' status: public title: Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2023' ... --- _id: '12817' abstract: - lang: eng 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. acknowledged_ssus: - _id: ScienComp - _id: Bio - _id: PreCl - _id: LifeSc - _id: M-Shop - _id: E-Lib 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. ' article_processing_charge: No author: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Danzl JG. Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” 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 chicago: Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria, 2023. 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. 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. short: J.G. Danzl, (2023). contributor: - first_name: Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Eder id: 3FB91342-F248-11E8-B48F-1D18A9856A87 last_name: Miguel Villalba - first_name: Julia M id: 443DB6DE-F248-11E8-B48F-1D18A9856A87 last_name: Michalska - first_name: Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Donglai last_name: Wei - first_name: Zudi last_name: Lin - first_name: Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Jakob last_name: Troidl - first_name: Johanna last_name: Beyer - first_name: Yoav id: 43DF3136-F248-11E8-B48F-1D18A9856A87 last_name: Ben Simon - first_name: Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Wiebke id: 425C1CE8-F248-11E8-B48F-1D18A9856A87 last_name: Jahr - first_name: Alban id: 9ac8f577-2357-11eb-997a-e566c5550886 last_name: Cenameri - first_name: Johannes last_name: Broichhagen - first_name: 'Seth G. N. ' last_name: Grant - first_name: Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Hanspeter last_name: Pfister - first_name: Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 date_created: 2023-04-07T11:37:40Z date_published: 2023-05-19T00:00:00Z date_updated: 2024-01-10T08:37:48Z day: '19' ddc: - '570' department: - _id: JoDa doi: 10.15479/AT:ISTA:12817 file: - access_level: open_access checksum: c1819889e72ec86ee1bba809e19739e0 content_type: text/plain creator: jdanzl date_created: 2023-05-18T17:06:12Z date_updated: 2023-05-18T17:06:12Z file_id: '13030' file_name: Readme.txt file_size: 651 relation: main_file success: 1 - access_level: open_access checksum: 8f6259fc5128ffcc0cd89d25d51995c1 content_type: image/tiff creator: jdanzl date_created: 2023-05-18T19:51:52Z date_updated: 2023-05-18T19:51:52Z file_id: '13031' file_name: Fig1a_LIONESS.tif file_size: 347448884 relation: main_file success: 1 - 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access_level: open_access checksum: 47db2185ff2c6ba9b059c9b1a8882832 content_type: application/zip creator: jdanzl date_created: 2023-05-18T15:03:10Z date_updated: 2023-05-18T15:03:10Z file_id: '13000' file_name: Segmentation model.zip file_size: 19052980 relation: main_file success: 1 file_date_updated: 2023-05-18T19:51:52Z has_accepted_license: '1' license: https://creativecommons.org/licenses/by-sa/4.0/ month: '05' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '13267' relation: used_in_publication status: public status: public title: Research data for the publication "Dense 4D nanoscale reconstruction of living brain tissue" tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13267' 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. acknowledged_ssus: - _id: ScienComp - _id: Bio - _id: PreCl - _id: E-Lib - _id: LifeSc - _id: M-Shop 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.)." article_processing_charge: Yes article_type: original author: - first_name: Philipp full_name: Velicky, Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Eder full_name: Miguel Villalba, Eder id: 3FB91342-F248-11E8-B48F-1D18A9856A87 last_name: Miguel Villalba orcid: 0000-0001-5665-0430 - first_name: Julia M full_name: Michalska, Julia M id: 443DB6DE-F248-11E8-B48F-1D18A9856A87 last_name: Michalska orcid: 0000-0003-3862-1235 - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Donglai full_name: Wei, Donglai last_name: Wei - first_name: Zudi full_name: Lin, Zudi last_name: Lin - first_name: Jake full_name: Watson, Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Jakob full_name: Troidl, Jakob last_name: Troidl - first_name: Johanna full_name: Beyer, Johanna last_name: Beyer - first_name: Yoav full_name: Ben Simon, Yoav id: 43DF3136-F248-11E8-B48F-1D18A9856A87 last_name: Ben Simon - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Wiebke full_name: Jahr, Wiebke id: 425C1CE8-F248-11E8-B48F-1D18A9856A87 last_name: Jahr - first_name: Alban full_name: Cenameri, Alban id: 9ac8f577-2357-11eb-997a-e566c5550886 last_name: Cenameri - first_name: Johannes full_name: Broichhagen, Johannes last_name: Broichhagen - first_name: Seth G.N. full_name: Grant, Seth G.N. last_name: Grant - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: 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 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 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. ieee: P. Velicky et al., “Dense 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023. 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. mla: Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:10.1038/s41592-023-01936-6. short: P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265. date_created: 2023-07-23T22:01:13Z date_published: 2023-08-01T00:00:00Z date_updated: 2024-01-10T08:37:48Z day: '01' department: - _id: PeJo - _id: GaNo - _id: BeBi - _id: JoDa - _id: Bio doi: 10.1038/s41592-023-01936-6 ec_funded: 1 external_id: isi: - '001025621500001' pmid: - '37429995' intvolume: ' 20' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41592-023-01936-6 month: '08' oa: 1 oa_version: Published Version page: 1256-1265 pmid: 1 project: - _id: 265CB4D0-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03600 name: Optical control of synaptic function via adhesion molecules - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize - _id: 23889792-32DE-11EA-91FC-C7463DDC885E name: High content imaging to decode human immune cell interactions in health and allergic disease - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9 call_identifier: H2020 grant_number: '101026635' name: Synaptic computations of the hippocampal CA3 circuitry - _id: 2668BFA0-B435-11E9-9278-68D0E5697425 grant_number: LT00057 name: High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration publication: Nature Methods publication_identifier: eissn: - 1548-7105 issn: - 1548-7091 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: software url: https://github.com/danzllab/LIONESS record: - id: '12817' relation: research_data status: public - id: '14770' relation: shorter_version status: public scopus_import: '1' status: public title: Dense 4D nanoscale reconstruction of living brain tissue type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2023' ... --- _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. 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. article_processing_charge: No author: - first_name: Eugenia B full_name: Iofinova, Eugenia B id: f9a17499-f6e0-11ea-865d-fdf9a3f77117 last_name: Iofinova orcid: 0000-0002-7778-3221 - first_name: Elena-Alexandra full_name: Peste, Elena-Alexandra id: 32D78294-F248-11E8-B48F-1D18A9856A87 last_name: Peste - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: 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' 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' 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.' 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.' 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.' 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. conference: end_date: 2023-06-24 location: Vancouver, BC, Canada name: 'CVPR: Conference on Computer Vision and Pattern Recognition' start_date: 2023-06-17 date_created: 2024-01-10T08:42:40Z date_published: 2023-08-22T00:00:00Z date_updated: 2024-01-10T08:59:26Z day: '22' department: - _id: DaAl - _id: ChLa doi: 10.1109/cvpr52729.2023.02334 ec_funded: 1 external_id: arxiv: - '2304.12622' isi: - '001062531308068' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2304.12622 month: '08' oa: 1 oa_version: Preprint page: 24364-24373 project: - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: ' W1260-N35' name: Vienna Graduate School on Computational Optimization - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition publication_identifier: eisbn: - '9798350301298' eissn: - 2575-7075 publication_status: published publisher: IEEE quality_controlled: '1' related_material: link: - relation: software url: https://github.com/IST-DASLab/pruned-vision-model-bias status: public title: 'Bias in pruned vision models: In-depth analysis and countermeasures' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14770' abstract: - lang: eng 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. article_processing_charge: No article_type: letter_note author: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Philipp full_name: Velicky, Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 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 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 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. 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. ista: Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142. 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. date_created: 2024-01-10T08:07:15Z date_published: 2023-08-01T00:00:00Z date_updated: 2024-01-10T08:37:48Z day: '01' department: - _id: JoDa doi: 10.1038/s41592-023-01937-5 external_id: isi: - '001025621500002' intvolume: ' 20' isi: 1 issue: '8' keyword: - Cell Biology - Molecular Biology - Biochemistry - Biotechnology language: - iso: eng month: '08' oa_version: None page: 1141-1142 publication: Nature Methods publication_identifier: eissn: - 1548-7105 issn: - 1548-7091 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '13267' relation: extended_version status: public scopus_import: '1' status: public title: LIONESS enables 4D nanoscale reconstruction of living brain tissue type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2023' ... --- _id: '14774' abstract: - lang: eng 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. 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." article_number: dev201559 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Rohit K full_name: Harish, Rohit K id: 1bae78aa-ee0e-11ec-9b76-bc42990f409d last_name: Harish - first_name: Mansi full_name: Gupta, Mansi last_name: Gupta - first_name: Daniela full_name: Zöller, Daniela last_name: Zöller - first_name: Hella full_name: Hartmann, Hella last_name: Hartmann - first_name: Ali full_name: Gheisari, Ali last_name: Gheisari - first_name: Anja full_name: Machate, Anja last_name: Machate - first_name: Stefan full_name: Hans, Stefan last_name: Hans - first_name: Michael full_name: Brand, Michael last_name: Brand citation: 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 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 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. 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. 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. 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). date_created: 2024-01-10T09:18:54Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-10T12:45:25Z day: '01' ddc: - '570' department: - _id: AnKi doi: 10.1242/dev.201559 external_id: isi: - '001097449100002' pmid: - '37665167' file: - access_level: open_access checksum: 2d6f52dc33260a9b2352b8f28374ba5f content_type: application/pdf creator: dernst date_created: 2024-01-10T12:41:13Z date_updated: 2024-01-10T12:41:13Z file_id: '14790' file_name: 2023_Development_Harish.pdf file_size: 12836306 relation: main_file success: 1 file_date_updated: 2024-01-10T12:41:13Z has_accepted_license: '1' intvolume: ' 150' isi: 1 issue: '19' keyword: - Developmental Biology - Molecular Biology language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Development publication_identifier: eissn: - 1477-9129 issn: - 0950-1991 publication_status: published publisher: The Company of Biologists quality_controlled: '1' status: public title: Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 150 year: '2023' ... --- _id: '14776' 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. 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." article_number: '16527' article_processing_charge: Yes article_type: original author: - first_name: Anastasiia full_name: Teplova, Anastasiia id: e3736151-106c-11ec-b916-c2558e2762c6 last_name: Teplova - first_name: Artemii A. full_name: Pigidanov, Artemii A. last_name: Pigidanov - first_name: Marina V. full_name: Serebryakova, Marina V. last_name: Serebryakova - first_name: Sergei A. full_name: Golyshev, Sergei A. last_name: Golyshev - first_name: Raisa A. full_name: Galiullina, Raisa A. last_name: Galiullina - first_name: Nina V. full_name: Chichkova, Nina V. last_name: Chichkova - first_name: Andrey B. full_name: Vartapetian, Andrey B. last_name: Vartapetian citation: 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 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 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. 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. 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. 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). date_created: 2024-01-10T09:24:35Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-10T13:41:10Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.3390/ijms242216527 external_id: isi: - '001113792600001' pmid: - '38003717' file: - access_level: open_access checksum: 4df7d206ba022b7f54eff1f0aec1659a content_type: application/pdf creator: dernst date_created: 2024-01-10T13:39:42Z date_updated: 2024-01-10T13:39:42Z file_id: '14791' file_name: 2023_IJMS_Teplova.pdf file_size: 2637784 relation: main_file success: 1 file_date_updated: 2024-01-10T13:39:42Z has_accepted_license: '1' intvolume: ' 24' isi: 1 issue: '22' keyword: - Inorganic Chemistry - Organic Chemistry - Physical and Theoretical Chemistry - Computer Science Applications - Spectroscopy - Molecular Biology - General Medicine - Catalysis language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: International Journal of Molecular Sciences publication_identifier: issn: - 1422-0067 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2023' ... --- _id: '14775' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original author: - first_name: Kevin full_name: Schnelli, Kevin id: 434AD0AE-F248-11E8-B48F-1D18A9856A87 last_name: Schnelli orcid: 0000-0003-0954-3231 - first_name: Yuanyuan full_name: Xu, Yuanyuan id: 7902bdb1-a2a4-11eb-a164-c9216f71aea3 last_name: Xu orcid: 0000-0003-1559-1205 citation: 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 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 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. 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. 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. 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. date_created: 2024-01-10T09:23:31Z date_published: 2023-02-01T00:00:00Z date_updated: 2024-01-10T13:31:46Z day: '01' department: - _id: LaEr doi: 10.1214/22-aap1826 ec_funded: 1 external_id: arxiv: - '2108.02728' isi: - '000946432400021' intvolume: ' 33' isi: 1 issue: '1' keyword: - Statistics - Probability and Uncertainty - Statistics and Probability language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2108.02728 month: '02' oa: 1 oa_version: Preprint page: 677-725 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: The Annals of Applied Probability publication_identifier: issn: - 1050-5164 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2023' ... --- _id: '14773' abstract: - lang: eng text: Through a combination of idealized simulations and real-world data, researchers are uncovering how internal feedbacks and large-scale motions influence cloud dynamics. article_number: '28' article_processing_charge: No article_type: original author: - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Sophie full_name: Abramian, Sophie last_name: Abramian citation: ama: Muller CJ, Abramian S. The cloud dynamics of convective storm systems. Physics Today. 2023;76(5). doi:10.1063/pt.3.5234 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 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. ieee: C. J. Muller and S. Abramian, “The cloud dynamics of convective storm systems,” Physics Today, vol. 76, no. 5. AIP Publishing, 2023. ista: Muller CJ, Abramian S. 2023. The cloud dynamics of convective storm systems. Physics Today. 76(5), 28. 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. short: C.J. Muller, S. Abramian, Physics Today 76 (2023). date_created: 2024-01-10T09:18:04Z date_published: 2023-05-01T00:00:00Z date_updated: 2024-01-10T12:38:02Z day: '01' department: - _id: CaMu doi: 10.1063/pt.3.5234 external_id: isi: - '000984516100007' intvolume: ' 76' isi: 1 issue: '5' keyword: - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://www.lmd.ens.fr/muller/Pubs/2023-MullerAbramianPhysToday.pdf month: '05' oa: 1 oa_version: Published Version publication: Physics Today publication_identifier: eissn: - 1945-0699 issn: - 0031-9228 publication_status: published publisher: AIP Publishing quality_controlled: '1' status: public title: The cloud dynamics of convective storm systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 76 year: '2023' ... --- _id: '14777' abstract: - lang: eng 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. 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). article_number: '125206' article_processing_charge: Yes article_type: original author: - first_name: Kosuke full_name: Sato, Kosuke last_name: Sato - first_name: Saurabh full_name: Singh, Saurabh id: 12d625da-9cb3-11ed-9667-af09d37d3f0a last_name: Singh orcid: 0000-0003-2209-5269 - first_name: Itsuki full_name: Yamazaki, Itsuki last_name: Yamazaki - first_name: Keisuke full_name: Hirata, Keisuke last_name: Hirata - first_name: Artoni Kevin R. full_name: Ang, Artoni Kevin R. last_name: Ang - first_name: Masaharu full_name: Matsunami, Masaharu last_name: Matsunami - first_name: Tsunehiro full_name: Takeuchi, Tsunehiro last_name: Takeuchi citation: 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 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 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. 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. 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. short: K. Sato, S. Singh, I. Yamazaki, K. Hirata, A.K.R. Ang, M. Matsunami, T. Takeuchi, AIP Advances 13 (2023). date_created: 2024-01-10T09:26:08Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-10T13:49:09Z day: '01' ddc: - '540' department: - _id: MaIb doi: 10.1063/5.0171888 external_id: isi: - '001114917200005' file: - access_level: open_access checksum: a7098388b8ff822b47f5ddd37ed3bdbc content_type: application/pdf creator: dernst date_created: 2024-01-10T13:47:31Z date_updated: 2024-01-10T13:47:31Z file_id: '14792' file_name: 2023_AIPAdvances_Sato.pdf file_size: 9676071 relation: main_file success: 1 file_date_updated: 2024-01-10T13:47:31Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '12' keyword: - General Physics and Astronomy language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: AIP Advances publication_identifier: eissn: - 2158-3226 publication_status: published publisher: AIP Publishing quality_controlled: '1' status: public title: Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2023' ... --- _id: '9651' 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. 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.' article_number: '15' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Michael full_name: Dymond, Michael last_name: Dymond - first_name: Vojtech full_name: Kaluza, Vojtech id: 21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E last_name: Kaluza orcid: 0000-0002-2512-8698 citation: ama: Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 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 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. 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. 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. short: M. Dymond, V. Kaluza, Geometriae Dedicata (2023). date_created: 2021-07-14T07:01:27Z date_published: 2023-11-17T00:00:00Z date_updated: 2024-01-11T13:06:32Z day: '17' department: - _id: UlWa doi: 10.1007/s10711-023-00862-3 external_id: arxiv: - '2102.13046' isi: - '001105681500001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s10711-023-00862-3 month: '11' oa: 1 oa_version: Published Version publication: Geometriae Dedicata publication_identifier: eissn: - 1572-9168 issn: - 0046-5755 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Divergence of separated nets with respect to displacement equivalence type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14768' abstract: - lang: eng 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.' 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." article_processing_charge: No author: - first_name: Vincent full_name: Cohen-Addad, Vincent last_name: Cohen-Addad - first_name: David full_name: Saulpic, David id: f8e48cf0-b0ff-11ed-b0e9-b4c35598f964 last_name: Saulpic - first_name: Chris full_name: Schwiegelshohn, Chris last_name: Schwiegelshohn citation: 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' 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' 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.' 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.' 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.' 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.' short: V. Cohen-Addad, D. Saulpic, C. Schwiegelshohn, in:, 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, IEEE, 2023, pp. 1105–1130. conference: end_date: 2023-11-09 location: Santa Cruz, CA, United States name: 'FOCS: Symposium on Foundations of Computer Science' start_date: 2023-11-06 date_created: 2024-01-09T16:20:09Z date_published: 2023-12-22T00:00:00Z date_updated: 2024-01-16T07:28:06Z day: '22' department: - _id: MoHe doi: 10.1109/focs57990.2023.00066 ec_funded: 1 external_id: arxiv: - '2310.04076' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2310.04076 month: '12' oa: 1 oa_version: Preprint page: 1105-1130 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62 call_identifier: H2020 grant_number: '101019564' name: The design and evaluation of modern fully dynamic data structures publication: 2023 IEEE 64th Annual Symposium on Foundations of Computer Science publication_identifier: eisbn: - '9798350318944' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: 'Deterministic clustering in high dimensional spaces: Sketches and approximation' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14784' 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. 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. article_number: adg1610 article_processing_charge: Yes article_type: original author: - first_name: Carlos J. full_name: Gallardo-Dodd, Carlos J. last_name: Gallardo-Dodd - first_name: Christian full_name: Oertlin, Christian last_name: Oertlin - first_name: Julien full_name: Record, Julien last_name: Record - first_name: Rômulo G. full_name: Galvani, Rômulo G. last_name: Galvani - first_name: Christian full_name: Sommerauer, Christian last_name: Sommerauer - first_name: Nikolai V. full_name: Kuznetsov, Nikolai V. last_name: Kuznetsov - first_name: Evangelos full_name: Doukoumopoulos, Evangelos last_name: Doukoumopoulos - first_name: Liaqat full_name: Ali, Liaqat last_name: Ali - first_name: Mariana M. S. full_name: Oliveira, Mariana M. S. last_name: Oliveira - first_name: Christina full_name: Seitz, Christina last_name: Seitz - first_name: Mathias full_name: Percipalle, Mathias id: 45adb726-eb97-11eb-a6c2-c7c3d3caabe9 last_name: Percipalle - first_name: Tijana full_name: Nikić, Tijana last_name: Nikić - first_name: Anastasia A. full_name: Sadova, Anastasia A. last_name: Sadova - first_name: Sofia M. full_name: Shulgina, Sofia M. last_name: Shulgina - first_name: Vjacheslav A. full_name: Shmarov, Vjacheslav A. last_name: Shmarov - first_name: Olga V. full_name: Kutko, Olga V. last_name: Kutko - first_name: Daria D. full_name: Vlasova, Daria D. last_name: Vlasova - first_name: Kseniya D. full_name: Orlova, Kseniya D. last_name: Orlova - first_name: Marina P. full_name: Rykova, Marina P. last_name: Rykova - first_name: John full_name: Andersson, John last_name: Andersson - first_name: Piergiorgio full_name: Percipalle, Piergiorgio last_name: Percipalle - first_name: Claudia full_name: Kutter, Claudia last_name: Kutter - first_name: Sergey A. full_name: Ponomarev, Sergey A. last_name: Ponomarev - first_name: Lisa S. full_name: Westerberg, Lisa S. last_name: Westerberg citation: 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 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 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. 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. 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. 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). date_created: 2024-01-10T09:48:01Z date_published: 2023-08-25T00:00:00Z date_updated: 2024-01-16T09:38:58Z day: '25' ddc: - '570' department: - _id: FlSc doi: 10.1126/sciadv.adg1610 external_id: isi: - '001054596800007' pmid: - '37624890' file: - access_level: open_access checksum: b9072e20e2d5d9d34d2c53319bafee41 content_type: application/pdf creator: dernst date_created: 2024-01-16T09:35:28Z date_updated: 2024-01-16T09:35:28Z file_id: '14809' file_name: 2023_ScienceAdvances_GallardoDodd.pdf file_size: 1596639 relation: main_file success: 1 file_date_updated: 2024-01-16T09:35:28Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '34' keyword: - Multidisciplinary language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' 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 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2023' ... --- _id: '14782' 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. 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Lucia full_name: Baldauf, Lucia last_name: Baldauf - first_name: Felix F full_name: Frey, Felix F id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3 last_name: Frey - first_name: Marcos full_name: Arribas Perez, Marcos last_name: Arribas Perez - first_name: Timon full_name: Idema, Timon last_name: Idema - first_name: Gijsje H. full_name: Koenderink, Gijsje H. last_name: Koenderink citation: 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 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 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. 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. 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. 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. date_created: 2024-01-10T09:45:48Z date_published: 2023-06-06T00:00:00Z date_updated: 2024-01-16T09:20:03Z day: '06' ddc: - '570' department: - _id: AnSa doi: 10.1016/j.bpj.2023.02.018 external_id: isi: - '001016792600001' pmid: - '36806830' file: - access_level: open_access checksum: 70566e54cd95ea6df340909ad44c5cd5 content_type: application/pdf creator: dernst date_created: 2024-01-16T09:09:29Z date_updated: 2024-01-16T09:09:29Z file_id: '14807' file_name: 2023_BiophysicalJournal_Baldauf.pdf file_size: 3285810 relation: main_file success: 1 file_date_updated: 2024-01-16T09:09:29Z has_accepted_license: '1' intvolume: ' 122' isi: 1 issue: '11' keyword: - Biophysics language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 2311-2324 pmid: 1 publication: Biophysical Journal publication_identifier: issn: - 0006-3495 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - relation: software url: https://github.com/BioSoftMatterGroup/actin-curvature-sensing status: public title: Branched actin cortices reconstituted in vesicles sense membrane curvature tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 122 year: '2023' ... --- _id: '14783' abstract: - lang: eng 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. 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.' article_number: '1133' article_processing_charge: Yes article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Oana full_name: Chever, Oana last_name: Chever - first_name: Astrid full_name: Rollenhagen, Astrid last_name: Rollenhagen - first_name: Nicole full_name: Quenech’du, Nicole last_name: Quenech’du - first_name: Pascal full_name: Ezan, Pascal last_name: Ezan - first_name: Joachim H. R. full_name: Lübke, Joachim H. R. last_name: Lübke - first_name: Nathalie full_name: Rouach, Nathalie last_name: Rouach citation: 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 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 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. ieee: G. T. Cheung et al., “Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses,” Cells, vol. 12, no. 8. MDPI, 2023. 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. 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). date_created: 2024-01-10T09:46:35Z date_published: 2023-04-11T00:00:00Z date_updated: 2024-01-16T09:29:35Z day: '11' ddc: - '570' department: - _id: SiHi doi: 10.3390/cells12081133 external_id: isi: - '000977445700001' pmid: - '37190042' file: - access_level: open_access checksum: 6798cd75d8857976fbc58a43fd173d68 content_type: application/pdf creator: dernst date_created: 2024-01-16T09:26:52Z date_updated: 2024-01-16T09:26:52Z file_id: '14808' file_name: 2023_Cells_Cheung.pdf file_size: 7931643 relation: main_file success: 1 file_date_updated: 2024-01-16T09:26:52Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '8' keyword: - General Medicine language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: Cells publication_identifier: issn: - 2073-4409 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2023' ... --- _id: '14785' abstract: - lang: eng 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. 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" article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Fabian full_name: Nies, Fabian last_name: Nies - first_name: Tanita full_name: Wein, Tanita last_name: Wein - first_name: Dustin M. full_name: Hanke, Dustin M. last_name: Hanke - first_name: Benjamin L full_name: Springstein, Benjamin L id: b4eb62ef-ac72-11ed-9503-ed3b4d66c083 last_name: Springstein orcid: 0000-0002-3461-5391 - first_name: Jaime full_name: Alcorta, Jaime last_name: Alcorta - first_name: Claudia full_name: Taubenheim, Claudia last_name: Taubenheim - first_name: Tal full_name: Dagan, Tal last_name: Dagan citation: 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 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 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. 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. 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. 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. date_created: 2024-01-10T10:41:07Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-16T09:46:12Z day: '01' ddc: - '570' department: - _id: MaLo doi: 10.1111/1758-2229.13203 external_id: isi: - '001080203100001' pmid: - '37794696' file: - access_level: open_access checksum: d09ebb68fee61f4e2e09ec286c9cf1d3 content_type: application/pdf creator: dernst date_created: 2024-01-16T09:42:10Z date_updated: 2024-01-16T09:42:10Z file_id: '14810' file_name: 2023_EnvirMicroBiolReports_Nies.pdf file_size: 1518350 relation: main_file success: 1 file_date_updated: 2024-01-16T09:42:10Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '6' keyword: - Agricultural and Biological Sciences (miscellaneous) - Ecology - Evolution - Behavior and Systematics language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 656-668 pmid: 1 publication: Environmental Microbiology Reports publication_identifier: eissn: - 1758-2229 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2023' ... --- _id: '14780' 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. 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Xiucai full_name: Ding, Xiucai last_name: Ding - first_name: Hong Chang full_name: Ji, Hong Chang id: dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d last_name: Ji citation: 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 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 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. 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. ista: Ding X, Ji HC. 2023. Spiked multiplicative random matrices and principal components. Stochastic Processes and their Applications. 163, 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. short: X. Ding, H.C. Ji, Stochastic Processes and Their Applications 163 (2023) 25–60. date_created: 2024-01-10T09:29:25Z date_published: 2023-09-01T00:00:00Z date_updated: 2024-01-16T08:49:51Z day: '01' ddc: - '510' department: - _id: LaEr doi: 10.1016/j.spa.2023.05.009 ec_funded: 1 external_id: arxiv: - '2302.13502' isi: - '001113615900001' file: - access_level: open_access checksum: 46a708b0cd5569a73d0f3d6c3e0a44dc content_type: application/pdf creator: dernst date_created: 2024-01-16T08:47:31Z date_updated: 2024-01-16T08:47:31Z file_id: '14806' file_name: 2023_StochasticProcAppl_Ding.pdf file_size: 1870349 relation: main_file success: 1 file_date_updated: 2024-01-16T08:47:31Z has_accepted_license: '1' intvolume: ' 163' isi: 1 keyword: - Applied Mathematics - Modeling and Simulation - Statistics and Probability language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 25-60 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Stochastic Processes and their Applications publication_identifier: eissn: - 1879-209X issn: - 0304-4149 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Spiked multiplicative random matrices and principal components tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 163 year: '2023' ... --- _id: '14779' abstract: - lang: eng 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. 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. article_number: e2023GL103043 article_processing_charge: No article_type: original author: - first_name: Thomas E. full_name: Shaw, Thomas E. last_name: Shaw - first_name: Pascal full_name: Buri, Pascal last_name: Buri - first_name: Michael full_name: McCarthy, Michael last_name: McCarthy - first_name: Evan S. full_name: Miles, Evan S. last_name: Miles - first_name: Álvaro full_name: Ayala, Álvaro last_name: Ayala - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti orcid: 0000-0002-5554-8087 citation: 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 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. 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. 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. short: T.E. Shaw, P. Buri, M. McCarthy, E.S. Miles, Á. Ayala, F. Pellicciotti, Geophysical Research Letters 50 (2023). date_created: 2024-01-10T09:28:34Z date_published: 2023-06-16T00:00:00Z date_updated: 2024-01-16T08:42:36Z day: '16' ddc: - '550' department: - _id: FrPe doi: 10.1029/2023gl103043 external_id: isi: - '000999436400001' file: - access_level: open_access checksum: 391a3005c95340a0ae129ce4fbdf2bae content_type: application/pdf creator: dernst date_created: 2024-01-16T08:35:02Z date_updated: 2024-01-16T08:35:02Z file_id: '14805' file_name: 2023_GeophysicalResearchLetter_Shaw.pdf file_size: 2529327 relation: main_file success: 1 file_date_updated: 2024-01-16T08:35:02Z has_accepted_license: '1' intvolume: ' 50' isi: 1 issue: '11' keyword: - General Earth and Planetary Sciences - Geophysics language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Geophysical Research Letters publication_identifier: eissn: - 1944-8007 issn: - 0094-8276 publication_status: published publisher: American Geophysical Union quality_controlled: '1' status: public title: The decaying near‐surface boundary layer of a retreating alpine glacier tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2023' ... --- _id: '14539' 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 article_processing_charge: No author: - first_name: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic orcid: 0000-0002-4681-1699 citation: ama: Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:10.15479/14539 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 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. ieee: D. Zikelic, “Automated verification and control of infinite state stochastic systems,” Institute of Science and Technology Austria, 2023. ista: Zikelic D. 2023. Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria. 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. date_created: 2023-11-15T13:39:10Z date_published: 2023-11-15T00:00:00Z date_updated: 2024-01-16T11:58:15Z day: '15' ddc: - '000' degree_awarded: PhD department: - _id: KrCh - _id: GradSch doi: 10.15479/14539 ec_funded: 1 file: - access_level: open_access checksum: f23e002b0059ca78e1fbb864da52dd7e content_type: application/pdf creator: cchlebak date_created: 2023-11-15T13:43:28Z date_updated: 2023-11-15T13:43:28Z file_id: '14540' file_name: main.pdf file_size: 2116426 relation: main_file success: 1 - access_level: closed checksum: 80ca37618a3c7b59866875f8be9b15ed content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-11-15T13:44:24Z date_updated: 2023-11-15T13:44:24Z file_id: '14541' file_name: thesis_source.zip file_size: 35884057 relation: source_file file_date_updated: 2023-11-15T13:44:24Z language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '11' oa: 1 oa_version: Published Version page: '256' project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-036-7 issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1194' relation: part_of_dissertation status: public - id: '12000' relation: part_of_dissertation status: public - id: '9644' relation: part_of_dissertation status: public - id: '12511' relation: part_of_dissertation status: public - id: '14600' relation: part_of_dissertation status: public - id: '14601' relation: part_of_dissertation status: public - id: '10414' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Automated verification and control of infinite state stochastic systems tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14788' 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." 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. article_number: e202206038 article_processing_charge: No article_type: original author: - first_name: Markus full_name: Mund, Markus last_name: Mund - first_name: Aline full_name: Tschanz, Aline last_name: Tschanz - first_name: Yu-Le full_name: Wu, Yu-Le last_name: Wu - first_name: Felix F full_name: Frey, Felix F id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3 last_name: Frey orcid: 0000-0001-8501-6017 - first_name: Johanna L. full_name: Mehl, Johanna L. last_name: Mehl - first_name: Marko full_name: Kaksonen, Marko last_name: Kaksonen - first_name: Ori full_name: Avinoam, Ori last_name: Avinoam - first_name: Ulrich S. full_name: Schwarz, Ulrich S. last_name: Schwarz - first_name: Jonas full_name: Ries, Jonas last_name: Ries citation: 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 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 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. 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. 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. 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. 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). date_created: 2024-01-10T10:45:55Z date_published: 2023-02-03T00:00:00Z date_updated: 2024-01-16T10:17:05Z day: '03' ddc: - '570' department: - _id: AnSa doi: 10.1083/jcb.202206038 external_id: isi: - '000978065000001' pmid: - '36734980' file: - access_level: open_access checksum: 505d5cac36c14b073b68c7fed1a92bd3 content_type: application/pdf creator: dernst date_created: 2024-01-16T10:15:09Z date_updated: 2024-01-16T10:15:09Z file_id: '14811' file_name: 2023_JCB_Mund.pdf file_size: 5678069 relation: main_file success: 1 file_date_updated: 2024-01-16T10:15:09Z has_accepted_license: '1' intvolume: ' 222' isi: 1 issue: '3' keyword: - Cell Biology language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Journal of Cell Biology publication_identifier: eissn: - 1540-8140 issn: - 0021-9525 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' status: public title: Clathrin coats partially preassemble and subsequently bend during endocytosis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 222 year: '2023' ... --- _id: '14787' 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. 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. article_processing_charge: No article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Madeline A. full_name: Chase, Madeline A. last_name: Chase - first_name: Hanna full_name: McIntosh, Hanna last_name: McIntosh - first_name: Matthew A. full_name: Streisfeld, Matthew A. last_name: Streisfeld citation: 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 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 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. 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. 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. 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. short: S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054. date_created: 2024-01-10T10:44:45Z date_published: 2023-04-01T00:00:00Z date_updated: 2024-01-16T10:10:00Z day: '01' department: - _id: NiBa doi: 10.1111/mec.16849 external_id: isi: - '000919244600001' pmid: - '36651268' intvolume: ' 32' isi: 1 issue: '8' keyword: - Genetics - Ecology - Evolution - Behavior and Systematics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2022.01.28.478139 month: '04' oa: 1 oa_version: Preprint page: 2041-2054 pmid: 1 publication: Molecular Ecology publication_identifier: eissn: - 1365-294X issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2023' ... --- _id: '12162' 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. 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." article_processing_charge: Yes (via OA deal) article_type: review author: - first_name: Bernat full_name: Corominas-Murtra, Bernat id: 43BE2298-F248-11E8-B48F-1D18A9856A87 last_name: Corominas-Murtra orcid: 0000-0001-9806-5643 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: 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 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 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. 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. ista: Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 150–151, 58–65. 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. date_created: 2023-01-12T12:09:47Z date_published: 2023-12-02T00:00:00Z date_updated: 2024-01-16T13:22:32Z day: '02' ddc: - '570' department: - _id: EdHa doi: 10.1016/j.semcdb.2022.11.005 ec_funded: 1 external_id: isi: - '001053522200001' pmid: - '36470715' file: - access_level: open_access checksum: c619887cf130f4649bf3035417186004 content_type: application/pdf creator: dernst date_created: 2024-01-08T10:16:04Z date_updated: 2024-01-08T10:16:04Z file_id: '14741' file_name: 2023_SeminarsCellDevBiology_CorominasMurtra.pdf file_size: 1343750 relation: main_file success: 1 file_date_updated: 2024-01-08T10:16:04Z has_accepted_license: '1' isi: 1 keyword: - Cell Biology - Developmental Biology language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 58-65 pmid: 1 project: - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publication: Seminars in Cell & Developmental Biology publication_identifier: issn: - 1084-9521 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Modelling the dynamics of mammalian gut homeostasis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 150-151 year: '2023' ... --- _id: '13268' 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. 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. article_processing_charge: No article_type: original author: - first_name: D. full_name: Huybrechts, D. last_name: Huybrechts - first_name: Mirko full_name: Mauri, Mirko id: 2cf70c34-09c1-11ed-bd8d-c34fac206130 last_name: Mauri citation: 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 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 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. 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. ista: Huybrechts D, Mauri M. 2023. On type II degenerations of hyperkähler manifolds. Mathematical Research Letters. 30(1), 125–141. 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. date_created: 2023-07-23T22:01:14Z date_published: 2023-06-21T00:00:00Z date_updated: 2024-01-16T12:00:47Z day: '21' department: - _id: TaHa doi: 10.4310/mrl.2023.v30.n1.a6 ec_funded: 1 external_id: arxiv: - '2108.01587' isi: - '001027656000006' intvolume: ' 30' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2108.01587 month: '06' oa: 1 oa_version: Preprint page: 125-141 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Mathematical Research Letters publication_identifier: eissn: - 1945-001X issn: - 1073-2780 publication_status: published publisher: International Press quality_controlled: '1' scopus_import: '1' status: public title: On type II degenerations of hyperkähler manifolds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2023' ... --- _id: '14661' 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.' article_processing_charge: No article_type: original author: - first_name: Marcello full_name: Carioni, Marcello last_name: Carioni - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Anja full_name: Schlömerkemper, Anja last_name: Schlömerkemper citation: 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.' 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.' 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.' 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.' short: M. Carioni, J.L. Fischer, A. Schlömerkemper, Journal of Convex Analysis 30 (2023) 217–247. date_created: 2023-12-10T23:00:59Z date_published: 2023-01-01T00:00:00Z date_updated: 2024-01-16T12:03:05Z day: '01' department: - _id: JuFi external_id: arxiv: - '1811.09857' isi: - '001115503400013' intvolume: ' 30' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1811.09857 month: '01' oa: 1 oa_version: Preprint page: 217-247 publication: Journal of Convex Analysis publication_identifier: eissn: - 2363-6394 issn: - 0944-6532 publication_status: published publisher: Heldermann Verlag quality_controlled: '1' scopus_import: '1' status: public title: 'External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2023' ... --- _id: '14778' abstract: - lang: eng 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.' 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. article_number: '11' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Ehsan full_name: Kafshdar Goharshady, Ehsan last_name: Kafshdar Goharshady - first_name: Petr full_name: Novotný, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotný - first_name: Jiří full_name: Zárevúcky, Jiří last_name: Zárevúcky - first_name: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic orcid: 0000-0002-4681-1699 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 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 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. 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. 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. 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). date_created: 2024-01-10T09:27:43Z date_published: 2023-06-23T00:00:00Z date_updated: 2024-01-17T08:19:41Z day: '23' ddc: - '000' department: - _id: KrCh doi: 10.1145/3585391 ec_funded: 1 external_id: arxiv: - '2108.02188' file: - access_level: open_access checksum: 3bb133eeb27ec01649a9a36445d952d9 content_type: application/pdf creator: dernst date_created: 2024-01-16T08:11:24Z date_updated: 2024-01-16T08:11:24Z file_id: '14804' file_name: 2023_FormalAspectsComputing_Chatterjee.pdf file_size: 502522 relation: main_file success: 1 file_date_updated: 2024-01-16T08:11:24Z has_accepted_license: '1' intvolume: ' 35' issue: '2' keyword: - Theoretical Computer Science - Software language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Formal Aspects of Computing publication_identifier: eissn: - 1433-299X issn: - 0934-5043 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '10414' relation: earlier_version status: public status: public title: On lexicographic proof rules for probabilistic termination tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2023' ... --- _id: '14798' abstract: - lang: eng 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.' 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." article_number: '90' article_processing_charge: Yes (in subscription journal) author: - first_name: Bin full_name: Chen, Bin last_name: Chen - first_name: Akshay full_name: Jindal, Akshay last_name: Jindal - first_name: Michael full_name: Piovarci, Michael id: 62E473F4-5C99-11EA-A40E-AF823DDC885E last_name: Piovarci orcid: 0000-0002-5062-4474 - first_name: Chao full_name: Wang, Chao last_name: Wang - first_name: Hans Peter full_name: Seidel, Hans Peter last_name: Seidel - first_name: Piotr full_name: Didyk, Piotr last_name: Didyk - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski - first_name: Ana full_name: Serrano, Ana last_name: Serrano - first_name: Rafał K. full_name: Mantiuk, Rafał K. last_name: Mantiuk citation: 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' 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. 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.' 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. 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. conference: end_date: 2023-12-15 location: Sydney, Australia name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2023-12-12 date_created: 2024-01-14T23:00:57Z date_published: 2023-12-10T00:00:00Z date_updated: 2024-01-17T08:38:35Z day: '10' ddc: - '000' department: - _id: BeBi doi: 10.1145/3610548.3618226 file: - access_level: open_access checksum: 8abe27432ed222b50d1af9b3388db1b0 content_type: application/pdf creator: dernst date_created: 2024-01-17T08:33:06Z date_updated: 2024-01-17T08:33:06Z file_id: '14823' file_name: 2023_SA_Chen.pdf file_size: 95967451 relation: main_file success: 1 file_date_updated: 2024-01-17T08:33:06Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: eb901961-77a9-11ec-83b8-f5c883a62027 grant_number: M03319 name: Perception-Aware Appearance Fabrication publication: Proceedings of the SIGGRAPH Asia 2023 Conference publication_identifier: isbn: - '9798400703157' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: The effect of display capabilities on the gloss consistency between real and virtual objects tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14815' abstract: - lang: eng 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. 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. ' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Aleksandr full_name: Beznosikov, Aleksandr last_name: Beznosikov - first_name: Samuel full_name: Horvath, Samuel last_name: Horvath - first_name: Peter full_name: Richtarik, Peter last_name: Richtarik - first_name: Mher full_name: Safaryan, Mher id: dd546b39-0804-11ed-9c55-ef075c39778d last_name: Safaryan citation: 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. 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. 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. 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. short: A. Beznosikov, S. Horvath, P. Richtarik, M. Safaryan, Journal of Machine Learning Research 24 (2023) 1–50. date_created: 2024-01-16T12:13:36Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-17T09:14:13Z day: '01' ddc: - '000' department: - _id: DaAl external_id: arxiv: - '2002.12410' isi: - '001111578500001' file: - access_level: open_access checksum: c50f2b9db53938b755e30a085f464059 content_type: application/pdf creator: dernst date_created: 2024-01-16T12:13:27Z date_updated: 2024-01-16T12:13:27Z file_id: '14816' file_name: 2023_JMLR_Beznosikov.pdf file_size: 1510993 relation: main_file success: 1 file_date_updated: 2024-01-16T12:13:27Z has_accepted_license: '1' intvolume: ' 24' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1-50 publication: Journal of Machine Learning Research publication_identifier: eissn: - 1533-7928 publication_status: published publisher: Journal of Machine Learning Research quality_controlled: '1' status: public title: On biased compression for distributed learning tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2023' ... --- _id: '14456' 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. alternative_title: - LNCS article_processing_charge: No author: - first_name: Jan Matyáš full_name: Křišťan, Jan Matyáš last_name: Křišťan - first_name: Jakub full_name: Svoboda, Jakub id: 130759D2-D7DD-11E9-87D2-DE0DE6697425 last_name: Svoboda orcid: 0000-0002-1419-3267 citation: 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' 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' 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. 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.' 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. short: J.M. Křišťan, J. Svoboda, in:, 24th International Symposium on Fundamentals of Computation Theory, Springer Nature, 2023, pp. 333–347. conference: end_date: 2023-09-21 location: Trier, Germany name: 'FCT: Fundamentals of Computation Theory' start_date: 2023-09-18 date_created: 2023-10-29T23:01:16Z date_published: 2023-09-21T00:00:00Z date_updated: 2024-01-22T08:10:49Z day: '21' department: - _id: KrCh doi: 10.1007/978-3-031-43587-4_24 external_id: arxiv: - '2307.10847' intvolume: ' 14292' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2307.10847 month: '09' oa: 1 oa_version: Preprint page: 333-347 publication: 24th International Symposium on Fundamentals of Computation Theory publication_identifier: eissn: - 1611-3349 isbn: - '9783031435867' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1007/978-3-031-43587-4_31 scopus_import: '1' status: public title: Shortest dominating set reconfiguration under token sliding type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14292 year: '2023' ... --- _id: '14829' abstract: - lang: eng 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.' 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.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Shir full_name: Cohen, Shir last_name: Cohen - first_name: Guy full_name: Goren, Guy last_name: Goren - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Alberto full_name: Sonnino, Alberto last_name: Sonnino - first_name: Alexander full_name: Spiegelman, Alexander last_name: Spiegelman citation: 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' 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' 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. 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. 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.' 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. conference: end_date: 2023-05-05 location: Bol, Brac, Croatia name: 'FC: Financial Cryptography and Data Security' start_date: 2023-05-01 date_created: 2024-01-18T07:41:12Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-22T13:58:07Z day: '01' department: - _id: ElKo doi: 10.1007/978-3-031-47751-5_3 intvolume: ' 13951' language: - iso: eng main_file_link: - open_access: '1' url: https://fc23.ifca.ai/preproceedings/150.pdf month: '12' oa: 1 oa_version: Submitted Version page: 36-53 project: - _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f grant_number: F8512 name: Secure Network and Hardware for Efficient Blockchains publication: 27th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - '9783031477515' eissn: - 1611-3349 isbn: - '9783031477508' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Proof of availability and retrieval in a modular blockchain architecture type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13951 year: '2023' ... --- _id: '14827' abstract: - lang: eng 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. 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 article_processing_charge: No article_type: original author: - first_name: Cornelia full_name: Schwayer, Cornelia id: 3436488C-F248-11E8-B48F-1D18A9856A87 last_name: Schwayer orcid: 0000-0001-5130-2226 - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 citation: 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 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 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. 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. ista: Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 136(24), 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). date_created: 2024-01-17T12:46:55Z date_published: 2023-12-27T00:00:00Z date_updated: 2024-01-22T13:35:48Z day: '27' department: - _id: EdHa - _id: CaHe doi: 10.1242/jcs.261515 external_id: pmid: - '38149871' intvolume: ' 136' issue: '24' keyword: - Cell Biology language: - iso: eng month: '12' oa_version: None pmid: 1 project: - _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b grant_number: 343-2022 name: A mechano-chemical theory for stem cell fate decisions in organoid development publication: Journal of Cell Science publication_identifier: eissn: - 1477-9137 issn: - 0021-9533 publication_status: published publisher: The Company of Biologists quality_controlled: '1' scopus_import: '1' status: public title: Connecting theory and experiment in cell and tissue mechanics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 136 year: '2023' ... --- _id: '14830' abstract: - lang: eng 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. 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. article_processing_charge: No author: - first_name: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic orcid: 0000-0002-4681-1699 - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: 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' 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' 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. 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. 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.' 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. 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. conference: end_date: 2023-02-14 location: Washington, DC, United States name: 'AAAI: Conference on Artificial Intelligence' start_date: 2023-02-07 date_created: 2024-01-18T07:44:31Z date_published: 2023-06-26T00:00:00Z date_updated: 2024-01-22T14:08:29Z day: '26' department: - _id: ToHe - _id: KrCh doi: 10.1609/aaai.v37i10.26407 ec_funded: 1 external_id: arxiv: - '2210.05308' intvolume: ' 37' issue: '10' keyword: - General Medicine language: - iso: eng month: '06' oa_version: Preprint page: 11926-11935 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Proceedings of the 37th AAAI Conference on Artificial Intelligence publication_identifier: eissn: - 2374-3468 issn: - 2159-5399 publication_status: published publisher: Association for the Advancement of Artificial Intelligence quality_controlled: '1' related_material: record: - id: '14600' relation: earlier_version status: public status: public title: Learning control policies for stochastic systems with reach-avoid guarantees type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2023' ... --- _id: '14833' abstract: - lang: eng 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. 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). article_number: kzad002 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Zuzanna B full_name: Zagrodzka, Zuzanna B last_name: Zagrodzka - first_name: Juan full_name: Galindo, Juan last_name: Galindo - first_name: Mauricio full_name: Montaño-Rendón, Mauricio last_name: Montaño-Rendón - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Natalia full_name: Mikhailova, Natalia last_name: Mikhailova - first_name: April M H full_name: Blakeslee, April M H last_name: Blakeslee - first_name: Einar full_name: Arnason, Einar last_name: Arnason - first_name: Thomas full_name: Broquet, Thomas last_name: Broquet - first_name: Hernán E full_name: Morales, Hernán E last_name: Morales - first_name: John W full_name: Grahame, John W last_name: Grahame - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K full_name: Butlin, Roger K last_name: Butlin 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 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 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. 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. 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. 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. 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). date_created: 2024-01-18T07:54:10Z date_published: 2023-08-17T00:00:00Z date_updated: 2024-01-23T08:13:43Z day: '17' ddc: - '570' department: - _id: NiBa doi: 10.1093/evolinnean/kzad002 file: - access_level: open_access checksum: ba6f9102d3a9fe6631c4fa398c5e4313 content_type: application/pdf creator: dernst date_created: 2024-01-23T08:10:00Z date_updated: 2024-01-23T08:10:00Z file_id: '14875' file_name: 2023_EvolJourLinneanSociety_Stankowski.pdf file_size: 3408944 relation: main_file success: 1 file_date_updated: 2024-01-23T08:10:00Z has_accepted_license: '1' intvolume: ' 2' issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '08' oa: 1 oa_version: Published Version publication: Evolutionary Journal of the Linnean Society publication_identifier: eissn: - 2752-938X publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Whole-genome phylogeography of the intertidal snail Littorina saxatilis tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2023' ... --- _id: '14831' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original author: - first_name: Yann full_name: Sakref, Yann last_name: Sakref - first_name: Maitane full_name: Muñoz Basagoiti, Maitane id: 1a8a7950-82cd-11ed-bd4f-9624c913a607 last_name: Muñoz Basagoiti orcid: 0000-0003-1483-1457 - first_name: Zorana full_name: Zeravcic, Zorana last_name: Zeravcic - first_name: Olivier full_name: Rivoire, Olivier last_name: Rivoire citation: 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 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 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. 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. 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. 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. date_created: 2024-01-18T07:47:11Z date_published: 2023-12-13T00:00:00Z date_updated: 2024-01-23T07:58:27Z day: '13' department: - _id: AnSa doi: 10.1021/acs.jpcb.3c04627 external_id: arxiv: - '2312.15940' isi: - '001134068000001' intvolume: ' 127' isi: 1 issue: '51' keyword: - Materials Chemistry - Surfaces - Coatings and Films - Physical and Theoretical Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2312.15940 month: '12' oa: 1 oa_version: Preprint page: 10950-10959 publication: The Journal of Physical Chemistry B publication_identifier: eissn: - 1520-5207 issn: - 1520-6106 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: On kinetic constraints that catalysis imposes on elementary processes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 127 year: '2023' ... --- _id: '14844' 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.' 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). article_processing_charge: No article_type: original author: - first_name: Ali full_name: Azadbakht, Ali last_name: Azadbakht - first_name: Billie full_name: Meadowcroft, Billie id: a4725fd6-932b-11ed-81e2-c098c7f37ae1 last_name: Meadowcroft orcid: 0000-0003-3441-1337 - first_name: Juraj full_name: Majek, Juraj id: 3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1 last_name: Majek - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Daniela J. full_name: Kraft, Daniela J. last_name: Kraft citation: 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 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 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. 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. 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. short: A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical Journal (n.d.). date_created: 2024-01-21T23:00:56Z date_published: 2023-12-29T00:00:00Z date_updated: 2024-01-23T09:26:35Z day: '29' ddc: - '570' department: - _id: AnSa doi: 10.1016/j.bpj.2023.12.020 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.bpj.2023.12.020 month: '12' oa: 1 oa_version: Published Version project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Biophysical Journal publication_identifier: eissn: - 1542-0086 issn: - 0006-3495 publication_status: inpress publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Nonadditivity in interactions between three membrane-wrapped colloidal spheres tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14861' abstract: - lang: eng text: Cover Page article_number: ' e202304138' article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Mélanie full_name: Berbon, Mélanie last_name: Berbon - first_name: Alicia full_name: Vallet, Alicia last_name: Vallet - first_name: Axelle full_name: Grelard, Axelle last_name: Grelard - first_name: Estelle full_name: Morvan, Estelle last_name: Morvan - first_name: Benjamin full_name: Bardiaux, Benjamin last_name: Bardiaux - first_name: Roman full_name: Lichtenecker, Roman last_name: Lichtenecker - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Antoine full_name: Loquet, Antoine last_name: Loquet - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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' 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' 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.' 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.' 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.' 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.' date_created: 2024-01-22T11:54:34Z date_published: 2023-05-02T00:00:00Z date_updated: 2024-01-23T08:48:14Z day: '02' department: - _id: PaSc doi: 10.1002/anie.202304138 intvolume: ' 62' issue: '19' keyword: - General Chemistry - Catalysis language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/anie.202304138 month: '05' oa: 1 oa_version: Published Version publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley related_material: link: - relation: translation url: https://doi.org/10.1002/ange.202304138 record: - id: '12675' relation: other status: public status: public title: 'Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues' type: other_academic_publication user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2023' ... --- _id: '14849' 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. 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." article_processing_charge: No article_type: original author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 - first_name: Yuanyuan full_name: Xu, Yuanyuan last_name: Xu citation: 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 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 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. 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. 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. 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. short: G. Cipolloni, L. Erdös, D.J. Schröder, Y. Xu, The Annals of Probability 51 (2023) 2192–2242. date_created: 2024-01-22T08:08:41Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-23T10:56:30Z day: '01' department: - _id: LaEr doi: 10.1214/23-aop1643 ec_funded: 1 external_id: arxiv: - '2206.04448' intvolume: ' 51' issue: '6' keyword: - Statistics - Probability and Uncertainty - Statistics and Probability language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2206.04448 month: '11' oa: 1 oa_version: Preprint page: 2192-2242 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: The Annals of Probability publication_identifier: issn: - 0091-1798 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' status: public title: On the rightmost eigenvalue of non-Hermitian random matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2023' ... --- _id: '14835' 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. 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. article_number: e202219314 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Mélanie full_name: Berbon, Mélanie last_name: Berbon - first_name: Alicia full_name: Vallet, Alicia last_name: Vallet - first_name: Axelle full_name: Grelard, Axelle last_name: Grelard - first_name: Estelle full_name: Morvan, Estelle last_name: Morvan - first_name: Benjamin full_name: Bardiaux, Benjamin last_name: Bardiaux - first_name: Roman full_name: Lichtenecker, Roman last_name: Lichtenecker - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Antoine full_name: Loquet, Antoine last_name: Loquet - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 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 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 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. 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. 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. 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). date_created: 2024-01-18T10:01:01Z date_published: 2023-05-02T00:00:00Z date_updated: 2024-01-23T12:23:35Z day: '02' ddc: - '540' department: - _id: PaSc doi: 10.1002/ange.202219314 file: - access_level: open_access checksum: 98e68d370159f7be52a3d7c8a8ee1198 content_type: application/pdf creator: dernst date_created: 2024-01-23T08:57:01Z date_updated: 2024-01-23T08:57:01Z file_id: '14876' file_name: 2023_AngewChem_Becker.pdf file_size: 1004676 relation: main_file success: 1 file_date_updated: 2024-01-23T08:57:01Z has_accepted_license: '1' intvolume: ' 135' issue: '19' keyword: - General Medicine language: - iso: ger month: '05' oa: 1 oa_version: Published Version publication: Angewandte Chemie publication_identifier: eissn: - 1521-3757 issn: - 0044-8249 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2023' ... --- _id: '14853' abstract: - lang: eng 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. alternative_title: - Geophysical Monograph Series article_processing_charge: No author: - first_name: Jan O. full_name: Haerter, Jan O. last_name: Haerter - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 citation: 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' 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 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. 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. 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.' 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. date_created: 2024-01-22T08:23:16Z date_published: 2023-12-15T00:00:00Z date_updated: 2024-01-23T12:40:36Z day: '15' department: - _id: CaMu doi: 10.1002/9781119700357.ch8 editor: - first_name: Sylvia full_name: Sullivan, Sylvia last_name: Sullivan - first_name: Corinna full_name: Hoose, Corinna last_name: Hoose language: - iso: eng month: '12' oa_version: None page: 179-193 publication: Clouds and Their Climatic Impacts publication_identifier: eisbn: - '9781119700357' isbn: - '9781119700319' issn: - 2328-8779 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Mechanisms for the Self‐Organization of Tropical Deep Convection type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14847' abstract: - lang: eng 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. alternative_title: - New Developments in NMR article_processing_charge: No author: - first_name: I. full_name: Sučec, I. last_name: Sučec - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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' 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 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. 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. 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.' 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. date_created: 2024-01-22T08:04:57Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-23T11:50:10Z day: '01' department: - _id: PaSc doi: 10.1039/bk9781839165986-00136 editor: - first_name: Sebastian full_name: Hiller, Sebastian last_name: Hiller - first_name: Maili full_name: Liu, Maili last_name: Liu - first_name: Lichun full_name: He, Lichun last_name: He intvolume: ' 29' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.26434/chemrxiv-2023-rpn28 month: '11' oa: 1 oa_version: Preprint page: 136-161 publication: Biophysics of Molecular Chaperones publication_identifier: eisbn: - '9781839165993' isbn: - '9781839162824' publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2023' ... --- _id: '14848' abstract: - lang: eng 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. alternative_title: - New Developments in NMR article_processing_charge: No author: - first_name: F. full_name: Wruck, F. last_name: Wruck - first_name: Mario full_name: Avellaneda Sarrió, Mario id: DC4BA84C-56E6-11EA-AD5D-348C3DDC885E last_name: Avellaneda Sarrió orcid: 0000-0001-6406-524X - first_name: M. M. full_name: Naqvi, M. M. last_name: Naqvi - first_name: E. J. full_name: Koers, E. J. last_name: Koers - first_name: K. full_name: Till, K. last_name: Till - first_name: L. full_name: Gross, L. last_name: Gross - first_name: F. full_name: Moayed, F. last_name: Moayed - first_name: A. full_name: Roland, A. last_name: Roland - first_name: L. W. H. J. full_name: Heling, L. W. H. J. last_name: Heling - first_name: A. full_name: Mashaghi, A. last_name: Mashaghi - first_name: S. J. full_name: Tans, S. J. last_name: Tans citation: 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' 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 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. 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. 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.' 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. date_created: 2024-01-22T08:07:02Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-23T12:01:53Z day: '01' department: - _id: MiSi doi: 10.1039/bk9781839165986-00278 editor: - first_name: Sebastian full_name: Hiller, Sebastian last_name: Hiller - first_name: Maili full_name: Liu, Maili last_name: Liu - first_name: Lichun full_name: He, Lichun last_name: He intvolume: ' 29' language: - iso: eng month: '11' oa_version: None page: 278-318 publication: Biophysics of Molecular Chaperones publication_identifier: eisbn: - '9781839165993' isbn: - '9781839162824' publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: Probing Single Chaperone Substrates type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2023' ... --- _id: '14854' abstract: - lang: eng 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." article_processing_charge: No article_type: original author: - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: 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 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 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. 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. 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. short: D.J. Mitrouskas, R. Seiringer, Pure and Applied Analysis 5 (2023) 973–1008. date_created: 2024-01-22T08:24:23Z date_published: 2023-12-15T00:00:00Z date_updated: 2024-01-23T12:55:12Z day: '15' department: - _id: RoSe doi: 10.2140/paa.2023.5.973 intvolume: ' 5' issue: '4' keyword: - General Medicine language: - iso: eng month: '12' oa_version: None page: 973-1008 publication: Pure and Applied Analysis publication_identifier: issn: - 2578-5885 - 2578-5893 publication_status: published publisher: Mathematical Sciences Publishers quality_controlled: '1' status: public title: Ubiquity of bound states for the strongly coupled polaron type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2023' ... --- _id: '14872' abstract: - lang: eng 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. article_number: LM1F.3 article_processing_charge: No author: - first_name: Rishabh full_name: Sahu, Rishabh id: 47D26E34-F248-11E8-B48F-1D18A9856A87 last_name: Sahu orcid: 0000-0001-6264-2162 - first_name: Liu full_name: Qiu, Liu last_name: Qiu - first_name: William J full_name: Hease, William J id: 29705398-F248-11E8-B48F-1D18A9856A87 last_name: Hease orcid: 0000-0001-9868-2166 - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 - first_name: Yuri full_name: Minoguchi, Yuri last_name: Minoguchi - first_name: Peter full_name: Rabl, Peter last_name: Rabl - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: 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' 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' 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. ieee: R. Sahu et al., “Entangling microwaves and telecom wavelength light,” in Frontiers in Optics + Laser Science 2023, Tacoma, WA, United States, 2023. 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. 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. conference: end_date: 2023-10-12 location: Tacoma, WA, United States name: Laser Science start_date: 2023-10-09 date_created: 2024-01-22T12:29:41Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-24T08:43:28Z day: '01' department: - _id: JoFi doi: 10.1364/ls.2023.lm1f.3 language: - iso: eng month: '10' oa_version: None publication: Frontiers in Optics + Laser Science 2023 publication_identifier: isbn: - '9781957171296' publication_status: published publisher: Optica Publishing Group quality_controlled: '1' status: public title: Entangling microwaves and telecom wavelength light type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14867' abstract: - lang: eng 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. 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" article_processing_charge: No author: - first_name: Michael full_name: Anastos, Michael id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb last_name: Anastos citation: 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' 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' 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. 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. 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.' 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. conference: end_date: 2023-09-01 location: Prague, Czech Republic name: 'EUROCOMB: European Conference on Combinatorics, Graph Theory and Applications' start_date: 2023-08-28 date_created: 2024-01-22T12:20:15Z date_published: 2023-09-01T00:00:00Z date_updated: 2024-01-24T09:38:44Z day: '01' ddc: - '510' department: - _id: MaKw doi: 10.5817/cz.muni.eurocomb23-005 ec_funded: 1 external_id: arxiv: - '2209.09860' file: - access_level: open_access checksum: fb1d9a1e7389d90ec0e5e76934373cf8 content_type: application/pdf creator: dernst date_created: 2024-01-24T09:34:43Z date_updated: 2024-01-24T09:34:43Z file_id: '14881' file_name: 2023_Eurocomb_Anastos.pdf file_size: 464230 relation: main_file success: 1 file_date_updated: 2024-01-24T09:34:43Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 36-41 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications publication_identifier: eissn: - 2788-3116 publication_status: published publisher: Masaryk University Press quality_controlled: '1' status: public title: Constructing Hamilton cycles and perfect matchings efficiently tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14864' acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Starting Grant (No. 949120). article_number: '6166' article_processing_charge: No author: - first_name: Andrea full_name: Stöllner, Andrea id: 4bdcf7f6-eb97-11eb-a6c2-9981bbdc3bed last_name: Stöllner orcid: 0000-0002-0464-8440 - first_name: Isaac C full_name: Lenton, Isaac C id: a550210f-223c-11ec-8182-e2d45e817efb last_name: Lenton orcid: 0000-0002-5010-6984 - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: 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' 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' 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. 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. 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. 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. Waitukaitis, in:, EGU General Assembly 2023, European Geosciences Union, 2023. conference: end_date: 2023-04-28 location: Vienna, Austria & Virtual name: EGU General Assembly start_date: 2023-04-23 date_created: 2024-01-22T12:09:07Z date_published: 2023-04-23T00:00:00Z date_updated: 2024-01-24T11:21:42Z day: '23' ddc: - '530' department: - _id: CaMu - _id: ScWa doi: 10.5194/egusphere-egu23-6166 ec_funded: 1 file: - access_level: open_access checksum: 8d6ddbb359e584b156f991f00196d86b content_type: application/pdf creator: dernst date_created: 2024-01-23T13:00:26Z date_updated: 2024-01-23T13:00:26Z file_id: '14880' file_name: 2023_EGU_Stoellner.pdf file_size: 419736 relation: main_file success: 1 file_date_updated: 2024-01-23T13:00:26Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication: EGU General Assembly 2023 publication_status: published publisher: European Geosciences Union status: public title: Measuring spontaneous charging of single aerosol particles tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14862' article_number: ckad160.597 article_processing_charge: No author: - first_name: Simon full_name: Rella, Simon id: B4765ACA-AA38-11E9-AC9A-0930E6697425 last_name: Rella - first_name: Y full_name: Kulikova, Y last_name: Kulikova - first_name: Aygul full_name: Minnegalieva, Aygul id: 87DF77F0-1D9A-11EA-B6AE-CE443DDC885E last_name: Minnegalieva - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: 'Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies prevent the emergence of vaccine resistance. In: European Journal of Public Health. Vol 33. Oxford University Press; 2023. doi:10.1093/eurpub/ckad160.597' apa: Rella, S., Kulikova, Y., Minnegalieva, A., & Kondrashov, F. (2023). Complex vaccination strategies prevent the emergence of vaccine resistance. In European Journal of Public Health (Vol. 33). Oxford University Press. https://doi.org/10.1093/eurpub/ckad160.597 chicago: Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In European Journal of Public Health, Vol. 33. Oxford University Press, 2023. https://doi.org/10.1093/eurpub/ckad160.597. ieee: S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in European Journal of Public Health, 2023, vol. 33, no. Supplement_2. ista: Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. 2023. Complex vaccination strategies prevent the emergence of vaccine resistance. European Journal of Public Health. vol. 33, ckad160.597. mla: Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” European Journal of Public Health, vol. 33, no. Supplement_2, ckad160.597, Oxford University Press, 2023, doi:10.1093/eurpub/ckad160.597. short: S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023. date_created: 2024-01-22T12:02:28Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-24T11:16:09Z day: '01' ddc: - '570' department: - _id: GaTk doi: 10.1093/eurpub/ckad160.597 file: - access_level: open_access checksum: 98706755bb4cc5d553818ade7660a7d2 content_type: application/pdf creator: dernst date_created: 2024-01-24T11:12:33Z date_updated: 2024-01-24T11:12:33Z file_id: '14882' file_name: 2023_EurJourPublicHealth_Rella.pdf file_size: 71057 relation: main_file success: 1 file_date_updated: 2024-01-24T11:12:33Z has_accepted_license: '1' intvolume: ' 33' issue: Supplement_2 keyword: - Public Health - Environmental and Occupational Health language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: European Journal of Public Health publication_identifier: eissn: - 1464-360X issn: - 1101-1262 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Complex vaccination strategies prevent the emergence of vaccine resistance tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2023' ... --- _id: '14863' article_number: EGU23-6157 article_processing_charge: No author: - first_name: Andrea full_name: Polesello, Andrea id: 74c777f4-32da-11ee-b498-874db0835561 last_name: Polesello - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Claudia full_name: Pasquero, Claudia last_name: Pasquero - first_name: Agostino N. full_name: Meroni, Agostino N. last_name: Meroni citation: ama: 'Polesello A, Muller CJ, Pasquero C, Meroni AN. 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' 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. 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. 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. short: A. Polesello, C.J. Muller, C. Pasquero, A.N. Meroni, in:, EGU General Assembly 2023, European Geosciences Union, 2023. conference: end_date: 2023-04-28 location: Vienna, Austria & Virtual name: EGU General Assembly start_date: 2023-04-23 date_created: 2024-01-22T12:08:12Z date_published: 2023-04-13T00:00:00Z date_updated: 2024-01-24T11:25:07Z day: '13' ddc: - '550' department: - _id: CaMu - _id: GradSch doi: 10.5194/egusphere-egu23-6157 file: - access_level: open_access checksum: 8cb88c1bc80ccee328478a62064d98f7 content_type: application/pdf creator: dernst date_created: 2024-01-24T11:19:54Z date_updated: 2024-01-24T11:19:54Z file_id: '14883' file_name: 2023_EGU_Polesello.pdf file_size: 296769 relation: main_file success: 1 file_date_updated: 2024-01-24T11:19:54Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: EGU General Assembly 2023 publication_status: published publisher: European Geosciences Union status: public title: Intensification mechanisms of tropical cyclones tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14732' 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.' article_processing_charge: No author: - first_name: Oluwafunmilola O full_name: Olusanya, Oluwafunmilola O id: 41AD96DC-F248-11E8-B48F-1D18A9856A87 last_name: Olusanya orcid: 0000-0003-1971-8314 - first_name: Kseniia full_name: Khudiakova, Kseniia id: 4E6DC800-AE37-11E9-AC72-31CAE5697425 last_name: Khudiakova orcid: 0000-0002-6246-1465 - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva citation: 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 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 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. ieee: O. O. Olusanya, K. Khudiakova, and H. Sachdeva, “Genetic load, eco-evolutionary feedback and extinction in a metapopulation,” bioRxiv. . ista: Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv, 10.1101/2023.12.02.569702. mla: Olusanya, Oluwafunmilola O., et al. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, doi:10.1101/2023.12.02.569702. short: O.O. Olusanya, K. Khudiakova, H. Sachdeva, BioRxiv (n.d.). date_created: 2024-01-04T09:35:54Z date_published: 2023-12-04T00:00:00Z date_updated: 2024-01-26T12:00:53Z day: '04' department: - _id: NiBa - _id: JaMa doi: 10.1101/2023.12.02.569702 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2023.12.02.569702v1 month: '12' oa: 1 oa_version: Preprint project: - _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8 grant_number: P32896 name: Causes and consequences of population fragmentation - _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8 grant_number: '26293' name: The impact of deleterious mutations on small populations - _id: 34c872fe-11ca-11ed-8bc3-8534b82131e6 grant_number: '26380' name: Polygenic Adaptation in a Metapopulation publication: bioRxiv publication_status: submitted related_material: record: - id: '14711' relation: dissertation_contains status: public status: public title: Genetic load, eco-evolutionary feedback and extinction in a metapopulation tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13049' 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." acknowledged_ssus: - _id: M-Shop 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). article_number: '142' article_processing_charge: No article_type: original author: - first_name: Marco full_name: Freire, Marco last_name: Freire - first_name: Manas full_name: Bhargava, Manas id: FF8FA64C-AA6A-11E9-99AD-50D4E5697425 last_name: Bhargava orcid: 0009-0007-6138-6890 - first_name: Camille full_name: Schreck, Camille id: 2B14B676-F248-11E8-B48F-1D18A9856A87 last_name: Schreck - first_name: Pierre-Alexandre full_name: Hugron, Pierre-Alexandre last_name: Hugron - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Sylvain full_name: Lefebvre, Sylvain last_name: Lefebvre citation: 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' 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' 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.' 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.' 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.' 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). conference: end_date: 2023-08-10 location: Los Angeles, CA, United States name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2023-08-06 date_created: 2023-05-22T08:37:04Z date_published: 2023-07-26T00:00:00Z date_updated: 2024-01-29T10:30:49Z day: '26' ddc: - '006' department: - _id: GradSch - _id: BeBi doi: 10.1145/3592411 ec_funded: 1 external_id: isi: - '001044671300108' file: - access_level: open_access checksum: a0b0ba3b36f43a94388e8824613d812a content_type: application/pdf creator: dernst date_created: 2023-06-19T11:02:23Z date_updated: 2023-06-19T11:02:23Z file_id: '13156' file_name: 2023_ACMToG_Freire.pdf file_size: 78940724 relation: main_file success: 1 - access_level: open_access checksum: b9206bbb67af82df49b7e7cdbde3410c content_type: application/pdf creator: dernst date_created: 2023-06-20T12:20:51Z date_updated: 2023-06-20T12:20:51Z file_id: '13157' file_name: 2023_ACMToG_SuppMaterial_Freire.pdf file_size: 34345905 relation: main_file success: 1 file_date_updated: 2023-06-20T12:20:51Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '4' keyword: - PCB design and layout - Mesh geometry models language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: 'PCBend: Light up your 3D shapes with foldable circuit boards' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2023' ... --- _id: '13212' abstract: - lang: eng 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. acknowledged_ssus: - _id: LifeSc - _id: Bio 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). article_processing_charge: Yes (via OA deal) article_type: letter_note author: - first_name: Huihuang full_name: Chen, Huihuang id: 83c96512-15b2-11ec-abd3-b7eede36184f last_name: Chen - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Minxia full_name: Zou, Minxia id: 5c243f41-03f3-11ec-841c-96faf48a7ef9 last_name: Zou - first_name: Linlin full_name: Qi, Linlin id: 44B04502-A9ED-11E9-B6FC-583AE6697425 last_name: Qi orcid: 0000-0001-5187-8401 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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 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 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. 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. 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. 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. date_created: 2023-07-12T07:32:46Z date_published: 2023-07-01T00:00:00Z date_updated: 2024-01-29T10:38:57Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.molp.2023.06.007 ec_funded: 1 external_id: isi: - '001044410900001' pmid: - '37393433' file: - access_level: open_access checksum: 6012b7e4a2f680ee6c1f84001e2b945f content_type: application/pdf creator: dernst date_created: 2024-01-29T10:37:05Z date_updated: 2024-01-29T10:37:05Z file_id: '14894' file_name: 2023_MolecularPlant_Chen.pdf file_size: 1000871 relation: main_file success: 1 file_date_updated: 2024-01-29T10:37:05Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1117-1119 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Molecular Plant publication_identifier: eissn: - 1674-2052 issn: - 1752-9867 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' scopus_import: '1' status: public title: Distinct functions of TIR1 and AFB1 receptors in auxin signalling. tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2023' ... --- _id: '12984' abstract: - lang: eng 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. acknowledged_ssus: - _id: M-Shop 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). article_number: '67' article_processing_charge: No article_type: original author: - first_name: Michael full_name: Piovarci, Michael id: 62E473F4-5C99-11EA-A40E-AF823DDC885E last_name: Piovarci orcid: 0000-0002-5062-4474 - first_name: Alexandre full_name: Chapiro, Alexandre last_name: Chapiro - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: 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' 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' 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.' 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.' ista: 'Piovarci M, Chapiro A, Bickel B. 2023. Skin-Screen: A computational fabrication framework for color tattoos. Transactions on Graphics. 42(4), 67.' 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). conference: end_date: 2023-08-10 location: Los Angeles, CA, United States name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2023-08-06 date_created: 2023-05-16T09:39:14Z date_published: 2023-07-26T00:00:00Z date_updated: 2024-01-29T10:27:23Z day: '26' ddc: - '004' department: - _id: BeBi doi: 10.1145/3592432 external_id: isi: - '001044671300033' file: - access_level: open_access checksum: 5f0a6867689e025a661bd0b4fd90b821 content_type: application/pdf creator: mpiovarc date_created: 2023-05-16T09:38:25Z date_updated: 2023-05-16T09:38:25Z file_id: '12985' file_name: Piovarci2023.pdf file_size: 30817343 relation: main_file success: 1 file_date_updated: 2023-05-16T09:38:25Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '4' keyword: - appearance - modeling - reproduction - tattoo - skin color - gamut mapping - ink-optimization - prosthetic language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: eb901961-77a9-11ec-83b8-f5c883a62027 grant_number: M03319 name: Perception-Aware Appearance Fabrication publication: Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: 'Skin-Screen: A computational fabrication framework for color tattoos' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2023' ... --- _id: '14892' abstract: - lang: eng 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.' article_processing_charge: No author: - first_name: Douglas full_name: Feitosa Tomé, Douglas id: 0eed2d40-3d48-11ec-8d38-f789cc2e40b2 last_name: Feitosa Tomé citation: ama: 'Feitosa Tomé D. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation. 2023. doi:10.5281/ZENODO.10251087' apa: 'Feitosa Tomé, D. (2023). douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation. Zenodo. https://doi.org/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.' ieee: 'D. Feitosa Tomé, “douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation.” Zenodo, 2023.' ista: 'Feitosa Tomé D. 2023. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation, Zenodo, 10.5281/ZENODO.10251087.' mla: 'Feitosa Tomé, Douglas. Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation. Zenodo, 2023, doi:10.5281/ZENODO.10251087.' short: D. Feitosa Tomé, (2023). date_created: 2024-01-29T09:06:43Z date_published: 2023-12-02T00:00:00Z date_updated: 2024-01-29T09:22:01Z day: '02' ddc: - '570' department: - _id: TiVo doi: 10.5281/ZENODO.10251087 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.10251087 month: '12' oa: 1 oa_version: None publisher: Zenodo related_material: record: - id: '14887' relation: used_in_publication status: public status: public title: 'douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14032' abstract: - lang: eng 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. acknowledged_ssus: - _id: M-Shop - _id: NanoFab 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.). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Soham full_name: Mukhopadhyay, Soham id: FDE60288-A89D-11E9-947F-1AF6E5697425 last_name: Mukhopadhyay - first_name: Jorden L full_name: Senior, Jorden L id: 5479D234-2D30-11EA-89CC-40953DDC885E last_name: Senior orcid: 0000-0002-0672-9295 - first_name: Jaime full_name: Saez Mollejo, Jaime id: e0390f72-f6e0-11ea-865d-862393336714 last_name: Saez Mollejo - first_name: Denise full_name: Puglia, Denise id: 4D495994-AE37-11E9-AC72-31CAE5697425 last_name: Puglia orcid: 0000-0003-1144-2763 - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 citation: 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 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 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. ieee: S. Mukhopadhyay et al., “Superconductivity from a melted insulator in Josephson junction arrays,” Nature Physics, vol. 19. Springer Nature, pp. 1630–1635, 2023. 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. 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. 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. date_created: 2023-08-11T07:41:17Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-29T11:27:49Z day: '01' ddc: - '530' department: - _id: GradSch - _id: AnHi - _id: JoFi doi: 10.1038/s41567-023-02161-w ec_funded: 1 external_id: isi: - '001054563800006' file: - access_level: open_access checksum: 1fc86d71bfbf836e221c1e925343adc5 content_type: application/pdf creator: dernst date_created: 2024-01-29T11:25:38Z date_updated: 2024-01-29T11:25:38Z file_id: '14899' file_name: 2023_NaturePhysics_Mukhopadhyay.pdf file_size: 1977706 relation: main_file success: 1 file_date_updated: 2024-01-29T11:25:38Z has_accepted_license: '1' intvolume: ' 19' isi: 1 keyword: - General Physics and Astronomy language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1630-1635 project: - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter - _id: bd5b4ec5-d553-11ed-ba76-a6eedb083344 name: Protected states of quantum matter publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Superconductivity from a melted insulator in Josephson junction arrays tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2023' ... --- _id: '13266' abstract: - lang: eng 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. 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.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Linlin full_name: Qi, Linlin id: 44B04502-A9ED-11E9-B6FC-583AE6697425 last_name: Qi orcid: 0000-0001-5187-8401 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 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 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 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. 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. ista: Qi L, Friml J. 2023. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 240(2), 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. short: L. Qi, J. Friml, New Phytologist 240 (2023) 489–495. date_created: 2023-07-23T22:01:13Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-29T11:21:55Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1111/nph.19123 external_id: isi: - '001026321500001' pmid: - '37434303' file: - access_level: open_access checksum: 6d9bbd45b8e7bb3ceee2586d447bacb2 content_type: application/pdf creator: dernst date_created: 2024-01-29T11:21:43Z date_updated: 2024-01-29T11:21:43Z file_id: '14898' file_name: 2023_NewPhytologist_Qi.pdf file_size: 974464 relation: main_file success: 1 file_date_updated: 2024-01-29T11:21:43Z has_accepted_license: '1' intvolume: ' 240' isi: 1 issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 489-495 pmid: 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 publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Tale of cAMP as a second messenger in auxin signaling and beyond tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 240 year: '2023' ... --- _id: '13136' abstract: - lang: eng 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. 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.' article_number: '100459' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Thomas full_name: Minchington, Thomas id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f last_name: Minchington - first_name: Stefanie full_name: Rus, Stefanie id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87 last_name: Rus orcid: 0000-0001-8703-1093 - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: 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 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 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. 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. 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. 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). date_created: 2023-06-18T22:00:46Z date_published: 2023-09-01T00:00:00Z date_updated: 2024-01-29T11:07:47Z day: '01' ddc: - '570' department: - _id: AnKi doi: 10.1016/j.coisb.2023.100459 file: - access_level: open_access checksum: 8a75c4e29fd9b62e3c50663c2265b173 content_type: application/pdf creator: dernst date_created: 2024-01-29T11:06:45Z date_updated: 2024-01-29T11:06:45Z file_id: '14896' file_name: 2023_CurrOpSystBioloy_Minchington.pdf file_size: 598842 relation: main_file success: 1 file_date_updated: 2024-01-29T11:06:45Z has_accepted_license: '1' intvolume: ' 35' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' 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 - _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A grant_number: SC19-011 name: The regulatory logic of pattern formation in the vertebrate dorsal neural tube publication: Current Opinion in Systems Biology publication_identifier: eissn: - 2452-3100 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Control of tissue dimensions in the developing neural tube and somites tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2023' ... --- _id: '13135' abstract: - lang: eng 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. 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). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Antonio full_name: Agresti, Antonio id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72 last_name: Agresti orcid: 0000-0002-9573-2962 - first_name: Mark full_name: Veraar, Mark last_name: Veraar citation: 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' 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' 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.' 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.' 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.' 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.' short: A. Agresti, M. Veraar, Journal of Differential Equations 368 (2023) 247–300. date_created: 2023-06-18T22:00:45Z date_published: 2023-09-25T00:00:00Z date_updated: 2024-01-29T11:04:41Z day: '25' ddc: - '510' department: - _id: JuFi doi: 10.1016/j.jde.2023.05.038 ec_funded: 1 external_id: isi: - '001019018700001' file: - access_level: open_access checksum: 246b703b091dfe047bfc79abf0891a63 content_type: application/pdf creator: dernst date_created: 2024-01-29T11:03:09Z date_updated: 2024-01-29T11:03:09Z file_id: '14895' file_name: 2023_JourDifferentialEquations_Agresti.pdf file_size: 834638 relation: main_file success: 1 file_date_updated: 2024-01-29T11:03:09Z has_accepted_license: '1' intvolume: ' 368' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 247-300 project: - _id: 0aa76401-070f-11eb-9043-b5bb049fa26d call_identifier: H2020 grant_number: '948819' name: Bridging Scales in Random Materials publication: Journal of Differential Equations publication_identifier: eissn: - 1090-2732 issn: - 0022-0396 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 368 year: '2023' ... --- _id: '13270' abstract: - lang: eng 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." acknowledgement: Open access funding provided by the Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Florestan R full_name: Brunck, Florestan R id: 6ab6e556-f394-11eb-9cf6-9dfb78f00d8d last_name: Brunck 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 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 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. 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. ista: Brunck FR. 2023. Iterated medial triangle subdivision in surfaces of constant curvature. Discrete and Computational Geometry. 70(3), 1059–1089. 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. date_created: 2023-07-23T22:01:14Z date_published: 2023-07-05T00:00:00Z date_updated: 2024-01-29T11:16:16Z day: '05' ddc: - '510' department: - _id: UlWa doi: 10.1007/s00454-023-00500-5 external_id: arxiv: - '2107.04112' isi: - '001023742800003' file: - access_level: open_access checksum: 865e68daafdd4edcfc280172ec50f5ea content_type: application/pdf creator: dernst date_created: 2024-01-29T11:15:22Z date_updated: 2024-01-29T11:15:22Z file_id: '14897' file_name: 2023_DiscreteComputGeometry_Brunck.pdf file_size: 1466020 relation: main_file success: 1 file_date_updated: 2024-01-29T11:15:22Z has_accepted_license: '1' intvolume: ' 70' isi: 1 issue: '3' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1059-1089 publication: Discrete and Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Iterated medial triangle subdivision in surfaces of constant curvature tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 70 year: '2023' ... --- _id: '13269' 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. 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]." article_processing_charge: No article_type: original author: - first_name: Nikita full_name: Polyanskii, Nikita last_name: Polyanskii - first_name: Yihan full_name: Zhang, Yihan id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c last_name: Zhang orcid: 0000-0002-6465-6258 citation: 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 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 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. 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. 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. short: N. Polyanskii, Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 6340–6357. date_created: 2023-07-23T22:01:14Z date_published: 2023-07-04T00:00:00Z date_updated: 2024-01-29T11:10:54Z day: '04' department: - _id: MaMo doi: 10.1109/TIT.2023.3292219 external_id: arxiv: - '2105.01427' isi: - '001069680100011' intvolume: ' 69' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2105.01427 month: '07' oa: 1 oa_version: Preprint page: 6340-6357 publication: IEEE Transactions on Information Theory publication_identifier: eissn: - 1557-9654 issn: - 0018-9448 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Codes for the Z-channel type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 69 year: '2023' ... --- _id: '13209' 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. 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. " article_number: '100632' article_processing_charge: Yes article_type: original author: - first_name: Jing full_name: Xia, Jing last_name: Xia - first_name: Mengjuan full_name: Kong, Mengjuan last_name: Kong - first_name: Zhisen full_name: Yang, Zhisen last_name: Yang - first_name: Lianghanxiao full_name: Sun, Lianghanxiao last_name: Sun - first_name: Yakun full_name: Peng, Yakun last_name: Peng - first_name: Yanbo full_name: Mao, Yanbo last_name: Mao - first_name: Hong full_name: Wei, Hong last_name: Wei - first_name: Wei full_name: Ying, Wei last_name: Ying - first_name: Yongxiao full_name: Gao, Yongxiao last_name: Gao - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jianping full_name: Weng, Jianping last_name: Weng - first_name: Xin full_name: Liu, Xin last_name: Liu - first_name: Linfeng full_name: Sun, Linfeng last_name: Sun - first_name: Shutang full_name: Tan, Shutang last_name: Tan citation: 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 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 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. 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. 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. 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). date_created: 2023-07-12T07:32:00Z date_published: 2023-11-13T00:00:00Z date_updated: 2024-01-30T10:55:34Z day: '13' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.xplc.2023.100632 external_id: isi: - '001113003000001' pmid: - '37254481' file: - access_level: open_access checksum: f8ef92af6096834f91ce38587fb1db9f content_type: application/pdf creator: dernst date_created: 2024-01-30T10:54:40Z date_updated: 2024-01-30T10:54:40Z file_id: '14900' file_name: 2023_PlantCommunications_Xia.pdf file_size: 1434862 relation: main_file success: 1 file_date_updated: 2024-01-30T10:54:40Z has_accepted_license: '1' intvolume: ' 4' isi: 1 issue: '6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Plant Communications publication_identifier: eissn: - 2590-3462 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' status: public title: Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2023' ... --- _id: '13971' abstract: - lang: eng 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. 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. article_processing_charge: Yes article_type: original author: - first_name: Daniel full_name: Grober, Daniel id: abdfc56f-34fb-11ee-bd33-fd766fce5a99 last_name: Grober - first_name: Ivan full_name: Palaia, Ivan id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa last_name: Palaia orcid: ' 0000-0002-8843-9485 ' - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 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 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 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. 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. 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. 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. short: D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature Physics 19 (2023) 1680–1688. date_created: 2023-08-06T22:01:11Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-30T12:26:55Z day: '01' ddc: - '530' department: - _id: EdHa - _id: AnSa - _id: JePa doi: 10.1038/s41567-023-02136-x ec_funded: 1 external_id: isi: - '001037346400005' file: - access_level: open_access checksum: 7e282c2ebc0ac82125a04f6b4742d4c1 content_type: application/pdf creator: dernst date_created: 2024-01-30T12:26:08Z date_updated: 2024-01-30T12:26:08Z file_id: '14906' file_name: 2023_NaturePhysics_Grober.pdf file_size: 6365607 relation: main_file success: 1 file_date_updated: 2024-01-30T12:26:08Z has_accepted_license: '1' intvolume: ' 19' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1680-1688 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Unconventional colloidal aggregation in chiral bacterial baths tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2023' ... --- _id: '10551' 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.' 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)." article_number: '76' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Federico full_name: Cornalba, Federico id: 2CEB641C-A400-11E9-A717-D712E6697425 last_name: Cornalba orcid: 0000-0002-6269-5149 - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: 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 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 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. 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. 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. 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). date_created: 2021-12-16T12:16:03Z date_published: 2023-08-04T00:00:00Z date_updated: 2024-01-30T12:10:10Z day: '04' ddc: - '510' department: - _id: JuFi doi: 10.1007/s00205-023-01903-7 ec_funded: 1 external_id: arxiv: - '2109.06500' isi: - '001043086800001' file: - access_level: open_access checksum: 4529eeff170b6745a461d397ee611b5a content_type: application/pdf creator: dernst date_created: 2024-01-30T12:09:34Z date_updated: 2024-01-30T12:09:34Z file_id: '14904' file_name: 2023_ArchiveRationalMech_Cornalba.pdf file_size: 1851185 relation: main_file success: 1 file_date_updated: 2024-01-30T12:09:34Z has_accepted_license: '1' intvolume: ' 247' isi: 1 issue: '5' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: Archive for Rational Mechanics and Analysis publication_identifier: eissn: - 1432-0673 issn: - 0003-9527 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 247 year: '2023' ...