TY - JOUR AB - The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous bouncing or steady-state floating. The effect embodies an unexplored interplay between thermodynamics, elasticity, and lubrication: despite being observed, its basic theoretical description remains a challenge. Here, we provide a theory of elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to the hot surface. By contrast, we discover an elasticity-dominated regime where the heavier the solid, the higher it floats. This geometry-governed behavior is reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this elastic regime is characterized by Hertzian behavior of the solid’s underbelly and derive how the float height scales with materials parameters. Introducing a dimensionless elastic Leidenfrost number, we capture the crossover between rigid and Hertzian behavior. Our results provide theoretical underpinning for recent experiments, and point to the design of novel soft machines. AU - Binysh, Jack AU - Chakraborty, Indrajit AU - Chubynsky, Mykyta V. AU - Diaz Melian, Vicente L AU - Waitukaitis, Scott R AU - Sprittles, James E. AU - Souslov, Anton ID - 14514 IS - 16 JF - Physical Review Letters SN - 0031-9007 TI - Modeling Leidenfrost levitation of soft elastic solids VL - 131 ER - TY - GEN AB - see Readme file AU - Binysh, Jack AU - Chakraborty, Indrajit AU - Chubynsky, Mykyta AU - Diaz Melian, Vicente L AU - Waitukaitis, Scott R AU - Sprittles, James AU - Souslov, Anton ID - 14523 TI - SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1 ER - TY - CONF AB - We consider bidding games, a class of two-player zero-sum graph games. The game proceeds as follows. Both players have bounded budgets. A token is placed on a vertex of a graph, in each turn the players simultaneously submit bids, and the higher bidder moves the token, where we break bidding ties in favor of Player 1. Player 1 wins the game iff the token visits a designated target vertex. We consider, for the first time, poorman discrete-bidding in which the granularity of the bids is restricted and the higher bid is paid to the bank. Previous work either did not impose granularity restrictions or considered Richman bidding (bids are paid to the opponent). While the latter mechanisms are technically more accessible, the former is more appealing from a practical standpoint. Our study focuses on threshold budgets, which is the necessary and sufficient initial budget required for Player 1 to ensure winning against a given Player 2 budget. We first show existence of thresholds. In DAGs, we show that threshold budgets can be approximated with error bounds by thresholds under continuous-bidding and that they exhibit a periodic behavior. We identify closed-form solutions in special cases. We implement and experiment with an algorithm to find threshold budgets. AU - Avni, Guy AU - Meggendorfer, Tobias AU - Sadhukhan, Suman AU - Tkadlec, Josef AU - Zikelic, Dorde ID - 14518 SN - 0922-6389 T2 - Frontiers in Artificial Intelligence and Applications TI - Reachability poorman discrete-bidding games VL - 372 ER - TY - JOUR AB - Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death. AU - Degen, Morris AU - Santos, José Carlos AU - Pluhackova, Kristyna AU - Cebrero, Gonzalo AU - Ramos, Saray AU - Jankevicius, Gytis AU - Hartenian, Ella AU - Guillerm, Undina AU - Mari, Stefania A. AU - Kohl, Bastian AU - Müller, Daniel J. AU - Schanda, Paul AU - Maier, Timm AU - Perez, Camilo AU - Sieben, Christian AU - Broz, Petr AU - Hiller, Sebastian ID - 13096 JF - Nature SN - 0028-0836 TI - Structural basis of NINJ1-mediated plasma membrane rupture in cell death VL - 618 ER - TY - JOUR AB - A series of triarylamines was synthesised and screened for their suitability as catholytes in redox flow batteries using cyclic voltammetry (CV). Tris(4-aminophenyl)amine was found to be the strongest candidate. Solubility and initial electrochemical performance were promising; however, polymerisation was observed during electrochemical cycling leading to rapid capacity fade prescribed to a loss of accessible active material and the limitation of ion transport processes within the cell. A mixed electrolyte system of H3PO4 and HCl was found to inhibit polymerisation producing oligomers that consumed less active material reducing rates of degradation in the redox flow battery. Under these conditions Coulombic efficiency improved by over 4 %, the maximum number of cycles more than quadrupled and an additional theoretical capacity of 20 % was accessed. This paper is, to our knowledge, the first example of triarylamines as catholytes in all-aqueous redox flow batteries and emphasises the impact supporting electrolytes can have on electrochemical performance. AU - Farag, Nadia L. AU - Jethwa, Rajesh B AU - Beardmore, Alice E. AU - Insinna, Teresa AU - O'Keefe, Christopher A. AU - Klusener, Peter A.A. AU - Grey, Clare P. AU - Wright, Dominic S. ID - 13041 IS - 13 JF - ChemSusChem SN - 1864-5631 TI - Triarylamines as catholytes in aqueous organic redox flow batteries VL - 16 ER - TY - JOUR AB - Under high pressures and temperatures, molecular systems with substantial polarization charges, such as ammonia and water, are predicted to form superionic phases and dense fluid states with dissociating molecules and high electrical conductivity. This behaviour potentially plays a role in explaining the origin of the multipolar magnetic fields of Uranus and Neptune, whose mantles are thought to result from a mixture of H2O, NH3 and CH4 ices. Determining the stability domain, melting curve and electrical conductivity of these superionic phases is therefore crucial for modelling planetary interiors and dynamos. Here we report the melting curve of superionic ammonia up to 300 GPa from laser-driven shock compression of pre-compressed samples and atomistic calculations. We show that ammonia melts at lower temperatures than water above 100 GPa and that fluid ammonia’s electrical conductivity exceeds that of water at conditions predicted by hot, super-adiabatic models for Uranus and Neptune, and enhances the conductivity in their fluid water-rich dynamo layers. AU - Hernandez, J.-A. AU - Bethkenhagen, Mandy AU - Ninet, S. AU - French, M. AU - Benuzzi-Mounaix, A. AU - Datchi, F. AU - Guarguaglini, M. AU - Lefevre, F. AU - Occelli, F. AU - Redmer, R. AU - Vinci, T. AU - Ravasio, A. ID - 13118 JF - Nature Physics SN - 1745-2473 TI - Melting curve of superionic ammonia at planetary interior conditions VL - 19 ER - TY - JOUR AB - A density wave (DW) is a fundamental type of long-range order in quantum matter tied to self-organization into a crystalline structure. The interplay of DW order with superfluidity can lead to complex scenarios that pose a great challenge to theoretical analysis. In the past decades, tunable quantum Fermi gases have served as model systems for exploring the physics of strongly interacting fermions, including most notably magnetic ordering1, pairing and superfluidity2, and the crossover from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here, we realize a Fermi gas featuring both strong, tunable contact interactions and photon-mediated, spatially structured long-range interactions in a transversely driven high-finesse optical cavity. Above a critical long-range interaction strength, DW order is stabilized in the system, which we identify via its superradiant light-scattering properties. We quantitatively measure the variation of the onset of DW order as the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field theory. The atomic DW susceptibility varies over an order of magnitude upon tuning the strength and the sign of the long-range interactions below the self-ordering threshold, demonstrating independent and simultaneous control over the contact and long-range interactions. Therefore, our experimental setup provides a fully tunable and microscopically controllable platform for the experimental study of the interplay of superfluidity and DW order. AU - Helson, Victor AU - Zwettler, Timo AU - Mivehvar, Farokh AU - Colella, Elvia AU - Roux, Kevin Etienne Robert AU - Konishi, Hideki AU - Ritsch, Helmut AU - Brantut, Jean Philippe ID - 13119 JF - Nature SN - 0028-0836 TI - Density-wave ordering in a unitary Fermi gas with photon-mediated interactions VL - 618 ER - TY - JOUR AB - This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground-state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem. AU - Feliciangeli, Dario AU - Gerolin, Augusto AU - Portinale, Lorenzo ID - 12911 IS - 4 JF - Journal of Functional Analysis SN - 0022-1236 TI - A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature VL - 285 ER - TY - JOUR AB - In this note we study the eigenvalue growth of infinite graphs with discrete spectrum. We assume that the corresponding Dirichlet forms satisfy certain Sobolev-type inequalities and that the total measure is finite. In this sense, the associated operators on these graphs display similarities to elliptic operators on bounded domains in the continuum. Specifically, we prove lower bounds on the eigenvalue growth and show by examples that corresponding upper bounds cannot be established. AU - Hua, Bobo AU - Keller, Matthias AU - Schwarz, Michael AU - Wirth, Melchior ID - 13177 IS - 8 JF - Proceedings of the American Mathematical Society SN - 0002-9939 TI - Sobolev-type inequalities and eigenvalue growth on graphs with finite measure VL - 151 ER - TY - JOUR AB - n the dynamic minimum set cover problem, the challenge is to minimize the update time while guaranteeing a close-to-optimal min{O(log n), f} approximation factor. (Throughout, n, m, f , and C are parameters denoting the maximum number of elements, the number of sets, the frequency, and the cost range.) In the high-frequency range, when f = Ω(log n) , this was achieved by a deterministic O(log n) -approximation algorithm with O(f log n) amortized update time by Gupta et al. [Online and dynamic algorithms for set cover, in Proceedings STOC 2017, ACM, pp. 537–550]. In this paper we consider the low-frequency range, when f = O(log n) , and obtain deterministic algorithms with a (1 + ∈)f -approximation ratio and the following guarantees on the update time. (1) O ((f/∈)-log(Cn)) amortized update time: Prior to our work, the best approximation ratio guaranteed by deterministic algorithms was O(f2) of Bhattacharya, Henzinger, and Italiano [Design of dynamic algorithms via primal-dual method, in Proceedings ICALP 2015, Springer, pp. 206–218]. In contrast, the only result with O(f) -approximation was that of Abboud et al. [Dynamic set cover: Improved algorithms and lower bounds, in Proceedings STOC 2019, ACM, pp. 114–125], who designed a randomized (1+∈)f -approximation algorithm with amortized update time. (2) O(f2/∈3 + (f/∈2).logC) amortized update time: This result improves the above update time bound for most values of f in the low-frequency range, i.e., f=o(log n) . It is also the first result that is independent of m and n. It subsumes the constant amortized update time of Bhattacharya and Kulkarni [Deterministically maintaining a (2 + ∈) -approximate minimum vertex cover in O(1/∈2) amortized update time, in Proceedings SODA 2019, SIAM, pp. 1872–1885] for unweighted dynamic vertex cover (i.e., when f = 2 and C = 1). (3) O((f/∈3).log2(Cn)) worst-case update time: No nontrivial worst-case update time was previously known for the dynamic set cover problem. Our bound subsumes and improves by a logarithmic factor the O(log3n/poly (∈)) worst-case update time for the unweighted dynamic vertex cover problem (i.e., when f = 2 and C =1) of Bhattacharya, Henzinger, and Nanongkai [Fully dynamic approximate maximum matching and minimum vertex cover in O(log3)n worst case update time, in Proceedings SODA 2017, SIAM, pp. 470–489]. We achieve our results via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. Prior work in dynamic algorithms that employs the primal-dual approach uses a local update scheme that maintains relaxed complementary slackness conditions for every set. For our first result we use instead a global update scheme that does not always maintain complementary slackness conditions. For our second result we combine the global and the local update schema. To achieve our third result we use a hierarchy of background schedulers. It is an interesting open question whether this background scheduler technique can also be used to transform algorithms with amortized running time bounds into algorithms with worst-case running time bounds. AU - Bhattacharya, Sayan AU - Henzinger, Monika H AU - Nanongkai, Danupon AU - Wu, Xiaowei ID - 14558 IS - 5 JF - SIAM Journal on Computing SN - 0097-5397 TI - Deterministic near-optimal approximation algorithms for dynamic set cover VL - 52 ER - TY - CONF AB - We consider the problem of learning control policies in discrete-time stochastic systems which guarantee that the system stabilizes within some specified stabilization region with probability 1. Our approach is based on the novel notion of stabilizing ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome the limitation of methods proposed in previous works whose applicability is restricted to systems in which the stabilizing region cannot be left once entered under any control policy. We present a learning procedure that learns a control policy together with an sRSM that formally certifies probability 1 stability, both learned as neural networks. We show that this procedure can also be adapted to formally verifying that, under a given Lipschitz continuous control policy, the stochastic system stabilizes within some stabilizing region with probability 1. Our experimental evaluation shows that our learning procedure can successfully learn provably stabilizing policies in practice. AU - Ansaripour, Matin AU - Chatterjee, Krishnendu AU - Henzinger, Thomas A AU - Lechner, Mathias AU - Zikelic, Dorde ID - 14559 SN - 0302-9743 T2 - 21st International Symposium on Automated Technology for Verification and Analysis TI - Learning provably stabilizing neural controllers for discrete-time stochastic systems VL - 14215 ER - TY - JOUR AB - The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations around the meanfield limit for large-scale particle systems in both particle density and momentum density. We focus on the following two aspects. Firstly, we set up a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide suitable definitions of numerical fluxes at the interface of the mesh elements which are consistent with the wave-type nature of the RIDK model and grant stability of the simulations, and we quantify the rate of convergence in mean square to the continuous RIDK model. Secondly, we introduce modifications of the RIDK model in order to preserve positivity of the density (such a feature only holds in a “high-probability sense” for the original RIDK model). By means of numerical simulations, we show that the modifications lead to physically realistic and positive density profiles. In one case, subject to additional regularity constraints, we also prove positivity. Finally, we present an application of our methodology to a system of diffusing and reacting particles. Our Python code is available in open-source format. AU - Cornalba, Federico AU - Shardlow, Tony ID - 14554 IS - 5 JF - ESAIM: Mathematical Modelling and Numerical Analysis SN - 2822-7840 TI - The regularised inertial Dean' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime VL - 57 ER - TY - JOUR AB - Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach. AU - Berdan, Emma L. AU - Barton, Nicholas H AU - Butlin, Roger AU - Charlesworth, Brian AU - Faria, Rui AU - Fragata, Inês AU - Gilbert, Kimberly J. AU - Jay, Paul AU - Kapun, Martin AU - Lotterhos, Katie E. AU - Mérot, Claire AU - Durmaz Mitchell, Esra AU - Pascual, Marta AU - Peichel, Catherine L. AU - Rafajlović, Marina AU - Westram, Anja M AU - Schaeffer, Stephen W. AU - Johannesson, Kerstin AU - Flatt, Thomas ID - 14556 JF - Journal of Evolutionary Biology SN - 1010-061X TI - How chromosomal inversions reorient the evolutionary process ER - TY - JOUR AB - The intricate regulatory processes behind actin polymerization play a crucial role in cellular biology, including essential mechanisms such as cell migration or cell division. However, the self-organizing principles governing actin polymerization are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky (BZ) reaction, a classic and well understood chemical oscillator known for its self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing actin. While the BZ reaction originates from the domain of inorganic chemistry, it shares remarkable similarities with actin polymerization, including the characteristic propagating waves, which are influenced by geometry and external fields, and the emergent collective behavior. Starting with a general description of emerging patterns, we elaborate on single droplets or cell-level dynamics, the influence of geometric confinements and conclude with collective interactions. Comparing these two systems sheds light on the universal nature of self-organization principles in both living and inanimate systems. AU - Riedl, Michael AU - Sixt, Michael K ID - 14555 JF - Frontiers in Cell and Developmental Biology TI - The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction VL - 11 ER - TY - JOUR AB - The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders. AU - Kaiyrzhanov, Rauan AU - Rad, Aboulfazl AU - Lin, Sheng-Jia AU - Bertoli-Avella, Aida AU - Kallemeijn, Wouter W AU - Godwin, Annie AU - Zaki, Maha S AU - Huang, Kevin AU - Lau, Tracy AU - Petree, Cassidy AU - Efthymiou, Stephanie AU - Ghayoor Karimiani, Ehsan AU - Hempel, Maja AU - Normand, Elizabeth A AU - Rudnik-Schöneborn, Sabine AU - Schatz, Ulrich A AU - Baggelaar, Marc P AU - Ilyas, Muhammad AU - Sultan, Tipu AU - Alvi, Javeria Raza AU - Ganieva, Manizha AU - Fowler, Ben AU - Aanicai, Ruxandra AU - Akay Tayfun, Gulsen AU - Al Saman, Abdulaziz AU - Alswaid, Abdulrahman AU - Amiri, Nafise AU - Asilova, Nilufar AU - Shotelersuk, Vorasuk AU - Yeetong, Patra AU - Azam, Matloob AU - Babaei, Meisam AU - Bahrami Monajemi, Gholamreza AU - Mohammadi, Pouria AU - Samie, Saeed AU - Banu, Selina Husna AU - Basto, Jorge Pinto AU - Kortüm, Fanny AU - Bauer, Mislen AU - Bauer, Peter AU - Beetz, Christian AU - Garshasbi, Masoud AU - Hameed Issa, Awatif AU - Eyaid, Wafaa AU - Ahmed, Hind AU - Hashemi, Narges AU - Hassanpour, Kazem AU - Herman, Isabella AU - Ibrohimov, Sherozjon AU - Abdul-Majeed, Ban A AU - Imdad, Maria AU - Isrofilov, Maksudjon AU - Kaiyal, Qassem AU - Khan, Suliman AU - Kirmse, Brian AU - Koster, Janet AU - Lourenço, Charles Marques AU - Mitani, Tadahiro AU - Moldovan, Oana AU - Murphy, David AU - Najafi, Maryam AU - Pehlivan, Davut AU - Rocha, Maria Eugenia AU - Salpietro, Vincenzo AU - Schmidts, Miriam AU - Shalata, Adel AU - Mahroum, Mohammad AU - Talbeya, Jawabreh Kassem AU - Taylor, Robert W AU - Vazquez, Dayana AU - Vetro, Annalisa AU - Waterham, Hans R AU - Zaman, Mashaya AU - Schrader, Tina A AU - Chung, Wendy K AU - Guerrini, Renzo AU - Lupski, James R AU - Gleeson, Joseph AU - Suri, Mohnish AU - Jamshidi, Yalda AU - Bhatia, Kailash P AU - Vona, Barbara AU - Schrader, Michael AU - Severino, Mariasavina AU - Guille, Matthew AU - Tate, Edward W AU - Varshney, Gaurav K AU - Houlden, Henry AU - Maroofian, Reza ID - 14543 JF - Brain KW - Neurology (clinical) SN - 0006-8950 TI - Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders ER - TY - JOUR AB - It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit. AU - Henheik, Sven Joscha AU - Lauritsen, Asbjørn Bækgaard AU - Roos, Barbara ID - 14542 JF - Reviews in Mathematical Physics SN - 0129-055X TI - Universality in low-dimensional BCS theory ER - TY - JOUR AB - Quantum state tomography is an essential component of modern quantum technology. In application to continuous-variable harmonic-oscillator systems, such as the electromagnetic field, existing tomography methods typically reconstruct the state in discrete bases, and are hence limited to states with relatively low amplitudes and energies. Here, we overcome this limitation by utilizing a feed-forward neural network to obtain the density matrix directly in the continuous position basis. An important benefit of our approach is the ability to choose specific regions in the phase space for detailed reconstruction. This results in a relatively slow scaling of the amount of resources required for the reconstruction with the state amplitude, and hence allows us to dramatically increase the range of amplitudes accessible with our method. AU - Fedotova, Ekaterina AU - Kuznetsov, Nikolai AU - Tiunov, Egor AU - Ulanov, A. E. AU - Lvovsky, A. I. ID - 14553 IS - 4 JF - Physical Review A SN - 2469-9926 TI - Continuous-variable quantum tomography of high-amplitude states VL - 108 ER - TY - JOUR AB - Motivated by a problem posed in [10], we investigate the closure operators of the category SLatt of join semilattices and its subcategory SLattO of join semilattices with bottom element. In particular, we show that there are only finitely many closure operators of both categories, and provide a complete classification. We use this result to deduce the known fact that epimorphisms of SLatt and SLattO are surjective. We complement the paper with two different proofs of this result using either generators or Isbell’s zigzag theorem. AU - Dikranjan, D. AU - Giordano Bruno, A. AU - Zava, Nicolò ID - 14557 IS - S1 JF - Quaestiones Mathematicae SN - 1607-3606 TI - Epimorphisms and closure operators of categories of semilattices VL - 46 ER - TY - JOUR AB - Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth. AU - Robinson, M. L. AU - Hahn, P. G. AU - Inouye, B. D. AU - Underwood, N. AU - Whitehead, S. R. AU - Abbott, K. C. AU - Bruna, E. M. AU - Cacho, N. I. AU - Dyer, L. A. AU - Abdala-Roberts, L. AU - Allen, W. J. AU - Andrade, J. F. AU - Angulo, D. F. AU - Anjos, D. AU - Anstett, D. N. AU - Bagchi, R. AU - Bagchi, S. AU - Barbosa, M. AU - Barrett, S. AU - Baskett, Carina AU - Ben-Simchon, E. AU - Bloodworth, K. J. AU - Bronstein, J. L. AU - Buckley, Y. M. AU - Burghardt, K. T. AU - Bustos-Segura, C. AU - Calixto, E. S. AU - Carvalho, R. L. AU - Castagneyrol, B. AU - Chiuffo, M. C. AU - Cinoğlu, D. AU - Cinto Mejía, E. AU - Cock, M. C. AU - Cogni, R. AU - Cope, O. L. AU - Cornelissen, T. AU - Cortez, D. R. AU - Crowder, D. W. AU - Dallstream, C. AU - Dáttilo, W. AU - Davis, J. K. AU - Dimarco, R. D. AU - Dole, H. E. AU - Egbon, I. N. AU - Eisenring, M. AU - Ejomah, A. AU - Elderd, B. D. AU - Endara, M. J. AU - Eubanks, M. D. AU - Everingham, S. E. AU - Farah, K. N. AU - Farias, R. P. AU - Fernandes, A. P. AU - Fernandes, G. W. AU - Ferrante, M. AU - Finn, A. AU - Florjancic, G. A. AU - Forister, M. L. AU - Fox, Q. N. AU - Frago, E. AU - França, F. M. AU - Getman-Pickering, A. S. AU - Getman-Pickering, Z. AU - Gianoli, E. AU - Gooden, B. AU - Gossner, M. M. AU - Greig, K. A. AU - Gripenberg, S. AU - Groenteman, R. AU - Grof-Tisza, P. AU - Haack, N. AU - Hahn, L. AU - Haq, S. M. AU - Helms, A. M. AU - Hennecke, J. AU - Hermann, S. L. AU - Holeski, L. M. AU - Holm, S. AU - Hutchinson, M. C. AU - Jackson, E. E. AU - Kagiya, S. AU - Kalske, A. AU - Kalwajtys, M. AU - Karban, R. AU - Kariyat, R. AU - Keasar, T. AU - Kersch-Becker, M. F. AU - Kharouba, H. M. AU - Kim, T. N. AU - Kimuyu, D. M. AU - Kluse, J. AU - Koerner, S. E. AU - Komatsu, K. J. AU - Krishnan, S. AU - Laihonen, M. AU - Lamelas-López, L. AU - Lascaleia, M. C. AU - Lecomte, N. AU - Lehn, C. R. AU - Li, X. AU - Lindroth, R. L. AU - Lopresti, E. F. AU - Losada, M. AU - Louthan, A. M. AU - Luizzi, V. J. AU - Lynch, S. C. AU - Lynn, J. S. AU - Lyon, N. J. AU - Maia, L. F. AU - Maia, R. A. AU - Mannall, T. L. AU - Martin, B. S. AU - Massad, T. J. AU - Mccall, A. C. AU - Mcgurrin, K. AU - Merwin, A. C. AU - Mijango-Ramos, Z. AU - Mills, C. H. AU - Moles, A. T. AU - Moore, C. M. AU - Moreira, X. AU - Morrison, C. R. AU - Moshobane, M. C. AU - Muola, A. AU - Nakadai, R. AU - Nakajima, K. AU - Novais, S. AU - Ogbebor, C. O. AU - Ohsaki, H. AU - Pan, V. S. AU - Pardikes, N. A. AU - Pareja, M. AU - Parthasarathy, N. AU - Pawar, R. R. AU - Paynter, Q. AU - Pearse, I. S. AU - Penczykowski, R. M. AU - Pepi, A. A. AU - Pereira, C. C. AU - Phartyal, S. S. AU - Piper, F. I. AU - Poveda, K. AU - Pringle, E. G. AU - Puy, J. AU - Quijano, T. AU - Quintero, C. AU - Rasmann, S. AU - Rosche, C. AU - Rosenheim, L. Y. AU - Rosenheim, J. A. AU - Runyon, J. B. AU - Sadeh, A. AU - Sakata, Y. AU - Salcido, D. M. AU - Salgado-Luarte, C. AU - Santos, B. A. AU - Sapir, Y. AU - Sasal, Y. AU - Sato, Y. AU - Sawant, M. AU - Schroeder, H. AU - Schumann, I. AU - Segoli, M. AU - Segre, H. AU - Shelef, O. AU - Shinohara, N. AU - Singh, R. P. AU - Smith, D. S. AU - Sobral, M. AU - Stotz, G. C. AU - Tack, A. J.M. AU - Tayal, M. AU - Tooker, J. F. AU - Torrico-Bazoberry, D. AU - Tougeron, K. AU - Trowbridge, A. M. AU - Utsumi, S. AU - Uyi, O. AU - Vaca-Uribe, J. L. AU - Valtonen, A. AU - Van Dijk, L. J.A. AU - Vandvik, V. AU - Villellas, J. AU - Waller, L. P. AU - Weber, M. G. AU - Yamawo, A. AU - Yim, S. AU - Zarnetske, P. L. AU - Zehr, L. N. AU - Zhong, Z. AU - Wetzel, W. C. ID - 14552 IS - 6671 JF - Science TI - Plant size, latitude, and phylogeny explain within-population variability in herbivory VL - 382 ER - TY - JOUR AB - Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale. AU - Briffa, Amy AU - Hollwey, Elizabeth AU - Shahzad, Zaigham AU - Moore, Jonathan D. AU - Lyons, David B. AU - Howard, Martin AU - Zilberman, Daniel ID - 14551 IS - 11 JF - Cell Systems SN - 2405-4712 TI - Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations VL - 14 ER - TY - GEN AB - This is associated with our paper "Plant size, latitude, and phylogeny explain within-population variability in herbivory" published in Science. AU - Wetzel, William ID - 14579 TI - HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0 ER - TY - JOUR AB - Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration. AU - Fäßler, Florian AU - Javoor, Manjunath AU - Datler, Julia AU - Döring, Hermann AU - Hofer, Florian AU - Dimchev, Georgi A AU - Hodirnau, Victor-Valentin AU - Faix, Jan AU - Rottner, Klemens AU - Schur, Florian KM ID - 12334 IS - 3 JF - Science Advances KW - Multidisciplinary SN - 2375-2548 TI - ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning VL - 9 ER - TY - DATA AB - Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration. AU - Schur, Florian KM ID - 14562 TI - Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning" ER - TY - COMP AB - A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner. AU - Dimchev, Georgi A AU - Amiri, Behnam AU - Fäßler, Florian AU - Falcke, Martin AU - Schur, Florian KM ID - 14502 KW - cryo-electron tomography KW - actin cytoskeleton KW - toolbox TI - Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data ER - TY - JOUR AB - Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the amoebaDictyostelium discoideum, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease. AU - Kroll, Janina AU - Hauschild, Robert AU - Kuznetcov, Arthur AU - Stefanowski, Kasia AU - Hermann, Monika D. AU - Merrin, Jack AU - Shafeek, Lubuna B AU - Müller-Taubenberger, Annette AU - Renkawitz, Jörg ID - 13342 JF - EMBO Journal SN - 0261-4189 TI - Adaptive pathfinding by nucleokinesis during amoeboid migration ER - TY - JOUR AB - AbstractEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3–7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host. AU - Bussi, Claudio AU - Mangiarotti, Agustín AU - Vanhille-Campos, Christian Eduardo AU - Aylan, Beren AU - Pellegrino, Enrica AU - Athanasiadi, Natalia AU - Fearns, Antony AU - Rodgers, Angela AU - Franzmann, Titus M. AU - Šarić, Anđela AU - Dimova, Rumiana AU - Gutierrez, Maximiliano G. ID - 14610 JF - Nature KW - Multidisciplinary SN - 0028-0836 TI - Stress granules plug and stabilize damaged endolysosomal membranes ER - TY - DATA AB - Data related to the following paper: "Stress granules plug and stabilize damaged endolysosomal membranes" (https://doi.org/10.1038/s41586-023-06726-w) Abstract: Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in "Stress granules plug and stabilize damaged endolysosomal membranes", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w. AU - Vanhille-Campos, Christian Eduardo AU - Šarić, Anđela ID - 14472 TI - Stress granules plug and stabilize damaged endolysosomal membranes ER - TY - JOUR AB - Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing. AU - Cikes, Domagoj AU - Elsayad, Kareem AU - Sezgin, Erdinc AU - Koitai, Erika AU - Ferenc, Torma AU - Orthofer, Michael AU - Yarwood, Rebecca AU - Heinz, Leonhard X. AU - Sedlyarov, Vitaly AU - Darwish-Miranda, Nasser AU - Taylor, Adrian AU - Grapentine, Sophie AU - al-Murshedi, Fathiya AU - Abot, Anne AU - Weidinger, Adelheid AU - Kutchukian, Candice AU - Sanchez, Colline AU - Cronin, Shane J. F. AU - Novatchkova, Maria AU - Kavirayani, Anoop AU - Schuetz, Thomas AU - Haubner, Bernhard AU - Haas, Lisa AU - Hagelkruys, Astrid AU - Jackowski, Suzanne AU - Kozlov, Andrey AU - Jacquemond, Vincent AU - Knauf, Claude AU - Superti-Furga, Giulio AU - Rullman, Eric AU - Gustafsson, Thomas AU - McDermot, John AU - Lowe, Martin AU - Radak, Zsolt AU - Chamberlain, Jeffrey S. AU - Bakovic, Marica AU - Banka, Siddharth AU - Penninger, Josef M. ID - 12747 JF - Nature Metabolism KW - Cell Biology KW - Physiology (medical) KW - Endocrinology KW - Diabetes and Metabolism KW - Internal Medicine SN - 2522-5812 TI - PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing VL - 5 ER - TY - JOUR AB - The phonon transport mechanisms and ultralow lattice thermal conductivities (κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein, we study the lattice dynamics and thermal property of AgX under the framework of perturbation theory and the two-channel Wigner thermal transport model based on accurate machine learning potentials. We find that an accurate extraction of the third-order atomic force constants from largely displaced configurations is significant for the calculation of the κL of AgX, and the coherence thermal transport is also non-negligible. In AgI, however, the calculated κL still considerably overestimates the experimental values even including four-phonon scatterings. Molecular dynamics (MD) simulations using machine learning potential suggest an important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency phonon linewidths of AgI at room temperature, which can be related to the simultaneous restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated using MD phonon lifetimes including full-order lattice anharmonicity shows a better agreement with experiments. AU - Ouyang, Niuchang AU - Zeng, Zezhu AU - Wang, Chen AU - Wang, Qi AU - Chen, Yue ID - 14605 IS - 17 JF - Physical Review B SN - 2469-9950 TI - Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I) VL - 108 ER - TY - CONF AB - Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted party. DKG is an essential building block to many decentralized protocols such as randomness beacons, threshold signatures, Byzantine consensus, and multiparty computation. While significant progress has been made recently, existing asynchronous DKG constructions are inefficient when the reconstruction threshold is larger than one-third of the total nodes. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t + 1 nodes that can tolerate up to t malicious nodes and support any reconstruction threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where κ is the security parameter, and only assumes the hardness of the Discrete Logarithm. The core ingredient of our ADKG protocol is an asynchronous protocol to secret share a random polynomial of degree ℓ ≥ t, which has other applications, such as asynchronous proactive secret sharing and asynchronous multiparty computation. We implement our high-threshold ADKG protocol and evaluate it using a network of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over the state-of-the-art. AU - Das, Sourav AU - Xiang, Zhuolun AU - Kokoris Kogias, Eleftherios AU - Ren, Ling ID - 14609 SN - 9781713879497 T2 - 32nd USENIX Security Symposium TI - Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling VL - 8 ER - TY - JOUR AB - Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances. AU - Reinhardt, Aleks AU - Chew, Pin Yu AU - Cheng, Bingqing ID - 14603 IS - 18 JF - Journal of Chemical Physics SN - 0021-9606 TI - A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals VL - 159 ER - TY - JOUR AB - Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders. AU - Toups, Melissa A AU - Vicoso, Beatriz ID - 14604 IS - 11 JF - Evolution TI - The X chromosome of insects likely predates the origin of class Insecta VL - 77 ER - TY - GEN AB - Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders. AU - Toups, Melissa A AU - Vicoso, Beatriz ID - 14616 TI - The X chromosome of insects likely predates the origin of Class Insecta ER - TY - GEN AB - Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders. AU - Toups, Melissa A AU - Vicoso, Beatriz ID - 14617 TI - The X chromosome of insects likely predates the origin of Class Insecta ER - TY - GEN AB - Data underlying the publication "A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals" (DOI https://doi.org/10.1063/5.0173341). AU - Cheng, Bingqing ID - 14619 TI - BingqingCheng/solubility: V1.0 ER - TY - JOUR AB - Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized. AU - Khouider, B. AU - GOSWAMI, BIDYUT B AU - Phani, R. AU - Majda, A. J. ID - 14564 IS - 11 JF - Journal of Advances in Modeling Earth Systems KW - General Earth and Planetary Sciences KW - Environmental Chemistry KW - Global and Planetary Change TI - A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model VL - 15 ER - TY - JOUR AB - Experiments have shown that charge distributions of granular materials are non-Gaussian, with broad tails that indicate many particles with high charge. This observation has consequences for the behavior of granular materials in many settings, and may bear relevance to the underlying charge transfer mechanism. However, there is the unaddressed possibility that broad tails arise due to experimental uncertainties, as determining the shapes of tails is nontrivial. Here we show that measurement uncertainties can indeed account for most of the tail broadening previously observed. The clue that reveals this is that distributions are sensitive to the electric field at which they are measured; ones measured at low (high) fields have larger (smaller) tails. Accounting for sources of uncertainty, we reproduce this broadening in silico. Finally, we use our results to back out the true charge distribution without broadening, which we find is still non-Guassian, though with substantially different behavior at the tails and indicating significantly fewer highly charged particles. These results have implications in many natural settings where electrostatic interactions, especially among highly charged particles, strongly affect granular behavior. AU - Mujica, Nicolás AU - Waitukaitis, Scott R ID - 12789 IS - 3 JF - Physical Review E SN - 2470-0045 TI - Accurate determination of the shapes of granular charge distributions VL - 107 ER - TY - CONF AB - We consider a natural problem dealing with weighted packet selection across a rechargeable link, which e.g., finds applications in cryptocurrency networks. The capacity of a link (u, v) is determined by how much nodes u and v allocate for this link. Specifically, the input is a finite ordered sequence of packets that arrive in both directions along a link. Given (u, v) and a packet of weight x going from u to v, node u can either accept or reject the packet. If u accepts the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity on (u, v) increases by x. If a node rejects the packet, this will entail a cost affinely linear in the weight of the packet. A link is “rechargeable” in the sense that the total capacity of the link has to remain constant, but the allocation of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions. The goal is to minimise the sum of the capacity injected into the link and the cost of rejecting packets. We show that the problem is NP-hard, but can be approximated efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0. . AU - Schmid, Stefan AU - Svoboda, Jakub AU - Yeo, Michelle X ID - 13238 SN - 0302-9743 T2 - SIROCCO 2023: Structural Information and Communication Complexity TI - Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation VL - 13892 ER - TY - THES AB - Payment channel networks are a promising approach to improve the scalability bottleneck of cryptocurrencies. Two design principles behind payment channel networks are efficiency and privacy. Payment channel networks improve efficiency by allowing users to transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding the lengthy process of consensus on the blockchain. Transacting over payment channel networks also improves privacy as these transactions are not broadcast to the blockchain. Despite the influx of recent protocols built on top of payment channel networks and their analysis, a common shortcoming of many of these protocols is that they typically focus only on either improving efficiency or privacy, but not both. Another limitation on the efficiency front is that the models used to model actions, costs and utilities of users are limited or come with unrealistic assumptions. This thesis aims to address some of the shortcomings of recent protocols and algorithms on payment channel networks, particularly in their privacy and efficiency aspects. We first present a payment route discovery protocol based on hub labelling and private information retrieval that hides the route query and is also efficient. We then present a rebalancing protocol that formulates the rebalancing problem as a linear program and solves the linear program using multiparty computation so as to hide the channel balances. The rebalancing solution as output by our protocol is also globally optimal. We go on to develop more realistic models of the action space, costs, and utilities of both existing and new users that want to join the network. In each of these settings, we also develop algorithms to optimise the utility of these users with good guarantees on the approximation and competitive ratios. AU - Yeo, Michelle X ID - 14506 SN - 2663 - 337X TI - Advances in efficiency and privacy in payment channel network analysis ER - TY - CONF AB - Payment channel networks (PCNs) are a promising solution to the scalability problem of cryptocurrencies. Any two users connected by a payment channel in the network can theoretically send an unbounded number of instant, costless transactions between them. Users who are not directly connected can also transact with each other in a multi-hop fashion. In this work, we study the incentive structure behind the creation of payment channel networks, particularly from the point of view of a single user that wants to join the network. We define a utility function for a new user in terms of expected revenue, expected fees, and the cost of creating channels, and then provide constant factor approximation algorithms that optimise the utility function given a certain budget. Additionally, we take a step back from a single user to the whole network and examine the parameter spaces under which simple graph topologies form a Nash equilibrium. AU - Avarikioti, Zeta AU - Lizurej, Tomasz AU - Michalak, Tomasz AU - Yeo, Michelle X ID - 14490 SN - 9798350339864 T2 - 43rd International Conference on Distributed Computing Systems TI - Lightning creation games VL - 2023 ER - TY - THES AB - Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self–sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub–population in the developing cortex. AU - Riedl, Michael ID - 12726 SN - 2663-337X TI - Synchronization in collectively moving active matter ER - TY - THES AB - Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex. AU - Riedl, Michael ID - 14530 KW - Synchronization KW - Collective Movement KW - Active Matter KW - Cell Migration KW - Active Colloids SN - 2663 - 337X TI - Synchronization in collectively moving active matter ER - TY - THES AB - Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation. Despite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood. In this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. The second focuses on a technological application, a gate-tunable Josephson parametric amplifier. In the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well. We embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance. The behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \pm ip$ pairing in InAs. Measuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory. We observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory. In contrast, the data can be captured quantitatively by fitting to a two-component model. We find the evidence of the intraband $p \pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\mathrm{T}$. From the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined. By systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle. Strong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data. In the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element. The device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator. By applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz. Modelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage. We observed gate-tunable Kerr nonlinearity qualitatively in line with expectation. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency. In general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared. The noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier. As a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account. We found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier. AU - Phan, Duc T ID - 14547 KW - superconductor-semiconductor KW - superconductivity KW - Al KW - InAs KW - p-wave KW - superconductivity KW - JPA KW - microwave SN - 2663 - 337X TI - Resonant microwave spectroscopy of Al-InAs ER - TY - JOUR AB - We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency. AU - Phan, Duc T AU - Falthansl-Scheinecker, Paul AU - Mishra, Umang AU - Strickland, W. M. AU - Langone, D. AU - Shabani, J. AU - Higginbotham, Andrew P ID - 13264 IS - 6 JF - Physical Review Applied TI - Gate-tunable superconductor-semiconductor parametric amplifier VL - 19 ER - TY - GEN AB - Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins. AU - Gnyliukh, Nataliia AU - Johnson, Alexander J AU - Nagel, Marie-Kristin AU - Monzer, Aline AU - Hlavata, Annamaria AU - Isono, Erika AU - Loose, Martin AU - Friml, Jiří ID - 14591 T2 - bioRxiv TI - Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants ER - TY - JOUR AB - Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship. Methods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity. Results: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy. Conclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”. AU - Lin, Sheng-Jia AU - Vona, Barbara AU - Lau, Tracy AU - Huang, Kevin AU - Zaki, Maha S. AU - Aldeen, Huda Shujaa AU - Karimiani, Ehsan Ghayoor AU - Rocca, Clarissa AU - Noureldeen, Mahmoud M. AU - Saad, Ahmed K. AU - Petree, Cassidy AU - Bartolomaeus, Tobias AU - Abou Jamra, Rami AU - Zifarelli, Giovanni AU - Gotkhindikar, Aditi AU - Wentzensen, Ingrid M. AU - Liao, Mingjuan AU - Cork, Emalyn Elise AU - Varshney, Pratishtha AU - Hashemi, Narges AU - Mohammadi, Mohammad Hasan AU - Rad, Aboulfazl AU - Neira, Juanita AU - Toosi, Mehran Beiraghi AU - Knopp, Cordula AU - Kurth, Ingo AU - Challman, Thomas D. AU - Smith, Rebecca AU - Abdalla, Asmahan AU - Haaf, Thomas AU - Suri, Mohnish AU - Joshi, Manali AU - Chung, Wendy K. AU - Moreno-De-Luca, Andres AU - Houlden, Henry AU - Maroofian, Reza AU - Varshney, Gaurav K. ID - 14639 JF - Genome Medicine KW - Genetics (clinical) KW - Genetics KW - Molecular Biology KW - Molecular Medicine SN - 1756-994X TI - Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity VL - 15 ER - TY - JOUR AB - We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration. AU - Makatura, Liane AU - Wang, Bohan AU - Chen, Yi-Lu AU - Deng, Bolei AU - Wojtan, Christopher J AU - Bickel, Bernd AU - Matusik, Wojciech ID - 14628 IS - 5 JF - ACM Transactions on Graphics KW - Computer Graphics and Computer-Aided Design SN - 0730-0301 TI - Procedural metamaterials: A unified procedural graph for metamaterial design VL - 42 ER - TY - GEN AB - Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression. AU - Tluckova, Katarina AU - Testa Salmazo, Anita P AU - Bernecky, Carrie A ID - 14644 TI - Mechanism of mammalian transcriptional repression by noncoding RNA ER - TY - JOUR AB - We investigate spin-charge separation of a spin- 1 2 Fermi system confined in a triple well where multiple bands are occupied. We assume that our finite fermionic system is close to fully spin polarized while being doped by a hole and an impurity fermion with opposite spin. Our setup involves ferromagnetic couplings among the particles in different bands, leading to the development of strong spin-transport correlations in an intermediate interaction regime. Interactions are then strong enough to lift the degeneracy among singlet and triplet spin configurations in the well of the spin impurity but not strong enough to prohibit hole-induced magnetic excitations to the singlet state. Despite the strong spin-hole correlations, the system exhibits spin-charge deconfinement allowing for long-range entanglement of the spatial and spin degrees of freedom. AU - Becker, J. M. AU - Koutentakis, Georgios AU - Schmelcher, P. ID - 14658 IS - 4 JF - Physical Review Research SN - 2643-1564 TI - Spin-charge correlations in finite one-dimensional multiband Fermi systems VL - 5 ER - TY - JOUR AB - We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e., impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the impurity-boson interaction. We show that the dipolar nature of the condensate and of the impurity results in anisotropic relaxation dynamics, in particular, anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench dynamics is strongly affected by the interplay between dipolar anisotropy and trap geometry. Our findings pave the way for simulating impurities in anisotropic media utilizing experiments with dipolar mixtures. AU - Volosniev, Artem AU - Bighin, Giacomo AU - Santos, Luis AU - Peña Ardila, Luisllu A. ID - 14650 IS - 6 JF - SciPost Physics KW - General Physics and Astronomy SN - 2542-4653 TI - Non-equilibrium dynamics of dipolar polarons VL - 15 ER - TY - JOUR AB - Mass spectrometry imaging (MSI) is a powerful analytical technique for the two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments require to predefine the surface of interest based on photographic or microscopic images. Typically, these boundaries can no longer be changed or adjusted once the experiment has been started. In terms of a more interactive approach we recently developed a pen-like ionization interface which is directly connected to the mass spectrometer. The device allows the user to ionize chemicals by desorption electrospray ionization (DESI) and to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI). For this application, we present a novel approach for a robust, optical flow-based motion detection. While the live video stream from the camera is used to track the pen's motion across the surface a post-acquisition algorithm correlates the coordinates of the pen trajectory with respective mass spectra obtained from a simultaneous mass spectrometric data acquisition. This algorithm is no longer dependent on a single, manually applied optical marker on the sample surface, which has to be visible on all video frames throughout the analysis. The advanced DESI-IMSI method was successfully tested on inkjet-printed letters as well as mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI with standard DESI-MSI data. AU - Kluibenschedl, Florian AU - Ploner, Anna AU - Meisenbichler, Christina AU - Konrat, Robert AU - Müller, Thomas ID - 14653 JF - International Journal of Mass Spectrometry SN - 1387-3806 TI - Advanced motion tracking for interactive mass spectrometry imaging (IMSI) VL - 495 ER - TY - GEN AB - In the developing vertebrate central nervous system, neurons and glia typically arise sequentially from common progenitors. Here, we report that the transcription factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and in postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic ligand FGF18 in new born neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons increases Fgf18 expression and enhances gliogenesis in the progenitors. These results fit well with the model that new born neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex. AU - Bose, Mahima AU - Suresh, Varun AU - Mishra, Urvi AU - Talwar, Ishita AU - Yadav, Anuradha AU - Biswas, Shiona AU - Hippenmeyer, Simon AU - Tole, Shubha ID - 14647 T2 - bioRxiv TI - Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway ER - TY - JOUR AB - The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments’ ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division. AU - Sorichetti, Valerio AU - Lenz, Martin ID - 14655 IS - 22 JF - Physical Review Letters SN - 0031-9007 TI - Transverse fluctuations control the assembly of semiflexible filaments VL - 131 ER - TY - JOUR AB - The classical Steinitz theorem states that if the origin belongs to the interior of the convex hull of a set 𝑆⊂ℝ𝑑, then there are at most 2𝑑 points of 𝑆 whose convex hull contains the origin in the interior. Bárány, Katchalski,and Pach proved the following quantitative version of Steinitz’s theorem. Let 𝑄 be a convex polytope in ℝ𝑑 containing the standard Euclidean unit ball 𝐁𝑑. Then there exist at most 2𝑑 vertices of 𝑄 whose convex hull 𝑄′ satisfies 𝑟𝐁𝑑⊂𝑄′ with 𝑟⩾𝑑−2𝑑. They conjectured that 𝑟⩾𝑐𝑑−1∕2 holds with a universal constant 𝑐>0. We prove 𝑟⩾15𝑑2, the first polynomial lower bound on 𝑟. Furthermore, we show that 𝑟 is not greater than 2/√𝑑. AU - Ivanov, Grigory AU - Naszódi, Márton ID - 14660 JF - Bulletin of the London Mathematical Society SN - 0024-6093 TI - Quantitative Steinitz theorem: A polynomial bound ER - TY - JOUR AB - So-called spontaneous activity is a central hallmark of most nervous systems. Such non-causal firing is contrary to the tenet of spikes as a means of communication, and its purpose remains unclear. We propose that self-initiated firing can serve as a release valve to protect neurons from the toxic conditions arising in mitochondria from lower-than-baseline energy consumption. To demonstrate the viability of our hypothesis, we built a set of models that incorporate recent experimental results indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP), adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing. We explore the relationship of metabolic cost of spiking with its effect on the temporal patterning of spikes and reproduce experimentally observed changes in intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with ROS-modulated potassium channels. We also show that metabolic spiking homeostasis can produce indefinitely sustained avalanche dynamics in cortical circuits. Our theory can account for key features of neuronal activity observed in many studies ranging from ion channel function all the way to resting state dynamics. We finish with a set of experimental predictions that would confirm an integrated, crucial role for metabolically regulated spiking and firmly link metabolic homeostasis and neuronal function. AU - Chintaluri, Chaitanya AU - Vogels, Tim P ID - 14666 IS - 48 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 0027-8424 TI - Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species VL - 120 ER - TY - JOUR AB - Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain. AU - Nardin, Michele AU - Csicsvari, Jozsef L AU - Tkačik, Gašper AU - Savin, Cristina ID - 14656 IS - 48 JF - The Journal of Neuroscience TI - The structure of hippocampal CA1 interactions optimizes spatial coding across experience VL - 43 ER - TY - JOUR AB - Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader’s fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader’s dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader’s connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader’s fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident. AU - Tkadlec, Josef AU - Kaveh, Kamran AU - Chatterjee, Krishnendu AU - Nowak, Martin A. ID - 14657 IS - 208 JF - Journal of the Royal Society, Interface TI - Evolutionary dynamics of mutants that modify population structure VL - 20 ER - TY - JOUR AB - The architecture of self-assembled host molecules can profoundly affect the properties of the encapsulated guests. For example, a rigid cage with small windows can efficiently protect its contents from the environment; in contrast, tube-shaped, flexible hosts with large openings and an easily accessible cavity are ideally suited for catalysis. Here, we report a “Janus” nature of a Pd6L4 coordination host previously reported to exist exclusively as a tube isomer (T). We show that upon encapsulating various tetrahedrally shaped guests, T can reconfigure into a cage-shaped host (C) in quantitative yield. Extracting the guest affords empty C, which is metastable and spontaneously relaxes to T, and the T⇄C interconversion can be repeated for multiple cycles. Reversible toggling between two vastly different isomers paves the way toward controlling functional properties of coordination hosts “on demand”. AU - Hema, Kuntrapakam AU - Grommet, Angela B. AU - Białek, Michał J. AU - Wang, Jinhua AU - Schneider, Laura AU - Drechsler, Christoph AU - Yanshyna, Oksana AU - Diskin-Posner, Yael AU - Clever, Guido H. AU - Klajn, Rafal ID - 14664 IS - 45 JF - Journal of the American Chemical Society SN - 0002-7863 TI - Guest encapsulation alters the thermodynamic landscape of a coordination host VL - 145 ER - TY - JOUR AB - As a bottleneck in the direct synthesis of hydrogen peroxide, the development of an efficient palladium-based catalyst has garnered great attention. However, elusive active centers and reaction mechanism issues inhibit further optimization of its performance. In this work, advanced microkinetic modeling with the adsorbate–adsorbate interaction and nanoparticle size effect based on first-principles calculations is developed. A full mechanism uncovering the significance of adsorbate–adsorbate interaction is determined on Pd nanoparticles. We demonstrate unambiguously that Pd(100) with main coverage species of O2 and H is beneficial to H2O2 production, being consistent with experimental operando observation, while H2O forms on Pd(111) covered by O species and Pd(211) covered by O and OH species. Kinetic analyses further enable quantitative estimation of the influence of temperature, pressure, and particle size. Large-size Pd nanoparticles are found to achieve a high H2O2 reaction rate when the operating conditions are moderate temperature and higher oxygen partial pressure. We reveal that specific facets of the Pd nanoparticles are crucial factors for their selectivity and activity. Consistent with the experiment, the production of H2O2 is discovered to be more favorable on Pd nanoparticles containing Pd(100) facets. The ratio of H2/O2 induces substantial variations in the coverage of intermediates of O2 and H on Pd(100), resulting in a change in product selectivity. AU - Zhao, Jinyan AU - Yao, Zihao AU - Bunting, Rhys AU - Hu, P. AU - Wang, Jianguo ID - 14663 IS - 22 JF - ACS Catalysis TI - Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles VL - 13 ER - TY - JOUR AB - For large dimensional non-Hermitian random matrices X with real or complex independent, identically distributed, centered entries, we consider the fluctuations of f (X) as a matrix where f is an analytic function around the spectrum of X. We prove that for a generic bounded square matrix A, the quantity Tr f (X)A exhibits Gaussian fluctuations as the matrix size grows to infinity, which consists of two independent modes corresponding to the tracial and traceless parts of A. We find a new formula for the variance of the traceless part that involves the Frobenius norm of A and the L2-norm of f on the boundary of the limiting spectrum. AU - Erdös, László AU - Ji, Hong Chang ID - 14667 IS - 4 JF - Annales de l'institut Henri Poincare (B) Probability and Statistics SN - 0246-0203 TI - Functional CLT for non-Hermitian random matrices VL - 59 ER - TY - JOUR AB - We consider a class of polaron models, including the Fröhlich model, at zero total momentum, and show that at sufficiently weak coupling there are no excited eigenvalues below the essential spectrum. AU - Seiringer, Robert ID - 14662 IS - 3 JF - Journal of Spectral Theory SN - 1664-039X TI - Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling VL - 13 ER - TY - JOUR AB - In order to demonstrate the stability of newly proposed iridium-based Ir2Cr(In,Sn) and IrRhCr(In,Sn) heusler alloys, we present ab-initio analysis of these alloys by examining various properties to prove their stability. The stability of these alloys can be inferred from different cohesive and formation energies as well as positive phonon frequencies. Their electronic structure results indicate that they are semi-metals in nature. The magnetic moments are computed using the Slater-Pauling formula and exhibit a high value, with the Cr atom contributing the most in all alloys. Mulliken’s charge analysis results show that our alloys contain a range of linkages, mainly ionic and covalent ones. The ductility and mechanical stability of these alloys are confirmed by elastic constants viz. Poisson’s ratio, Pugh’s ratio, and many different types of elastic moduli. AU - Gupta, Shyam Lal AU - Singh, Saurabh AU - Kumar, Sumit AU - Anupam, Unknown AU - Thakur, Samjeet Singh AU - Kumar, Ashish AU - Panwar, Sanjay AU - Diwaker, D. ID - 14652 JF - Physica B: Condensed Matter SN - 0921-4526 TI - Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys VL - 674 ER - TY - JOUR AB - Sleep plays a key role in preserving brain function, keeping the brain network in a state that ensures optimal computational capabilities. Empirical evidence indicates that such a state is consistent with criticality, where scale-free neuronal avalanches emerge. However, the relationship between sleep, emergent avalanches, and criticality remains poorly understood. Here we fully characterize the critical behavior of avalanches during sleep, and study their relationship with the sleep macro- and micro-architecture, in particular the cyclic alternating pattern (CAP). We show that avalanche size and duration distributions exhibit robust power laws with exponents approximately equal to −3/2 e −2, respectively. Importantly, we find that sizes scale as a power law of the durations, and that all critical exponents for neuronal avalanches obey robust scaling relations, which are consistent with the mean-field directed percolation universality class. Our analysis demonstrates that avalanche dynamics depends on the position within the NREM-REM cycles, with the avalanche density increasing in the descending phases and decreasing in the ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche occurrence correlates with CAP activation phases, particularly A1, which are the expression of slow wave sleep propensity and have been proposed to be beneficial for cognitive processes. The results suggest that neuronal avalanches, and thus tuning to criticality, actively contribute to sleep development and play a role in preserving network function. Such findings, alongside characterization of the universality class for avalanches, open new avenues to the investigation of functional role of criticality during sleep with potential clinical application.Significance statementWe fully characterize the critical behavior of neuronal avalanches during sleep, and show that avalanches follow precise scaling laws that are consistent with the mean-field directed percolation universality class. The analysis provides first evidence of a functional relationship between avalanche occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of CAP phase A during NREM sleep. Because CAP is considered one of the major guardians of NREM sleep that allows the brain to dynamically react to external perturbation and contributes to the cognitive consolidation processes occurring in sleep, our observations suggest that neuronal avalanches at criticality are associated with flexible response to external inputs and to cognitive processes, a key assumption of the critical brain hypothesis. AU - Scarpetta, Silvia AU - Morrisi, Niccolò AU - Mutti, Carlotta AU - Azzi, Nicoletta AU - Trippi, Irene AU - Ciliento, Rosario AU - Apicella, Ilenia AU - Messuti, Giovanni AU - Angiolelli, Marianna AU - Lombardi, Fabrizio AU - Parrino, Liborio AU - Vaudano, Anna Elisabetta ID - 12487 IS - 10 JF - iScience TI - Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture VL - 26 ER - TY - JOUR AB - Background: Fighting disease while fighting rivals exposes males to constraints and tradeoffs during male-male competition. We here tested how both the stage and intensity of infection with the fungal pathogen Metarhizium robertsii interfered with fighting success in Cardiocondyla obscurior ant males. Males of this species have evolved long lifespans during which they can gain many matings with the young queens of the colony, if successful in male-male competition. Since male fights occur inside the colony, the outcome of male-male competition can further be biased by interference of the colony’s worker force. Results: We found that severe, but not yet mild, infection strongly impaired male fighting success. In late-stage infection, this could be attributed to worker aggression directed towards the infected rather than the healthy male and an already very high male morbidity even in the absence of fighting. Shortly after pathogen exposure, however, male mortality was particularly increased during combat. Since these males mounted a strong immune response, their reduced fighting success suggests a trade-off between immune investment and competitive ability already early in the infection. Even if the males themselves showed no difference in the number of attacks they raised against their healthy rivals across infection stages and levels, severely infected males were thus losing in male-male competition from an early stage of infection on. Conclusions: Males of the ant C. obscurior have evolved high immune investment, triggering an effective immune response very fast after fungal exposure. This allows them to cope with mild pathogen exposures without cost to their success in male-male competition, and hence to gain multiple mating opportunities with the emerging virgin queens of the colony. Under severe infection, however, they are weak fighters and rarely survive a combat already at early infection when raising an immune response, as well as at progressed infection, when they are morbid and preferentially targeted by worker aggression. Workers thereby remove males that pose a future disease threat by biasing male-male competition. Our study thus revealed a novel social immunity mechanism how social insect workers protect the colony against disease risk. AU - Metzler, Sina AU - Kirchner, Jessica AU - Grasse, Anna V AU - Cremer, Sylvia ID - 12696 JF - BMC Ecology and Evolution SN - 2730-7182 TI - Trade-offs between immunity and competitive ability in fighting ant males VL - 23 ER - TY - JOUR AB - Understanding the response of Himalayan glaciers to global warming is vital because of their role as a water source for the Asian subcontinent. However, great uncertainties still exist on the climate drivers of past and present glacier changes across scales. Here, we analyse continuous hourly climate station data from a glacierized elevation (Pyramid station, Mount Everest) since 1994 together with other ground observations and climate reanalysis. We show that a decrease in maximum air temperature and precipitation occurred during the last three decades at Pyramid in response to global warming. Reanalysis data suggest a broader occurrence of this effect in the glacierized areas of the Himalaya. We hypothesize that the counterintuitive cooling is caused by enhanced sensible heat exchange and the associated increase in glacier katabatic wind, which draws cool air downward from higher elevations. The stronger katabatic winds have also lowered the elevation of local wind convergence, thereby diminishing precipitation in glacial areas and negatively affecting glacier mass balance. This local cooling may have partially preserved glaciers from melting and could help protect the periglacial environment. AU - Salerno, Franco AU - Guyennon, Nicolas AU - Yang, Kun AU - Shaw, Thomas AU - Lin, Changgui AU - Colombo, Nicola AU - Romano, Emanuele AU - Gruber, Stephan AU - Bolch, Tobias AU - Alessandri, Andrea AU - Cristofanelli, Paolo AU - Putero, Davide AU - Diolaiuti, Guglielmina AU - Tartari, Gianni AU - Verza, Gianpietro AU - Thakuri, Sudeep AU - Balsamo, Gianpaolo AU - Miles, Evan S. AU - Pellicciotti, Francesca ID - 14659 JF - Nature Geoscience SN - 1752-0894 TI - Local cooling and drying induced by Himalayan glaciers under global warming VL - 16 ER - TY - JOUR AB - AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three potent, chemically diverse ligands. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators. AU - Zhang, Danyang AU - Lape, Remigijus AU - Shaikh, Saher A. AU - Kohegyi, Bianka K. AU - Watson, Jake AU - Cais, Ondrej AU - Nakagawa, Terunaga AU - Greger, Ingo H. ID - 12786 JF - Nature Communications TI - Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics VL - 14 ER - TY - DATA AB - See Readme File for further information. AU - Cremer, Sylvia ID - 12693 TI - Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males ER - TY - JOUR AB - Urban-living individuals are exposed to many environmental factors that may combine and interact to influence mental health. While individual factors of an urban environment have been investigated in isolation, no attempt has been made to model how complex, real-life exposure to living in the city relates to brain and mental health, and how this is moderated by genetic factors. Using the data of 156,075 participants from the UK Biobank, we carried out sparse canonical correlation analyses to investigate the relationships between urban environments and psychiatric symptoms. We found an environmental profile of social deprivation, air pollution, street network and urban land-use density that was positively correlated with an affective symptom group (r = 0.22, Pperm < 0.001), mediated by brain volume differences consistent with reward processing, and moderated by genes enriched for stress response, including CRHR1, explaining 2.01% of the variance in brain volume differences. Protective factors such as greenness and generous destination accessibility were negatively correlated with an anxiety symptom group (r = 0.10, Pperm < 0.001), mediated by brain regions necessary for emotion regulation and moderated by EXD3, explaining 1.65% of the variance. The third urban environmental profile was correlated with an emotional instability symptom group (r = 0.03, Pperm < 0.001). Our findings suggest that different environmental profiles of urban living may influence specific psychiatric symptom groups through distinct neurobiological pathways. AU - Xu, Jiayuan AU - Liu, Nana AU - Polemiti, Elli AU - Garcia-Mondragon, Liliana AU - Tang, Jie AU - Liu, Xiaoxuan AU - Lett, Tristram AU - Yu, Le AU - Nöthen, Markus M. AU - Feng, Jianfeng AU - Yu, Chunshui AU - Marquand, Andre AU - Schumann, Gunter AU - Walter, Henrik AU - Heinz, Andreas AU - Ralser, Markus AU - Twardziok, Sven AU - Vaidya, Nilakshi AU - Serin, Emin AU - Jentsch, Marcel AU - Hitchen, Esther AU - Eils, Roland AU - Taron, Ulrike Helene AU - Schütz, Tatjana AU - Schepanski, Kerstin AU - Banks, Jamie AU - Banaschewski, Tobias AU - Jansone, Karina AU - Christmann, Nina AU - Meyer-Lindenberg, Andreas AU - Tost, Heike AU - Holz, Nathalie AU - Schwarz, Emanuel AU - Stringaris, Argyris AU - Neidhart, Maja AU - Nees, Frauke AU - Siehl, Sebastian AU - A. Andreassen, Ole AU - T. Westlye, Lars AU - Van Der Meer, Dennis AU - Fernandez, Sara AU - Kjelkenes, Rikka AU - Ask, Helga AU - Rapp, Michael AU - Tschorn, Mira AU - Böttger, Sarah Jane AU - Novarino, Gaia AU - Marr, Lena AU - Slater, Mel AU - Viapiana, Guillem Feixas AU - Orosa, Francisco Eiroa AU - Gallego, Jaime AU - Pastor, Alvaro AU - Forstner, Andreas AU - Hoffmann, Per AU - M. Nöthen, Markus AU - J. Forstner, Andreas AU - Claus, Isabelle AU - Miller, Abbi AU - Heilmann-Heimbach, Stefanie AU - Sommer, Peter AU - Boye, Mona AU - Wilbertz, Johannes AU - Schmitt, Karen AU - Jirsa, Viktor AU - Petkoski, Spase AU - Pitel, Séverine AU - Otten, Lisa AU - Athanasiadis, Anastasios Polykarpos AU - Pearmund, Charlie AU - Spanlang, Bernhard AU - Alvarez, Elena AU - Sanchez, Mavi AU - Giner, Arantxa AU - Hese, Sören AU - Renner, Paul AU - Jia, Tianye AU - Gong, Yanting AU - Xia, Yunman AU - Chang, Xiao AU - Calhoun, Vince AU - Liu, Jingyu AU - Thompson, Paul AU - Clinton, Nicholas AU - Desrivieres, Sylvane AU - H. Young, Allan AU - Stahl, Bernd AU - Ogoh, George ID - 13168 JF - Nature Medicine SN - 1078-8956 TI - Effects of urban living environments on mental health in adults VL - 29 ER - TY - CONF AB - 3D printing based on continuous deposition of materials, such as filament-based 3D printing, has seen widespread adoption thanks to its versatility in working with a wide range of materials. An important shortcoming of this type of technology is its limited multi-material capabilities. While there are simple hardware designs that enable multi-material printing in principle, the required software is heavily underdeveloped. A typical hardware design fuses together individual materials fed into a single chamber from multiple inlets before they are deposited. This design, however, introduces a time delay between the intended material mixture and its actual deposition. In this work, inspired by diverse path planning research in robotics, we show that this mechanical challenge can be addressed via improved printer control. We propose to formulate the search for optimal multi-material printing policies in a reinforcement learning setup. We put forward a simple numerical deposition model that takes into account the non-linear material mixing and delayed material deposition. To validate our system we focus on color fabrication, a problem known for its strict requirements for varying material mixtures at a high spatial frequency. We demonstrate that our learned control policy outperforms state-of-the-art hand-crafted algorithms. AU - Liao, Kang AU - Tricard, Thibault AU - Piovarci, Michael AU - Seidel, Hans-Peter AU - Babaei, Vahid ID - 12976 KW - reinforcement learning KW - deposition KW - control KW - color KW - multi-filament SN - 1050-4729 T2 - 2023 IEEE International Conference on Robotics and Automation TI - Learning deposition policies for fused multi-material 3D printing VL - 2023 ER - TY - JOUR AB - Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization. AU - Gert, Krista R.B. AU - Panser, Karin AU - Surm, Joachim AU - Steinmetz, Benjamin S. AU - Schleiffer, Alexander AU - Jovine, Luca AU - Moran, Yehu AU - Kondrashov, Fyodor AU - Pauli, Andrea ID - 13164 JF - Nature Communications TI - Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries VL - 14 ER - TY - JOUR AB - Let P be a nontorsion point on an elliptic curve defined over a number field K and consider the sequence {Bn}n∈N of the denominators of x(nP). We prove that every term of the sequence of the Bn has a primitive divisor for n greater than an effectively computable constant that we will explicitly compute. This constant will depend only on the model defining the curve. AU - Verzobio, Matteo ID - 12313 IS - 2 JF - Pacific Journal of Mathematics TI - Some effectivity results for primitive divisors of elliptic divisibility sequences VL - 325 ER - TY - JOUR AB - We prove a characterization of the Dirichlet–Ferguson measure over an arbitrary finite diffuse measure space. We provide an interpretation of this characterization in analogy with the Mecke identity for Poisson point processes. AU - Dello Schiavo, Lorenzo AU - Lytvynov, Eugene ID - 13145 JF - Electronic Communications in Probability TI - A Mecke-type characterization of the Dirichlet–Ferguson measure VL - 28 ER - TY - JOUR AB - We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let 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 . 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 for finite fields. In this paper, we derive the best known lower bounds on the optimal density of list-decodable infinite constellations for constant L under a stronger notion called average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory. AU - Zhang, Yihan AU - Vatedka, Shashank ID - 12838 IS - 7 JF - IEEE Transactions on Information Theory SN - 0018-9448 TI - Multiple packing: Lower bounds via infinite constellations VL - 69 ER - TY - CONF AB - A machine-learned system that is fair in static decision-making tasks may have biased societal impacts in the long-run. This may happen when the system interacts with humans and feedback patterns emerge, reinforcing old biases in the system and creating new biases. While existing works try to identify and mitigate long-run biases through smart system design, we introduce techniques for monitoring fairness in real time. Our goal is to build and deploy a monitor that will continuously observe a long sequence of events generated by the system in the wild, and will output, with each event, a verdict on how fair the system is at the current point in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated at run-time, which is important because unfair behaviors may not be eliminated a priori, at design-time, due to partial knowledge about the system and the environment, as well as uncertainties and dynamic changes in the system and the environment, such as the unpredictability of human behavior. Secondly, monitors are by design oblivious to how the monitored system is constructed, which makes them suitable to be used as trusted third-party fairness watchdogs. They function as computationally lightweight statistical estimators, and their correctness proofs rely on the rigorous analysis of the stochastic process that models the assumptions about the underlying dynamics of the system. We show, both in theory and experiments, how monitors can warn us (1) if a bank’s credit policy over time has created an unfair distribution of credit scores among the population, and (2) if a resource allocator’s allocation policy over time has made unfair allocations. Our experiments demonstrate that the monitors introduce very low overhead. We believe that runtime monitoring is an important and mathematically rigorous new addition to the fairness toolbox. AU - Henzinger, Thomas A AU - Karimi, Mahyar AU - Kueffner, Konstantin AU - Mallik, Kaushik ID - 13228 SN - 9781450372527 T2 - FAccT '23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency TI - Runtime monitoring of dynamic fairness properties ER - TY - JOUR AB - Recently the leading order of the correlation energy of a Fermi gas in a coupled mean-field and semiclassical scaling regime has been derived, under the assumption of an interaction potential with a small norm and with compact support in Fourier space. We generalize this result to large interaction potentials, requiring only |⋅|V^∈ℓ1(Z3). Our proof is based on approximate, collective bosonization in three dimensions. Significant improvements compared to recent work include stronger bounds on non-bosonizable terms and more efficient control on the bosonization of the kinetic energy. AU - Benedikter, Niels P AU - Porta, Marcello AU - Schlein, Benjamin AU - Seiringer, Robert ID - 13225 IS - 4 JF - Archive for Rational Mechanics and Analysis SN - 0003-9527 TI - Correlation energy of a weakly interacting Fermi gas with large interaction potential VL - 247 ER - TY - JOUR AB - We consider the ground state and the low-energy excited states of a system of N identical bosons with interactions in the mean-field scaling regime. For the ground state, we derive a weak Edgeworth expansion for the fluctuations of bounded one-body operators, which yields corrections to a central limit theorem to any order in 1/N−−√. For suitable excited states, we show that the limiting distribution is a polynomial times a normal distribution, and that higher-order corrections are given by an Edgeworth-type expansion. AU - Bossmann, Lea AU - Petrat, Sören P ID - 13226 IS - 4 JF - Letters in Mathematical Physics SN - 0377-9017 TI - Weak Edgeworth expansion for the mean-field Bose gas VL - 113 ER - TY - JOUR AB - Currently available quantum processors are dominated by noise, which severely limits their applicability and motivates the search for new physical qubit encodings. In this work, we introduce the inductively shunted transmon, a weakly flux-tunable superconducting qubit that offers charge offset protection for all levels and a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting in a constant coherence over a full flux quantum. The parabolic confinement provided by the inductive shunt as well as the linearity of the geometric superinductor facilitates a high-power readout that resolves quantum jumps with a fidelity and QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover, the device reveals quantum tunneling physics between the two prepared fluxon ground states with a measured average decay time of up to 3.5 h. In the future, fast time-domain control of the transition matrix elements could offer a new path forward to also achieve full qubit control in the decay-protected fluxon basis. AU - Hassani, Farid AU - Peruzzo, Matilda AU - Kapoor, Lucky AU - Trioni, Andrea AU - Zemlicka, Martin AU - Fink, Johannes M ID - 13227 JF - Nature Communications TI - Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours VL - 14 ER - TY - CONF AB - We consider the problem of reconstructing the signal and the hidden variables from observations coming from a multi-layer network with rotationally invariant weight matrices. The multi-layer structure models inference from deep generative priors, and the rotational invariance imposed on the weights generalizes the i.i.d. Gaussian assumption by allowing for a complex correlation structure, which is typical in applications. In this work, we present a new class of approximate message passing (AMP) algorithms and give a state evolution recursion which precisely characterizes their performance in the large system limit. In contrast with the existing multi-layer VAMP (ML-VAMP) approach, our proposed AMP – dubbed multilayer rotationally invariant generalized AMP (ML-RI-GAMP) – provides a natural generalization beyond Gaussian designs, in the sense that it recovers the existing Gaussian AMP as a special case. Furthermore, ML-RI-GAMP exhibits a significantly lower complexity than ML-VAMP, as the computationally intensive singular value decomposition is replaced by an estimation of the moments of the design matrices. Finally, our numerical results show that this complexity gain comes at little to no cost in the performance of the algorithm. AU - Xu, Yizhou AU - Hou, Tian Qi AU - Liang, Shan Suo AU - Mondelli, Marco ID - 13321 SN - 9798350301496 T2 - 2023 IEEE Information Theory Workshop TI - Approximate message passing for multi-layer estimation in rotationally invariant models ER - TY - JOUR AB - In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality. AU - Zhong, Fanchao AU - Xu, Yonglai AU - Zhao, Haisen AU - Lu, Lin ID - 13265 IS - 3 JF - ACM Transactions on Graphics SN - 0730-0301 TI - As-Continuous-As-Possible extrusion-based fabrication of surface models VL - 42 ER - TY - JOUR AB - Bohnenblust–Hille inequalities for Boolean cubes have been proven with dimension-free constants that grow subexponentially in the degree (Defant et al. in Math Ann 374(1):653–680, 2019). Such inequalities have found great applications in learning low-degree Boolean functions (Eskenazis and Ivanisvili in Proceedings of the 54th annual ACM SIGACT symposium on theory of computing, pp 203–207, 2022). Motivated by learning quantum observables, a qubit analogue of Bohnenblust–Hille inequality for Boolean cubes was recently conjectured in Rouzé et al. (Quantum Talagrand, KKL and Friedgut’s theorems and the learnability of quantum Boolean functions, 2022. arXiv preprint arXiv:2209.07279). The conjecture was resolved in Huang et al. (Learning to predict arbitrary quantum processes, 2022. arXiv preprint arXiv:2210.14894). In this paper, we give a new proof of these Bohnenblust–Hille inequalities for qubit system with constants that are dimension-free and of exponential growth in the degree. As a consequence, we obtain a junta theorem for low-degree polynomials. Using similar ideas, we also study learning problems of low degree quantum observables and Bohr’s radius phenomenon on quantum Boolean cubes. AU - Volberg, Alexander AU - Zhang, Haonan ID - 13318 JF - Mathematische Annalen SN - 0025-5831 TI - Noncommutative Bohnenblust–Hille inequalities ER - TY - JOUR AB - In this paper, we prove the convexity of trace functionals (A,B,C)↦Tr|BpACq|s, for parameters (p, q, s) that are best possible, where B and C are any n-by-n positive-definite matrices, and A is any n-by-n matrix. We also obtain the monotonicity versions of trace functionals of this type. As applications, we extend some results in Carlen et al. (Linear Algebra Appl 490:174–185, 2016), Hiai and Petz (Publ Res Inst Math Sci 48(3):525-542, 2012) and resolve a conjecture in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) in the matrix setting. Other conjectures in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) will also be discussed. We also show that some related trace functionals are not concave in general. Such concavity results were expected to hold in different problems. AU - Zhang, Haonan ID - 13271 JF - Annales Henri Poincare SN - 1424-0637 TI - Some convexity and monotonicity results of trace functionals ER - TY - JOUR AB - Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation. AU - Kleshnina, Maria AU - Hilbe, Christian AU - Simsa, Stepan AU - Chatterjee, Krishnendu AU - Nowak, Martin A. ID - 13258 JF - Nature Communications TI - The effect of environmental information on evolution of cooperation in stochastic games VL - 14 ER - TY - JOUR AB - Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date. Results: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models. AU - Trinh, Van Giang AU - Benhamou, Belaid AU - Henzinger, Thomas A AU - Pastva, Samuel ID - 13263 IS - Supplement_1 JF - Bioinformatics SN - 1367-4803 TI - Trap spaces of multi-valued networks: Definition, computation, and applications VL - 39 ER - TY - JOUR AB - Although budding yeast has been extensively used as a model organism for studying organelle functions and intracellular vesicle trafficking, whether it possesses an independent endocytic early/sorting compartment that sorts endocytic cargos to the endo-lysosomal pathway or the recycling pathway has long been unclear. The structure and properties of the endocytic early/sorting compartment differ significantly between organisms; in plant cells, the trans-Golgi network (TGN) serves this role, whereas in mammalian cells a separate intracellular structure performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic vesicles, but which compartment is the direct target for endocytic vesicles remained unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within the TGN functions as the early/sorting compartment. After arriving here, endocytic cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing endosomal compartment through the pathway requiring the clathrin adaptors GGAs. Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment, and the deletion of GGAs has little effect on another TGN region where Sec7p is present but suppresses dynamics of the Tlg2-residing early/sorting compartment, indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting compartment and function independently of the Sec7p-residing region within the TGN. AU - Toshima, Junko Y. AU - Tsukahara, Ayana AU - Nagano, Makoto AU - Tojima, Takuro AU - Siekhaus, Daria E AU - Nakano, Akihiko AU - Toshima, Jiro ID - 13316 JF - eLife TI - The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network VL - 12 ER - TY - JOUR AB - We prove the Eigenstate Thermalisation Hypothesis (ETH) for local observables in a typical translation invariant system of quantum spins with L-body interactions, where L is the number of spins. This mathematically verifies the observation first made by Santos and Rigol (Phys Rev E 82(3):031130, 2010, https://doi.org/10.1103/PhysRevE.82.031130) that the ETH may hold for systems with additional translational symmetries for a naturally restricted class of observables. We also present numerical support for the same phenomenon for Hamiltonians with local interaction. AU - Sugimoto, Shoki AU - Henheik, Sven Joscha AU - Riabov, Volodymyr AU - Erdös, László ID - 13317 IS - 7 JF - Journal of Statistical Physics SN - 0022-4715 TI - Eigenstate thermalisation hypothesis for translation invariant spin systems VL - 190 ER - TY - JOUR AB - We present a numerical analysis of spin-1/2 fermions in a one-dimensional harmonic potential in the presence of a magnetic point-like impurity at the center of the trap. The model represents a few-body analogue of a magnetic impurity in the vicinity of an s-wave superconductor. Already for a few particles we find a ground-state level crossing between sectors with different fermion parities. We interpret this crossing as a few-body precursor of a quantum phase transition, which occurs when the impurity "breaks" a Cooper pair. This picture is further corroborated by analyzing density-density correlations in momentum space. Finally, we discuss how the system may be realized with existing cold-atoms platforms. AU - Rammelmüller, Lukas AU - Huber, David AU - Čufar, Matija AU - Brand, Joachim AU - Hammer, Hans-Werner AU - Volosniev, Artem ID - 13278 IS - 1 JF - SciPost Physics KW - General Physics and Astronomy SN - 2542-4653 TI - Magnetic impurity in a one-dimensional few-fermion system VL - 14 ER - TY - JOUR AB - Viscous flows through pipes and channels are steady and ordered until, with increasing velocity, the laminar motion catastrophically breaks down and gives way to turbulence. How this apparently discontinuous change from low- to high-dimensional motion can be rationalized within the framework of the Navier-Stokes equations is not well understood. Exploiting geometrical properties of transitional channel flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible and identify the complete path that reversibly links fully turbulent motion to an invariant solution. This precursor of turbulence destabilizes rapidly with Re, and the accompanying explosive increase in attractor dimension effectively marks the transition between deterministic and de facto stochastic dynamics. AU - Paranjape, Chaitanya S AU - Yalniz, Gökhan AU - Duguet, Yohann AU - Budanur, Nazmi B AU - Hof, Björn ID - 13274 IS - 3 JF - Physical Review Letters KW - General Physics and Astronomy SN - 0031-9007 TI - Direct path from turbulence to time-periodic solutions VL - 131 ER - TY - JOUR AB - Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression. AU - Brückner, David AU - Chen, Hongtao AU - Barinov, Lev AU - Zoller, Benjamin AU - Gregor, Thomas ID - 13261 IS - 6652 JF - Science TI - Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome VL - 380 ER - TY - GEN AU - Kleshnina, Maria ID - 13336 TI - kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games ER - TY - JOUR AB - The ages of solar-like stars have been at the center of many studies such as exoplanet characterization or Galactic-archeology. While ages are usually computed from stellar evolution models, relations linking ages to other stellar properties, such as rotation and magnetic activity, have been investigated. With the large catalog of 55,232 rotation periods, Prot, and photometric magnetic activity index, Sph from Kepler data, we have the opportunity to look for such magneto-gyro-chronology relations. Stellar ages are obtained with two stellar evolution codes that include treatment of angular momentum evolution, hence using Prot as input in addition to classical atmospheric parameters. We explore two different ways of predicting stellar ages on three subsamples with spectroscopic observations: solar analogs, late-F and G dwarfs, and K dwarfs. We first perform a Bayesian analysis to derive relations between Sph and ages between 1 and 5 Gyr, and other stellar properties. For late-F and G dwarfs, and K dwarfs, the multivariate regression favors the model with Prot and Sph with median differences of 0.1% and 0.2%, respectively. We also apply Machine Learning techniques with a Random Forest algorithm to predict ages up to 14 Gyr with the same set of input parameters. For late-F, G and K dwarfs together, predicted ages are on average within 5.3% of the model ages and improve to 3.1% when including Prot. These are very promising results for a quick age estimation for solar-like stars with photometric observations, especially with current and future space missions. AU - Mathur, Savita AU - Claytor, Zachary R. AU - Santos, Ângela R. G. AU - García, Rafael A. AU - Amard, Louis AU - Bugnet, Lisa Annabelle AU - Corsaro, Enrico AU - Bonanno, Alfio AU - Breton, Sylvain N. AU - Godoy-Rivera, Diego AU - Pinsonneault, Marc H. AU - van Saders, Jennifer ID - 13443 IS - 2 JF - The Astrophysical Journal KW - Space and Planetary Science KW - Astronomy and Astrophysics SN - 0004-637X TI - Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations VL - 952 ER - TY - JOUR AB - Plants can regenerate their bodies via de novo establishment of shoot apical meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells is eventually specified into SAMs but the molecular mechanisms underlying fate specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX 13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana. WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2–based single cell transcriptome revealed that WOX13 plays key roles in determining cellular identity of callus cell population. We propose that reciprocal inhibition between WUS and WOX13 mediates critical cell fate determination in pluripotent cell population, which has a major impact on regeneration efficiency. AU - Ogura, Nao AU - Sasagawa, Yohei AU - Ito, Tasuku AU - Tameshige, Toshiaki AU - Kawai, Satomi AU - Sano, Masaki AU - Doll, Yuki AU - Iwase, Akira AU - Kawamura, Ayako AU - Suzuki, Takamasa AU - Nikaido, Itoshi AU - Sugimoto, Keiko AU - Ikeuchi, Momoko ID - 13259 IS - 27 JF - Science Advances TI - WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus VL - 9 ER - TY - JOUR AB - Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades’ worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery. AU - Wolfsberger, Walter AU - Chhugani, Karishma AU - Shchubelka, Khrystyna AU - Frolova, Alina AU - Salyha, Yuriy AU - Zlenko, Oksana AU - Arych, Mykhailo AU - Dziuba, Dmytro AU - Parkhomenko, Andrii AU - Smolanka, Volodymyr AU - Gümüş, Zeynep H. AU - Sezgin, Efe AU - Diaz-Lameiro, Alondra AU - Toth, Viktor R. AU - Maci, Megi AU - Bortz, Eric AU - Kondrashov, Fyodor AU - Morton, Patricia M. AU - Łabaj, Paweł P. AU - Romero, Veronika AU - Hlávka, Jakub AU - Mangul, Serghei AU - Oleksyk, Taras K. ID - 13976 JF - GigaScience TI - Scientists without borders: Lessons from Ukraine VL - 12 ER - TY - JOUR AB - We construct families of log K3 surfaces and study the arithmetic of their members. We use this to produce explicit surfaces with an order 5 Brauer–Manin obstruction to the integral Hasse principle. AU - Lyczak, Julian ID - 13973 IS - 2 JF - Annales de l'Institut Fourier SN - 0373-0956 TI - Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces VL - 73 ER - TY - JOUR AB - The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r−1)+1 points in Rd, one can find a partition X=X1∪⋯∪Xr of X, such that the convex hulls of the Xi, i=1,…,r, all share a common point. In this paper, we prove a trengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span ⌊n/3⌋ vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Álvarez-Rebollar et al. guarantees ⌊n/6⌋pairwise crossing triangles. Our result generalizes to a result about simplices in Rd, d≥2. AU - Fulek, Radoslav AU - Gärtner, Bernd AU - Kupavskii, Andrey AU - Valtr, Pavel AU - Wagner, Uli ID - 13974 JF - Discrete and Computational Geometry SN - 0179-5376 TI - The crossing Tverberg theorem ER - TY - JOUR AB - We consider the spectrum of random Laplacian matrices of the form Ln=An−Dn where An is a real symmetric random matrix and Dn is a diagonal matrix whose entries are equal to the corresponding row sums of An. If An is a Wigner matrix with entries in the domain of attraction of a Gaussian distribution, the empirical spectral measure of Ln is known to converge to the free convolution of a semicircle distribution and a standard real Gaussian distribution. We consider real symmetric random matrices An with independent entries (up to symmetry) whose row sums converge to a purely non-Gaussian infinitely divisible distribution, which fall into the class of Lévy–Khintchine random matrices first introduced by Jung [Trans Am Math Soc, 370, (2018)]. Our main result shows that the empirical spectral measure of Ln converges almost surely to a deterministic limit. A key step in the proof is to use the purely non-Gaussian nature of the row sums to build a random operator to which Ln converges in an appropriate sense. This operator leads to a recursive distributional equation uniquely describing the Stieltjes transform of the limiting empirical spectral measure. AU - Campbell, Andrew J AU - O’Rourke, Sean ID - 13975 JF - Journal of Theoretical Probability SN - 0894-9840 TI - Spectrum of Lévy–Khintchine random laplacian matrices ER - TY - JOUR AB - The magnetotropic susceptibility is the thermodynamic coefficient associated with the rotational anisotropy of the free energy in an external magnetic field and is closely related to the magnetic susceptibility. It emerges naturally in frequency-shift measurements of oscillating mechanical cantilevers, which are becoming an increasingly important tool in the quantitative study of the thermodynamics of modern condensed-matter systems. Here we discuss the basic properties of the magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift measurements, as well as to the interpretation of those experiments in terms of the intrinsic properties of the system under study. AU - Shekhter, A. AU - Mcdonald, R. D. AU - Ramshaw, B. J. AU - Modic, Kimberly A ID - 13257 IS - 3 JF - Physical Review B SN - 2469-9950 TI - Magnetotropic susceptibility VL - 108 ER - TY - JOUR AB - This Special Collection is dedicated to the field of photocatalytic synthesis and contains a diverse selection of original research contributions. It includes studies on catalyst development, mechanistic investigations, method development and the use of enabling technologies, illustrating the many facets of state-of-the-art research in photocatalytic synthesis. Further, emerging topics are surveyed and discussed in three reviews and a concept article. AU - Næsborg, Line AU - Pieber, Bartholomäus AU - Wenger, Oliver S. ID - 13972 JF - ChemCatChem SN - 1867-3880 TI - Special Collection: Photocatalytic synthesis ER - TY - JOUR AB - The use of multimodal readout mechanisms next to label-free real-time monitoring of biomolecular interactions can provide valuable insight into surface-based reaction mechanisms. To this end, the combination of an electrolyte-gated field-effect transistor (EG-FET) with a fiber optic-coupled surface plasmon resonance (FO-SPR) probe serving as gate electrode has been investigated to deconvolute surface mass and charge density variations associated to surface reactions. However, applying an electrochemical potential on such gold-coated FO-SPR gate electrodes can induce gradual morphological changes of the thin gold film, leading to an irreversible blue-shift of the SPR wavelength and a substantial signal drift. We show that mild annealing leads to optical and electronic signal stabilization (20-fold lower signal drift than as-sputtered fiber optic gates) and improved overall analytical performance characteristics. The thermal treatment prevents morphological changes of the thin gold-film occurring during operation, hence providing reliable and stable data immediately upon gate voltage application. Thus, the readout output of both transducing principles, the optical FO-SPR and electronic EG-FET, stays constant throughout the whole sensing time-window and the long-term effect of thermal treatment is also improved, providing stable signals even after 1 year of storage. Annealing should therefore be considered a necessary modification for applying fiber optic gate electrodes in real-time multimodal investigations of surface reactions at the solid-liquid interface. AU - Hasler, Roger AU - Steger-Polt, Marie Helene AU - Reiner-Rozman, Ciril AU - Fossati, Stefan AU - Lee, Seungho AU - Aspermair, Patrik AU - Kleber, Christoph AU - Ibáñez, Maria AU - Dostalek, Jakub AU - Knoll, Wolfgang ID - 13968 JF - Frontiers in Physics TI - Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing VL - 11 ER - TY - JOUR AB - Long-time and large-data existence of weak solutions for initial- and boundary-value problems concerning three-dimensional flows of incompressible fluids is nowadays available not only for Navier–Stokes fluids but also for various fluid models where the relation between the Cauchy stress tensor and the symmetric part of the velocity gradient is nonlinear. The majority of such studies however concerns models where such a dependence is explicit (the stress is a function of the velocity gradient), which makes the class of studied models unduly restrictive. The same concerns boundary conditions, or more precisely the slipping mechanisms on the boundary, where the no-slip is still the most preferred condition considered in the literature. Our main objective is to develop a robust mathematical theory for unsteady internal flows of implicitly constituted incompressible fluids with implicit relations between the tangential projections of the velocity and the normal traction on the boundary. The theory covers numerous rheological models used in chemistry, biorheology, polymer and food industry as well as in geomechanics. It also includes, as special cases, nonlinear slip as well as stick–slip boundary conditions. Unlike earlier studies, the conditions characterizing admissible classes of constitutive equations are expressed by means of tools of elementary calculus. In addition, a fully constructive proof (approximation scheme) is incorporated. Finally, we focus on the question of uniqueness of such weak solutions. AU - Bulíček, Miroslav AU - Málek, Josef AU - Maringová, Erika ID - 14042 IS - 3 JF - Journal of Mathematical Fluid Mechanics SN - 1422-6928 TI - On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary VL - 25 ER - TY - JOUR AB - Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering. AU - Méhes, Elod AU - Mones, Enys AU - Varga, Máté AU - Zsigmond, Áron AU - Biri-Kovács, Beáta AU - Nyitray, László AU - Barone, Vanessa AU - Krens, Gabriel AU - Heisenberg, Carl-Philipp J AU - Vicsek, Tamás ID - 14041 JF - Communications Biology TI - 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation VL - 6 ER -