0 there exists a large subset of a ∈ F×p such that for kl a,1,p : x → e((ax+x) / p) we have M(kla,1,p) ≥ (1−ε/√2π + o(1)) log log p, as p→∞. Finally, we prove a result on the growth of the moments of {M (kla,1,p)}a∈F×p. 2020 Mathematics Subject Classification: 11L03, 11T23 (Primary); 14F20, 60F10 (Secondary).},
author = {Bonolis, Dante},
issn = {14698064},
journal = {Mathematical Proceedings of the Cambridge Philosophical Society},
publisher = {Cambridge University Press},
title = {{On the size of the maximum of incomplete Kloosterman sums}},
doi = {10.1017/S030500412100030X},
year = {2021},
}
@article{9380,
abstract = {Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands.},
author = {Seferbekova, Zaira and Zabelkin, Alexey and Yakovleva, Yulia and Afasizhev, Robert and Dranenko, Natalia O. and Alexeev, Nikita and Gelfand, Mikhail S. and Bochkareva, Olga},
issn = {1664302X},
journal = {Frontiers in Microbiology},
title = {{High rates of genome rearrangements and pathogenicity of Shigella spp.}},
doi = {10.3389/fmicb.2021.628622},
volume = {12},
year = {2021},
}
@article{9381,
abstract = {A game of rock-paper-scissors is an interesting example of an interaction where none of the pure strategies strictly dominates all others, leading to a cyclic pattern. In this work, we consider an unstable version of rock-paper-scissors dynamics and allow individuals to make behavioural mistakes during the strategy execution. We show that such an assumption can break a cyclic relationship leading to a stable equilibrium emerging with only one strategy surviving. We consider two cases: completely random mistakes when individuals have no bias towards any strategy and a general form of mistakes. Then, we determine conditions for a strategy to dominate all other strategies. However, given that individuals who adopt a dominating strategy are still prone to behavioural mistakes in the observed behaviour, we may still observe extinct strategies. That is, behavioural mistakes in strategy execution stabilise evolutionary dynamics leading to an evolutionary stable and, potentially, mixed co-existence equilibrium.},
author = {Kleshnina, Maria and Streipert, Sabrina S. and Filar, Jerzy A. and Chatterjee, Krishnendu},
issn = {15537358},
journal = {PLoS Computational Biology},
number = {4},
title = {{Mistakes can stabilise the dynamics of rock-paper-scissors games}},
doi = {10.1371/journal.pcbi.1008523},
volume = {17},
year = {2021},
}
@inproceedings{9210,
abstract = {Modern neural networks can easily fit their training set perfectly. Surprisingly, despite being “overfit” in this way, they tend to generalize well to future data, thereby defying the classic bias–variance trade-off of machine learning theory. Of the many possible explanations, a prevalent one is that training by stochastic gradient descent (SGD) imposes an implicit bias that leads it to learn simple functions, and these simple functions generalize well. However, the specifics of this implicit bias are not well understood.
In this work, we explore the smoothness conjecture which states that SGD is implicitly biased towards learning functions that are smooth. We propose several measures to formalize the intuitive notion of smoothness, and we conduct experiments to determine whether SGD indeed implicitly optimizes for these measures. Our findings rule out the possibility that smoothness measures based on first-order derivatives are being implicitly enforced. They are supportive, though, of the smoothness conjecture for measures based on second-order derivatives.},
author = {Volhejn, Vaclav and Lampert, Christoph},
booktitle = {42nd German Conference on Pattern Recognition },
isbn = {9783030712778},
issn = {16113349},
location = {Virtual},
pages = {246--259},
publisher = {Springer},
title = {{Does SGD implicitly optimize for smoothness?}},
doi = {10.1007/978-3-030-71278-5_18},
volume = {12544 LNCS},
year = {2021},
}
@article{9383,
abstract = {A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.},
author = {Stankowski, Sean and Ravinet, Mark},
issn = {15585646},
journal = {Evolution},
title = {{Defining the speciation continuum}},
doi = {10.1111/evo.14215},
year = {2021},
}
@article{9379,
author = {Bolger-Munro, Madison and Choi, Kate and Cheung, Faith and Liu, Yi Tian and Dang-Lawson, May and Deretic, Nikola and Keane, Connor and Gold, Michael R.},
issn = {2296634X},
journal = {Frontiers in Cell and Developmental Biology},
keywords = {B cell, actin, immune synapse, cell spreading, cofilin, WDR1 (AIP1), LIM domain kinase, B cell receptor (BCR)},
title = {{The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse}},
doi = {10.3389/fcell.2021.649433},
volume = {9},
year = {2021},
}
@article{9387,
abstract = {We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift.},
author = {Khudiakova, Kseniia and Neretina, Tatiana Yu. and Kondrashov, Alexey S.},
issn = {0022-5193},
journal = {Journal of Theoretical Biology},
keywords = {General Biochemistry, Genetics and Molecular Biology, Modelling and Simulation, Statistics and Probability, General Immunology and Microbiology, Applied Mathematics, General Agricultural and Biological Sciences, General Medicine},
publisher = {Elsevier BV},
title = {{Two linked loci under mutation-selection balance and Muller’s ratchet}},
doi = {10.1016/j.jtbi.2021.110729},
volume = {524},
year = {2021},
}
@article{9393,
abstract = {We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff, the ratio, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with bounded treewidth—a class that contains the control flow graphs of most programs. Let n denote the number of nodes of a graph, m the number of edges (for bounded treewidth 𝑚=𝑂(𝑛)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for the minimum initial credit problem we show that (1) for general graphs the problem can be solved in 𝑂(𝑛2⋅𝑚) time and the associated decision problem in 𝑂(𝑛⋅𝑚) time, improving the previous known 𝑂(𝑛3⋅𝑚⋅log(𝑛⋅𝑊)) and 𝑂(𝑛2⋅𝑚) bounds, respectively; and (2) for bounded treewidth graphs we present an algorithm that requires 𝑂(𝑛⋅log𝑛) time. Second, for bounded treewidth graphs we present an algorithm that approximates the mean-payoff value within a factor of 1+𝜖 in time 𝑂(𝑛⋅log(𝑛/𝜖)) as compared to the classical exact algorithms on general graphs that require quadratic time. Third, for the ratio property we present an algorithm that for bounded treewidth graphs works in time 𝑂(𝑛⋅log(|𝑎⋅𝑏|))=𝑂(𝑛⋅log(𝑛⋅𝑊)), when the output is 𝑎𝑏, as compared to the previously best known algorithm on general graphs with running time 𝑂(𝑛2⋅log(𝑛⋅𝑊)). We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas},
issn = {15728102},
journal = {Formal Methods in System Design},
publisher = {Springer},
title = {{Faster algorithms for quantitative verification in bounded treewidth graphs}},
doi = {10.1007/s10703-021-00373-5},
year = {2021},
}
@article{9394,
abstract = {Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.},
author = {Koch, Eva L. and Morales, Hernán E. and Larsson, Jenny and Westram, Anja M and Faria, Rui and Lemmon, Alan R. and Lemmon, E. Moriarty and Johannesson, Kerstin and Butlin, Roger K.},
issn = {20563744},
journal = {Evolution Letters},
publisher = {Wiley},
title = {{Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis}},
doi = {10.1002/evl3.227},
year = {2021},
}
@misc{9389,
abstract = {This .zip File contains the transport data for "Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states" by M. Valentini, et. al.
The measurements were done using Labber Software and the data is stored in the hdf5 file format.
Instructions of how to read the data are in "Notebook_Valentini.pdf".},
author = {Valentini, Marco},
publisher = {IST Austria},
title = {{Research data for "Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states"}},
doi = {10.15479/AT:ISTA:9389},
year = {2021},
}
@article{9392,
author = {Stankowski, Sean and Ravinet, Mark},
issn = {18790445},
journal = {Current Biology},
number = {9},
pages = {R428--R429},
publisher = {Cell Press},
title = {{Quantifying the use of species concepts}},
doi = {10.1016/j.cub.2021.03.060},
volume = {31},
year = {2021},
}
@article{9402,
abstract = {Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability.},
author = {Schmid, Laura and Chatterjee, Krishnendu and Hilbe, Christian and Nowak, Martin A.},
issn = {2397-3374},
journal = {Nature Human Behaviour},
publisher = {Springer Nature},
title = {{A unified framework of direct and indirect reciprocity}},
doi = {10.1038/s41562-021-01114-8},
year = {2021},
}
@inbook{9403,
abstract = {Optimal decision making requires individuals to know their available options and to anticipate correctly what consequences these options have. In many social interactions, however, we refrain from gathering all relevant information, even if this information would help us make better decisions and is costless to obtain. This chapter examines several examples of “deliberate ignorance.” Two simple models are proposed to illustrate how ignorance can evolve among self-interested and payoff - maximizing individuals, and open problems are highlighted that lie ahead for future research to explore.},
author = {Schmid, Laura and Hilbe, Christian},
booktitle = {Deliberate Ignorance: Choosing Not To Know},
editor = {Hertwig, Ralph and Engel, Christoph},
isbn = {978-0-262-04559-9},
pages = {139--152},
publisher = {MIT Press},
title = {{The evolution of strategic ignorance in strategic interaction}},
volume = {29},
year = {2021},
}
@article{9412,
abstract = {We extend our recent result [22] on the central limit theorem for the linear eigenvalue statistics of non-Hermitian matrices X with independent, identically distributed complex entries to the real symmetry class. We find that the expectation and variance substantially differ from their complex counterparts, reflecting (i) the special spectral symmetry of real matrices onto the real axis; and (ii) the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes the previously known special cases where either the test function is analytic [49] or the first four moments of the matrix elements match the real Gaussian [59, 44]. The key element of the proof is the analysis of several weakly dependent Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared with [22] is that the correlation structure of the stochastic differentials in each individual DBM is non-trivial, potentially even jeopardising its well-posedness.},
author = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J},
issn = {10836489},
journal = {Electronic Journal of Probability},
publisher = {Institute of Mathematical Statistics},
title = {{Fluctuation around the circular law for random matrices with real entries}},
doi = {10.1214/21-EJP591},
volume = {26},
year = {2021},
}
@article{9411,
abstract = {The dynamics of a triangular magnetocapillary swimmer is studied using the lattice Boltzmann method. We extend on our previous work, which deals with the self-assembly and a specific type of the swimmer motion characterized by the swimmer’s maximum velocity centred around the particle’s inverse viscous time. Here, we identify additional regimes of motion. First, modifying the ratio of surface tension and magnetic forces allows to study the swimmer propagation in the regime of significantly lower frequencies mainly defined by the strength of the magnetocapillary potential. Second, introducing a constant magnetic contribution in each of the particles in addition to their magnetic moment induced by external fields leads to another regime characterized by strong in-plane swimmer reorientations that resemble experimental observations.},
author = {Sukhov, Alexander and Hubert, Maxime and Grosjean, Galien M and Trosman, Oleg and Ziegler, Sebastian and Collard, Ylona and Vandewalle, Nicolas and Smith, Ana Sunčana and Harting, Jens},
issn = {1292895X},
journal = {European Physical Journal E},
number = {4},
publisher = {Springer},
title = {{Regimes of motion of magnetocapillary swimmers}},
doi = {10.1140/epje/s10189-021-00065-2},
volume = {44},
year = {2021},
}
@article{9414,
abstract = {Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density.},
author = {Ishihara, Keisuke and Decker, Franziska and Dos Santos Caldas, Paulo R and Pelletier, James F. and Loose, Martin and Brugués, Jan and Mitchison, Timothy J.},
issn = {19394586},
journal = {Molecular Biology of the Cell},
number = {9},
pages = {869--879},
publisher = {American Society for Cell Biology},
title = {{Spatial variation of microtubule depolymerization in large asters}},
doi = {10.1091/MBC.E20-11-0723},
volume = {32},
year = {2021},
}
@inproceedings{9200,
abstract = {Formal design of embedded and cyber-physical systems relies on mathematical modeling. In this paper, we consider the model class of hybrid automata whose dynamics are defined by affine differential equations. Given a set of time-series data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting behavior that is close to the data, up to a specified precision, and changes in synchrony with the data. A fundamental problem in our synthesis algorithm is to check membership of a time series in a hybrid automaton. Our solution integrates reachability and optimization techniques for affine dynamical systems to obtain both a sufficient and a necessary condition for membership, combined in a refinement framework. The algorithm processes one time series at a time and hence can be interrupted, provide an intermediate result, and be resumed. We report experimental results demonstrating the applicability of our synthesis approach.},
author = {Garcia Soto, Miriam and Henzinger, Thomas A and Schilling, Christian},
booktitle = {HSCC '21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control},
isbn = {9781450383394},
keywords = {hybrid automaton, membership, system identification},
location = {Online},
pages = {2102.12734},
publisher = {Association for Computing Machinery},
title = {{Synthesis of hybrid automata with affine dynamics from time-series data}},
doi = {10.1145/3447928.3456704},
year = {2021},
}
@article{9408,
abstract = {We present a computational design system that assists users to model, optimize, and fabricate quad-robots with soft skins. Our system addresses the challenging task of predicting their physical behavior by fully integrating the multibody dynamics of the mechanical skeleton and the elastic behavior of the soft skin. The developed motion control strategy uses an alternating optimization scheme to avoid expensive full space time-optimization, interleaving space-time optimization for the skeleton, and frame-by-frame optimization for the full dynamics. The output are motor torques to drive the robot to achieve a user prescribed motion trajectory. We also provide a collection of convenient engineering tools and empirical manufacturing guidance to support the fabrication of the designed quad-robot. We validate the feasibility of designs generated with our system through physics simulations and with a physically-fabricated prototype.},
author = {Feng, Xudong and Liu, Jiafeng and Wang, Huamin and Yang, Yin and Bao, Hujun and Bickel, Bernd and Xu, Weiwei},
issn = {10772626},
journal = {IEEE Transactions on Visualization and Computer Graphics},
number = {6},
publisher = {IEEE},
title = {{Computational design of skinned Quad-Robots}},
doi = {10.1109/TVCG.2019.2957218},
volume = {27},
year = {2021},
}
@article{9410,
abstract = {Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains.},
author = {Lagator, Mato and Uecker, Hildegard and Neve, Paul},
issn = {1744957X},
journal = {Biology letters},
number = {5},
publisher = {Royal Society of London},
title = {{Adaptation at different points along antibiotic concentration gradients}},
doi = {10.1098/rsbl.2020.0913},
volume = {17},
year = {2021},
}
@article{9376,
abstract = {This paper presents a method for designing planar multistable compliant structures. Given a sequence of desired stable states and the corresponding poses of the structure, we identify the topology and geometric realization of a mechanism—consisting of bars and joints—that is able to physically reproduce the desired multistable behavior. In order to solve this problem efficiently, we build on insights from minimally rigid graph theory to identify simple but effective topologies for the mechanism. We then optimize its geometric parameters, such as joint positions and bar lengths, to obtain correct transitions between the given poses. Simultaneously, we ensure adequate stability of each pose based on an effective approximate error metric related to the elastic energy Hessian of the bars in the mechanism. As demonstrated by our results, we obtain functional multistable mechanisms of manageable complexity that can be fabricated using 3D printing. Further, we evaluated the effectiveness of our method on a large number of examples in the simulation and fabricated several physical prototypes.},
author = {Zhang, Ran and Auzinger, Thomas and Bickel, Bernd},
journal = {ACM Transactions on Graphics},
keywords = {multistability, mechanism, computational design, rigidity},
title = {{Computational design of planar multistable compliant structures}},
doi = {10.1145/3453477},
year = {2021},
}
@article{7901,
abstract = {We derive rigorously the leading order of the correlation energy of a Fermi gas in a scaling regime of high density and weak interaction. The result verifies the prediction of the random-phase approximation. Our proof refines the method of collective bosonization in three dimensions. We approximately diagonalize an effective Hamiltonian describing approximately bosonic collective excitations around the Hartree–Fock state, while showing that gapless and non-collective excitations have only a negligible effect on the ground state energy.},
author = {Benedikter, Niels P and Nam, Phan Thành and Porta, Marcello and Schlein, Benjamin and Seiringer, Robert},
issn = {14321297},
journal = {Inventiones Mathematicae},
publisher = {Springer},
title = {{Correlation energy of a weakly interacting Fermi gas}},
doi = {10.1007/s00222-021-01041-5},
year = {2021},
}
@article{9437,
abstract = {The synaptic connection from medial habenula (MHb) to interpeduncular nucleus (IPN) is critical for emotion-related behaviors and uniquely expresses R-type Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates or inhibits transmitter release from MHb terminals depending on the IPN subnucleus, but the role of KCTDs is unknown. We therefore examined the localization and function of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3 currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3 co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3 with KCTDs therefore scales synaptic strength independent of GBR activation.},
author = {Bhandari, Pradeep and Vandael, David H and Fernández-Fernández, Diego and Fritzius, Thorsten and Kleindienst, David and Önal, Hüseyin C and Montanaro-Punzengruber, Jacqueline-Claire and Gassmann, Martin and Jonas, Peter M and Kulik, Akos and Bettler, Bernhard and Shigemoto, Ryuichi and Koppensteiner, Peter},
issn = {2050-084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial habenula terminals}},
doi = {10.7554/ELIFE.68274},
volume = {10},
year = {2021},
}
@article{9439,
abstract = {The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks.},
author = {Mlynarski, Wiktor F and Hermundstad, Ann M.},
issn = {15461726},
journal = {Nature Neuroscience},
publisher = {Springer Nature},
title = {{Efficient and adaptive sensory codes}},
doi = {10.1038/s41593-021-00846-0},
year = {2021},
}
@unpublished{9435,
abstract = {For any given positive integer l, we prove that every plane deformation of a circlewhich preserves the 1/2and 1/ (2l + 1) -rational caustics is trivial i.e. the deformationconsists only of similarities (rescalings and isometries).},
author = {Kaloshin, Vadim and Koudjinan, Edmond},
title = {{Non co-preservation of the 1/2 and 1/(2l+1)-rational caustics along deformations of circles}},
year = {2021},
}
@article{9438,
abstract = {Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system.},
author = {Vandael, David H and Okamoto, Yuji and Borges Merjane, Carolina and Vargas Barroso, Victor M and Suter, Benjamin and Jonas, Peter M},
issn = {17502799},
journal = {Nature Protocols},
number = {6},
pages = {2947–2967},
publisher = {Springer Nature},
title = {{Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses}},
doi = {10.1038/s41596-021-00526-0},
volume = {16},
year = {2021},
}
@article{9316,
abstract = {Embryo morphogenesis is impacted by dynamic changes in tissue material properties, which have been proposed to occur via processes akin to phase transitions (PTs). Here, we show that rigidity percolation provides a simple and robust theoretical framework to predict material/structural PTs of embryonic tissues from local cell connectivity. By using percolation theory, combined with directly monitoring dynamic changes in tissue rheology and cell contact mechanics, we demonstrate that the zebrafish blastoderm undergoes a genuine rigidity PT, brought about by a small reduction in adhesion-dependent cell connectivity below a critical value. We quantitatively predict and experimentally verify hallmarks of PTs, including power-law exponents and associated discontinuities of macroscopic observables. Finally, we show that this uniform PT depends on blastoderm cells undergoing meta-synchronous divisions causing random and, consequently, uniform changes in cell connectivity. Collectively, our theoretical and experimental findings reveal the structural basis of material PTs in an organismal context.},
author = {Petridou, Nicoletta and Corominas-Murtra, Bernat and Heisenberg, Carl-Philipp J and Hannezo, Edouard B},
issn = {10974172},
journal = {Cell},
number = {7},
pages = {1914--1928.e19},
publisher = {Elsevier},
title = {{Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions}},
doi = {10.1016/j.cell.2021.02.017},
volume = {184},
year = {2021},
}
@article{9257,
abstract = {The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing emergent kinetics, but this has received considerably less attention. Using recent advances in automatic differentiation, we show how kinetic pathways can be precisely designed by directly differentiating through statistical physics models, namely free energy calculations and molecular dynamics simulations. We consider two systems that are crucial to our understanding of structural self-assembly: bulk crystallization and small nanoclusters. In each case, we are able to assemble precise dynamical features. Using gradient information, we manipulate interactions among constituent particles to tune the rate at which these systems yield specific structures of interest. Moreover, we use this approach to learn nontrivial features about the high-dimensional design space, allowing us to accurately predict when multiple kinetic features can be simultaneously and independently controlled. These results provide a concrete and generalizable foundation for studying nonstructural self-assembly, including kinetic properties as well as other complex emergent properties, in a vast array of systems.},
author = {Goodrich, Carl Peter and King, Ella M. and Schoenholz, Samuel S. and Cubuk, Ekin D. and Brenner, Michael P.},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences},
number = {10},
publisher = {National Academy of Sciences},
title = {{Designing self-assembling kinetics with differentiable statistical physics models}},
doi = {10.1073/pnas.2024083118},
volume = {118},
year = {2021},
}
@article{9301,
abstract = {Electrodepositing insulating lithium peroxide (Li2O2) is the key process during discharge of aprotic Li–O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved lithium superoxide governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, better understanding governing factors for Li2O2 packing density and capacity requires structural sensitive in situ metrologies. Here, we establish in situ small- and wide-angle X-ray scattering (SAXS/WAXS) as a suitable method to record the Li2O2 phase evolution with atomic to submicrometer resolution during cycling a custom-built in situ Li–O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multiphase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets potentially forming large toroidal particles. Li2O2 solution growth is further justified by rotating ring-disk electrode measurements and electron microscopy. Higher discharge overpotentials lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. Hence, mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in weakly solvating electrolytes. The currently accepted Li–O2 reaction mechanism ought to be reconsidered.},
author = {Prehal, Christian and Samojlov, Aleksej and Nachtnebel, Manfred and Lovicar, Ludek and Kriechbaum, Manfred and Amenitsch, Heinz and Freunberger, Stefan Alexander},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
keywords = {small-angle X-ray scattering, oxygen reduction, disproportionation, Li-air battery},
number = {14},
publisher = {National Academy of Sciences},
title = {{In situ small-angle X-ray scattering reveals solution phase discharge of Li–O2 batteries with weakly solvating electrolytes}},
doi = {10.1073/pnas.2021893118},
volume = {118},
year = {2021},
}
@inproceedings{9345,
abstract = {Modeling a crystal as a periodic point set, we present a fingerprint consisting of density functionsthat facilitates the efficient search for new materials and material properties. We prove invarianceunder isometries, continuity, and completeness in the generic case, which are necessary featuresfor the reliable comparison of crystals. The proof of continuity integrates methods from discretegeometry and lattice theory, while the proof of generic completeness combines techniques fromgeometry with analysis. The fingerprint has a fast algorithm based on Brillouin zones and relatedinclusion-exclusion formulae. We have implemented the algorithm and describe its application tocrystal structure prediction.},
author = {Edelsbrunner, Herbert and Heiss, Teresa and Kurlin , Vitaliy and Smith, Philip and Wintraecken, Mathijs},
booktitle = {37th International Symposium on Computational Geometry (SoCG 2021)},
issn = {1868-8969},
location = {Online},
pages = {32:1--32:16},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{The density fingerprint of a periodic point set}},
doi = {10.4230/LIPIcs.SoCG.2021.32},
volume = {189},
year = {2021},
}
@inproceedings{9441,
abstract = {Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of ℝ^d defined as the zero set of some multivariate multivalued smooth function f: ℝ^d → ℝ^{d-n}, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation M̂ based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ = 1/D (and unavoidably exponential in n). Since it is known that for δ = Ω (d^{2.5}), M̂ is O(D²)-close and isotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M̂ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. },
author = {Boissonnat, Jean-Daniel and Kachanovich, Siargey and Wintraecken, Mathijs},
booktitle = {37th International Symposium on Computational Geometry (SoCG 2021)},
isbn = {978-3-95977-184-9},
issn = {1868-8969},
location = {Online},
pages = {17:1--17:16},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations}},
doi = {10.4230/LIPIcs.SoCG.2021.17},
volume = {189},
year = {2021},
}
@article{9443,
abstract = {Endoplasmic reticulum–plasma membrane contact sites (ER–PM CS) play fundamental roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER–PM protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an ER–PM tether that also functions in maintaining PM integrity. The ER–PM CS localization of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated by abiotic stress. Lipidomic analysis revealed that cold stress increased the accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to wild-type while the levels of most glycerolipid species remain unchanged. In addition, the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol at the PM produced during episodes of abiotic stress.},
author = {Ruiz-Lopez, N and Pérez-Sancho, J and Esteban Del Valle, A and Haslam, RP and Vanneste, S and Catalá, R and Perea-Resa, C and Van Damme, D and García-Hernández, S and Albert, A and Vallarino, J and Lin, J and Friml, Jiří and Macho, AP and Salinas, J and Rosado, A and Napier, JA and Amorim-Silva, V and Botella, MA},
issn = {1040-4651},
journal = {Plant Cell},
publisher = {American Society of Plant Biologists},
title = {{Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress}},
doi = {10.1093/plcell/koab122},
year = {2021},
}
@article{9447,
abstract = {Lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) based water-in-salt electrolytes (WiSEs) has recently emerged as a new promising class of electrolytes, primarily owing to their wide electrochemical stability windows (~3–4 V), that by far exceed the thermodynamic stability window of water (1.23 V). Upon increasing the salt concentration towards superconcentration the onset of the oxygen evolution reaction (OER) shifts more significantly than the hydrogen evolution reaction (HER) does. The OER shift has been explained by the accumulation of hydrophobic anions blocking water access to the electrode surface, hence by double layer theory. Here we demonstrate that the processes during oxidation are much more complex, involving OER, carbon and salt decomposition by OER intermediates, and salt precipitation upon local oversaturation. The positive shift in the onset potential of oxidation currents was elucidated by combining several advanced analysis techniques: rotating ring-disk electrode voltammetry, online electrochemical mass spectrometry, and X-ray photoelectron spectroscopy, using both dilute and superconcentrated electrolytes. The results demonstrate the importance of reactive OER intermediates and surface films for electrolyte and electrode stability and motivate further studies of the nature of the electrode.},
author = {Maffre, Marion and Bouchal, Roza and Freunberger, Stefan Alexander and Lindahl, Niklas and Johansson, Patrik and Favier, Frédéric and Fontaine, Olivier and Bélanger, Daniel},
issn = {0013-4651},
journal = {Journal of The Electrochemical Society},
keywords = {Renewable Energy, Sustainability and the Environment, Electrochemistry, Materials Chemistry, Electronic, Optical and Magnetic Materials, Surfaces, Coatings and Films, Condensed Matter Physics},
number = {5},
publisher = {IOP Publishing},
title = {{Investigation of electrochemical and chemical processes occurring at positive potentials in “Water-in-Salt” electrolytes}},
doi = {10.1149/1945-7111/ac0300},
volume = {168},
year = {2021},
}
@article{8909,
abstract = {Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies.},
author = {Jirovec, Daniel and Hofmann, Andrea C and Ballabio, Andrea and Mutter, Philipp M. and Tavani, Giulio and Botifoll, Marc and Crippa, Alessandro and Kukucka, Josip and Sagi, Oliver and Martins, Frederico and Saez Mollejo, Jaime and Prieto Gonzalez, Ivan and Borovkov, Maksim and Arbiol, Jordi and Chrastina, Daniel and Isella, Giovanni and Katsaros, Georgios},
issn = {1476-4660},
journal = {Nature Materials},
publisher = {Springer Nature},
title = {{A singlet triplet hole spin qubit in planar Ge}},
doi = {10.1038/s41563-021-01022-2},
year = {2021},
}
@misc{9323,
abstract = {This .zip File contains the data for figures presented in the main text and supplementary material of "A singlet triplet hole spin qubit in planar Ge" by D. Jirovec, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. The code for simulations is as well provided in Python.},
author = {Jirovec, Daniel},
publisher = {IST Austria},
title = {{Research data for "A singlet-triplet hole spin qubit planar Ge"}},
doi = {10.15479/AT:ISTA:9323},
year = {2021},
}
@article{9465,
abstract = {Given a locally finite set 𝑋⊆ℝ𝑑 and an integer 𝑘≥0, we consider the function 𝐰𝑘:Del𝑘(𝑋)→ℝ on the dual of the order-k Voronoi tessellation, whose sublevel sets generalize the notion of alpha shapes from order-1 to order-k (Edelsbrunner et al. in IEEE Trans Inf Theory IT-29:551–559, 1983; Krasnoshchekov and Polishchuk in Inf Process Lett 114:76–83, 2014). While this function is not necessarily generalized discrete Morse, in the sense of Forman (Adv Math 134:90–145, 1998) and Freij (Discrete Math 309:3821–3829, 2009), we prove that it satisfies similar properties so that its increments can be meaningfully classified into critical and non-critical steps. This result extends to the case of weighted points and sheds light on k-fold covers with balls in Euclidean space.},
author = {Edelsbrunner, Herbert and Nikitenko, Anton and Osang, Georg F},
issn = {14208997},
journal = {Journal of Geometry},
number = {1},
publisher = {Springer Nature},
title = {{A step in the Delaunay mosaic of order k}},
doi = {10.1007/s00022-021-00577-4},
volume = {112},
year = {2021},
}
@inproceedings{9466,
abstract = {In this work, we apply the dynamical systems analysis of Hanrot et al. (CRYPTO’11) to a class of lattice block reduction algorithms that includes (natural variants of) slide reduction and block-Rankin reduction. This implies sharper bounds on the polynomial running times (in the query model) for these algorithms and opens the door to faster practical variants of slide reduction. We give heuristic arguments showing that such variants can indeed speed up slide reduction significantly in practice. This is confirmed by experimental evidence, which also shows that our variants are competitive with state-of-the-art reduction algorithms.},
author = {Walter, Michael},
isbn = {9783030752446},
issn = {16113349},
location = {Virtual},
pages = {45--67},
publisher = {Springer Nature},
title = {{The convergence of slide-type reductions}},
doi = {10.1007/978-3-030-75245-3_3},
volume = {12710},
year = {2021},
}
@inproceedings{9464,
abstract = {We firstly introduce the self-assembled growth of highly uniform Ge quantum wires with controllable position, distance and length on patterned Si (001) substrates. We then present the electrically tunable strong spin-orbit coupling, the first Ge hole spin qubit and ultrafast operation of hole spin qubit in the Ge/Si quantum wires.},
author = {Gao, Fei and Zhang, Jie Yin and Wang, Jian Huan and Ming, Ming and Wang, Tina and Zhang, Jian Jun and Watzinger, Hannes and Kukucka, Josip and Vukušić, Lada and Katsaros, Georgios and Wang, Ke and Xu, Gang and Li, Hai Ou and Guo, Guo Ping},
booktitle = {2021 5th IEEE Electron Devices Technology and Manufacturing Conference, EDTM 2021},
isbn = {9781728181769},
location = {Virtual},
publisher = {IEEE},
title = {{Ge/Si quantum wires for quantum computing}},
doi = {10.1109/EDTM50988.2021.9420817},
year = {2021},
}
@article{9469,
abstract = {In this paper, we consider reflected three-operator splitting methods for monotone inclusion problems in real Hilbert spaces. To do this, we first obtain weak convergence analysis and nonasymptotic O(1/n) convergence rate of the reflected Krasnosel'skiĭ-Mann iteration for finding a fixed point of nonexpansive mapping in real Hilbert spaces under some seemingly easy to implement conditions on the iterative parameters. We then apply our results to three-operator splitting for the monotone inclusion problem and consequently obtain the corresponding convergence analysis. Furthermore, we derive reflected primal-dual algorithms for highly structured monotone inclusion problems. Some numerical implementations are drawn from splitting methods to support the theoretical analysis.},
author = {Iyiola, Olaniyi S. and Enyi, Cyril D. and Shehu, Yekini},
issn = {10294937},
journal = {Optimization Methods and Software},
publisher = {Taylor and Francis},
title = {{Reflected three-operator splitting method for monotone inclusion problem}},
doi = {10.1080/10556788.2021.1924715},
year = {2021},
}
@article{9470,
abstract = {A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.},
author = {Berdan, Emma L. and Blanckaert, Alexandre and Slotte, Tanja and Suh, Alexander and Westram, Anja M and Fragata, Inês},
issn = {1365294X},
journal = {Molecular Ecology},
number = {12},
pages = {2710--2723},
publisher = {Wiley},
title = {{Unboxing mutations: Connecting mutation types with evolutionary consequences}},
doi = {10.1111/mec.15936},
volume = {30},
year = {2021},
}
@article{9467,
abstract = {Turbulence in the flow of fluid through a pipe can be suppressed by buoyancy forces. As the suppression of turbulence leads to severe heat transfer deterioration, this is an important and undesirable phenomenon in both heating and cooling applications. Vertical flow is often considered, as the axial buoyancy force can help drive the flow. With heating measured by the buoyancy parameter 𝐶, our direct numerical simulations show that shear-driven turbulence may either be completely laminarised or it transitions to a relatively quiescent convection-driven state. Buoyancy forces cause a flattening of the base flow profile, which in isothermal pipe flow has recently been linked to complete suppression of turbulence (Kühnen et al., Nat. Phys., vol. 14, 2018, pp. 386–390), and the flattened laminar base profile has enhanced nonlinear stability (Marensi et al., J. Fluid Mech., vol. 863, 2019, pp. 50–875). In agreement with these findings, the nonlinear lower-branch travelling-wave solution analysed here, which is believed to mediate transition to turbulence in isothermal pipe flow, is shown to be suppressed by buoyancy. A linear instability of the laminar base flow is responsible for the appearance of the relatively quiescent convection driven state for 𝐶≳4 across the range of Reynolds numbers considered. In the suppression of turbulence, however, i.e. in the transition from turbulence, we find clearer association with the analysis of He et al. (J. Fluid Mech., vol. 809, 2016, pp. 31–71) than with the above dynamical systems approach, which describes better the transition to turbulence. The laminarisation criterion He et al. propose, based on an apparent Reynolds number of the flow as measured by its driving pressure gradient, is found to capture the critical 𝐶=𝐶𝑐𝑟(𝑅𝑒) above which the flow will be laminarised or switch to the convection-driven type. Our analysis suggests that it is the weakened rolls, rather than the streaks, which appear to be critical for laminarisation.},
author = {Marensi, Elena and He, Shuisheng and Willis, Ashley P.},
issn = {14697645},
journal = {Journal of Fluid Mechanics},
publisher = {Cambridge University Press},
title = {{Suppression of turbulence and travelling waves in a vertical heated pipe}},
doi = {10.1017/jfm.2021.371},
volume = {919},
year = {2021},
}
@article{9468,
abstract = {Motivated by the successful application of geometry to proving the Harary--Hill conjecture for “pseudolinear” drawings of $K_n$, we introduce “pseudospherical” drawings of graphs. A spherical drawing of a graph $G$ is a drawing in the unit sphere $\mathbb{S}^2$ in which the vertices of $G$ are represented as points---no three on a great circle---and the edges of $G$ are shortest-arcs in $\mathbb{S}^2$ connecting pairs of vertices. Such a drawing has three properties: (1) every edge $e$ is contained in a simple closed curve $\gamma_e$ such that the only vertices in $\gamma_e$ are the ends of $e$; (2) if $e\ne f$, then $\gamma_e\cap\gamma_f$ has precisely two crossings; and (3) if $e\ne f$, then $e$ intersects $\gamma_f$ at most once, in either a crossing or an end of $e$. We use properties (1)--(3) to define a pseudospherical drawing of $G$. Our main result is that for the complete graph, properties (1)--(3) are equivalent to the same three properties but with “precisely two crossings” in (2) replaced by “at most two crossings.” The proof requires a result in the geometric transversal theory of arrangements of pseudocircles. This is proved using the surprising result that the absence of special arcs (coherent spirals) in an arrangement of simple closed curves characterizes the fact that any two curves in the arrangement have at most two crossings. Our studies provide the necessary ideas for exhibiting a drawing of $K_{10}$ that has no extension to an arrangement of pseudocircles and a drawing of $K_9$ that does extend to an arrangement of pseudocircles, but no such extension has all pairs of pseudocircles crossing twice.
},
author = {Arroyo Guevara, Alan M and Richter, R. Bruce and Sunohara, Matthew},
issn = {08954801},
journal = {SIAM Journal on Discrete Mathematics},
number = {2},
pages = {1050--1076},
publisher = {Society for Industrial and Applied Mathematics},
title = {{Extending drawings of complete graphs into arrangements of pseudocircles}},
doi = {10.1137/20M1313234},
volume = {35},
year = {2021},
}
@article{8546,
abstract = {Brain neurons arise from relatively few progenitors generating an enormous diversity of neuronal types. Nonetheless, a cardinal feature of mammalian brain neurogenesis is thought to be that excitatory and inhibitory neurons derive from separate, spatially segregated progenitors. Whether bi-potential progenitors with an intrinsic capacity to generate both lineages exist and how such a fate decision may be regulated are unknown. Using cerebellar development as a model, we discover that individual progenitors can give rise to both inhibitory and excitatory lineages. Gradations of Notch activity determine the fates of the progenitors and their daughters. Daughters with the highest levels of Notch activity retain the progenitor fate, while intermediate levels of Notch activity generate inhibitory neurons, and daughters with very low levels of Notch signaling adopt the excitatory fate. Therefore, Notch-mediated binary cell fate choice is a mechanism for regulating the ratio of excitatory to inhibitory neurons from common progenitors.},
author = {Zhang, Tingting and Liu, Tengyuan and Mora, Natalia and Guegan, Justine and Bertrand, Mathilde and Contreras, Ximena and Hansen, Andi H and Streicher, Carmen and Anderle, Marica and Danda, Natasha and Tiberi, Luca and Hippenmeyer, Simon and Hassan, Bassem A.},
issn = { 22111247},
journal = {Cell Reports},
number = {10},
publisher = {Elsevier},
title = {{Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum}},
doi = {10.1016/j.celrep.2021.109208},
volume = {35},
year = {2021},
}
@article{9550,
abstract = {We prove that the energy of any eigenvector of a sum of several independent large Wigner matrices is equally distributed among these matrices with very high precision. This shows a particularly strong microcanonical form of the equipartition principle for quantum systems whose components are modelled by Wigner matrices. },
author = {Bao, Zhigang and Erdös, László and Schnelli, Kevin},
issn = {20505094},
journal = {Forum of Mathematics, Sigma},
publisher = {Cambridge University Press},
title = {{Equipartition principle for Wigner matrices}},
doi = {10.1017/fms.2021.38},
volume = {9},
year = {2021},
}
@article{9548,
abstract = {We extend the notion of the minimal volume ellipsoid containing a convex body in Rd to the setting of logarithmically concave functions. We consider a vast class of logarithmically concave functions whose superlevel sets are concentric ellipsoids. For a fixed function from this class, we consider the set of all its “affine” positions. For any log-concave function f on Rd, we consider functions belonging to this set of “affine” positions, and find the one with the minimal integral under the condition that it is pointwise greater than or equal to f. We study the properties of existence and uniqueness of the solution to this problem. For any s∈[0,+∞), we consider the construction dual to the recently defined John s-function (Ivanov and Naszódi in Functional John ellipsoids. arXiv preprint: arXiv:2006.09934, 2020). We prove that such a construction determines a unique function and call it the Löwner s-function of f. We study the Löwner s-functions as s tends to zero and to infinity. Finally, extending the notion of the outer volume ratio, we define the outer integral ratio of a log-concave function and give an asymptotically tight bound on it.},
author = {Ivanov, Grigory and Tsiutsiurupa, Igor},
issn = {1559-002X},
journal = {Journal of Geometric Analysis},
publisher = {Springer},
title = {{Functional Löwner ellipsoids}},
doi = {10.1007/s12220-021-00691-4},
year = {2021},
}
@article{9429,
abstract = {De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs.},
author = {Morandell, Jasmin and Schwarz, Lena A and Basilico, Bernadette and Tasciyan, Saren and Dimchev, Georgi A and Nicolas, Armel and Sommer, Christoph M and Kreuzinger, Caroline and Dotter, Christoph and Knaus, Lisa and Dobler, Zoe and Cacci, Emanuele and Schur, Florian KM and Danzl, Johann G and Novarino, Gaia},
issn = {2041-1723},
journal = {Nature Communications},
keywords = {General Biochemistry, Genetics and Molecular Biology},
number = {1},
publisher = {Springer Nature},
title = {{Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development}},
doi = {10.1038/s41467-021-23123-x},
volume = {12},
year = {2021},
}
@article{9431,
abstract = {Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.},
author = {Obr, Martin and Ricana, Clifton L. and Nikulin, Nadia and Feathers, Jon-Philip R. and Klanschnig, Marco and Thader, Andreas and Johnson, Marc C. and Vogt, Volker M. and Schur, Florian KM and Dick, Robert A.},
issn = {2041-1723},
journal = {Nature Communications},
keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry},
number = {1},
publisher = {Nature Research},
title = {{Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer}},
doi = {10.1038/s41467-021-23506-0},
volume = {12},
year = {2021},
}
@article{9540,
abstract = {The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.},
author = {Prattes, Michael and Grishkovskaya, Irina and Hodirnau, Victor-Valentin and Rössler, Ingrid and Klein, Isabella and Hetzmannseder, Christina and Zisser, Gertrude and Gruber, Christian C. and Gruber, Karl and Haselbach, David and Bergler, Helmut},
issn = {2041-1723},
journal = {Nature Communications},
keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry},
number = {1},
publisher = {Springer Nature},
title = {{Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine}},
doi = {10.1038/s41467-021-23854-x},
volume = {12},
year = {2021},
}
@article{9407,
abstract = {High impact epidemics constitute one of the largest threats humanity is facing in the 21st century. In the absence of pharmaceutical interventions, physical distancing together with testing, contact tracing and quarantining are crucial in slowing down epidemic dynamics. Yet, here we show that if testing capacities are limited, containment may fail dramatically because such combined countermeasures drastically change the rules of the epidemic transition: Instead of continuous, the response to countermeasures becomes discontinuous. Rather than following the conventional exponential growth, the outbreak that is initially strongly suppressed eventually accelerates and scales faster than exponential during an explosive growth period. As a consequence, containment measures either suffice to stop the outbreak at low total case numbers or fail catastrophically if marginally too weak, thus implying large uncertainties in reliably estimating overall epidemic dynamics, both during initial phases and during second wave scenarios.},
author = {Scarselli, Davide and Budanur, Nazmi B and Timme, Marc and Hof, Björn},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Springer Nature},
title = {{Discontinuous epidemic transition due to limited testing}},
doi = {10.1038/s41467-021-22725-9},
volume = {12},
year = {2021},
}
@article{9549,
abstract = {AMPA receptors (AMPARs) mediate the majority of excitatory transmission in the brain and enable the synaptic plasticity that underlies learning1. A diverse array of AMPAR signalling complexes are established by receptor auxiliary subunits, which associate with the AMPAR in various combinations to modulate trafficking, gating and synaptic strength2. However, their mechanisms of action are poorly understood. Here we determine cryo-electron microscopy structures of the heteromeric GluA1–GluA2 receptor assembled with both TARP-γ8 and CNIH2, the predominant AMPAR complex in the forebrain, in both resting and active states. Two TARP-γ8 and two CNIH2 subunits insert at distinct sites beneath the ligand-binding domains of the receptor, with site-specific lipids shaping each interaction and affecting the gating regulation of the AMPARs. Activation of the receptor leads to asymmetry between GluA1 and GluA2 along the ion conduction path and an outward expansion of the channel triggers counter-rotations of both auxiliary subunit pairs, promoting the active-state conformation. In addition, both TARP-γ8 and CNIH2 pivot towards the pore exit upon activation, extending their reach for cytoplasmic receptor elements. CNIH2 achieves this through its uniquely extended M2 helix, which has transformed this endoplasmic reticulum-export factor into a powerful AMPAR modulator that is capable of providing hippocampal pyramidal neurons with their integrative synaptic properties. },
author = {Zhang, Danyang and Watson, Jake and Matthews, Peter M. and Cais, Ondrej and Greger, Ingo H.},
issn = {14764687},
journal = {Nature},
publisher = {Springer Nature},
title = {{Gating and modulation of a hetero-octameric AMPA glutamate receptor}},
doi = {10.1038/s41586-021-03613-0},
year = {2021},
}
@article{9428,
abstract = {Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology.},
author = {Serbyn, Maksym and Abanin, Dmitry A. and Papić, Zlatko},
issn = {1745-2481},
journal = {Nature Physics},
number = {6},
pages = {675–685},
title = {{Quantum many-body scars and weak breaking of ergodicity}},
doi = {10.1038/s41567-021-01230-2},
volume = {17},
year = {2021},
}
@article{9462,
abstract = {We consider a system of N trapped bosons with repulsive interactions in a combined semiclassical mean-field limit at positive temperature. We show that the free energy is well approximated by the minimum of the Hartree free energy functional – a natural extension of the Hartree energy functional to positive temperatures. The Hartree free energy functional converges in the same limit to a semiclassical free energy functional, and we show that the system displays Bose–Einstein condensation if and only if it occurs in the semiclassical free energy functional. This allows us to show that for weak coupling the critical temperature decreases due to the repulsive interactions.},
author = {Deuchert, Andreas and Seiringer, Robert},
issn = {10960783},
journal = {Journal of Functional Analysis},
number = {6},
publisher = {Elsevier},
title = {{Semiclassical approximation and critical temperature shift for weakly interacting trapped bosons}},
doi = {10.1016/j.jfa.2021.109096},
volume = {281},
year = {2021},
}
@article{9547,
abstract = {With the wider availability of full-color 3D printers, color-accurate 3D-print preparation has received increased attention. A key challenge lies in the inherent translucency of commonly used print materials that blurs out details of the color texture. Previous work tries to compensate for these scattering effects through strategic assignment of colored primary materials to printer voxels. To date, the highest-quality approach uses iterative optimization that relies on computationally expensive Monte Carlo light transport simulation to predict the surface appearance from subsurface scattering within a given print material distribution; that optimization, however, takes in the order of days on a single machine. In our work, we dramatically speed up the process by replacing the light transport simulation with a data-driven approach. Leveraging a deep neural network to predict the scattering within a highly heterogeneous medium, our method performs around two orders of magnitude faster than Monte Carlo rendering while yielding optimization results of similar quality level. The network is based on an established method from atmospheric cloud rendering, adapted to our domain and extended by a physically motivated weight sharing scheme that substantially reduces the network size. We analyze its performance in an end-to-end print preparation pipeline and compare quality and runtime to alternative approaches, and demonstrate its generalization to unseen geometry and material values. This for the first time enables full heterogenous material optimization for 3D-print preparation within time frames in the order of the actual printing time.},
author = {Rittig, Tobias and Sumin, Denis and Babaei, Vahid and Didyk, Piotr and Voloboy, Alexey and Wilkie, Alexander and Bickel, Bernd and Myszkowski, Karol and Weyrich, Tim and Křivánek, Jaroslav},
issn = {14678659},
journal = {Computer Graphics Forum},
number = {2},
pages = {205--219},
publisher = {Wiley},
title = {{Neural acceleration of scattering-aware color 3D printing}},
doi = {10.1111/cgf.142626},
volume = {40},
year = {2021},
}
@article{9541,
abstract = {The Massively Parallel Computation (MPC) model is an emerging model that distills core aspects of distributed and parallel computation, developed as a tool to solve combinatorial (typically graph) problems in systems of many machines with limited space. Recent work has focused on the regime in which machines have sublinear (in n, the number of nodes in the input graph) space, with randomized algorithms presented for the fundamental problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms. A major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all edges incident to a single node. This poses a considerable obstacle compared to classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier, we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph, with the additional property that solving the problem on this subgraph provides significant progress towards solving the problem for the original input graph. Using this framework to derandomize the well-known algorithm of Luby [SICOMP’86], we obtain O(log Δ + log log n)-round deterministic MPC algorithms for solving the problems of Maximal Matching and Maximal Independent Set with O(nɛ) space on each machine for any constant ɛ > 0. These algorithms also run in O(log Δ) rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of O(log 2Δ) rounds by Censor-Hillel et al. [DISC’17].},
author = {Czumaj, Artur and Davies, Peter and Parter, Merav},
issn = {1549-6333},
journal = {ACM Transactions on Algorithms},
number = {2},
publisher = {ACM},
title = {{Graph sparsification for derandomizing massively parallel computation with low space}},
doi = {10.1145/3451992},
volume = {17},
year = {2021},
}
@phdthesis{9418,
abstract = {Deep learning is best known for its empirical success across a wide range of applications
spanning computer vision, natural language processing and speech. Of equal significance,
though perhaps less known, are its ramifications for learning theory: deep networks have
been observed to perform surprisingly well in the high-capacity regime, aka the overfitting
or underspecified regime. Classically, this regime on the far right of the bias-variance curve
is associated with poor generalisation; however, recent experiments with deep networks
challenge this view.
This thesis is devoted to investigating various aspects of underspecification in deep learning.
First, we argue that deep learning models are underspecified on two levels: a) any given
training dataset can be fit by many different functions, and b) any given function can be
expressed by many different parameter configurations. We refer to the second kind of
underspecification as parameterisation redundancy and we precisely characterise its extent.
Second, we characterise the implicit criteria (the inductive bias) that guide learning in the
underspecified regime. Specifically, we consider a nonlinear but tractable classification
setting, and show that given the choice, neural networks learn classifiers with a large margin.
Third, we consider learning scenarios where the inductive bias is not by itself sufficient to
deal with underspecification. We then study different ways of ‘tightening the specification’: i)
In the setting of representation learning with variational autoencoders, we propose a hand-
crafted regulariser based on mutual information. ii) In the setting of binary classification, we
consider soft-label (real-valued) supervision. We derive a generalisation bound for linear
networks supervised in this way and verify that soft labels facilitate fast learning. Finally, we
explore an application of soft-label supervision to the training of multi-exit models.},
author = {Bui Thi Mai, Phuong},
pages = {125},
publisher = {IST Austria},
title = {{Underspecification in Deep Learning}},
doi = {10.15479/AT:ISTA:9418},
year = {2021},
}
@inproceedings{9543,
abstract = {We consider the problem ofdistributed mean estimation (DME), in which n machines are each given a local d-dimensional vector xv∈Rd, and must cooperate to estimate the mean of their inputs μ=1n∑nv=1xv, while minimizing total communication cost. DME is a fundamental construct in distributed machine learning, and there has been considerable work on variants of this problem, especially in the context of distributed variance reduction for stochastic gradients in parallel SGD. Previous work typically assumes an upper bound on the norm of the input vectors, and achieves an error bound in terms of this norm. However, in many real applications, the input vectors are concentrated around the correct output μ, but μ itself has large norm. In such cases, previous output error bounds perform poorly. In this paper, we show that output error bounds need not depend on input norm. We provide a method of quantization which allows distributed mean estimation to be performed with solution quality dependent only on the distance between inputs, not on input norm, and show an analogous result for distributed variance reduction. The technique is based on a new connection with lattice theory. We also provide lower bounds showing that the communication to error trade-off of our algorithms is asymptotically optimal. As the lattices achieving optimal bounds under l2-norm can be computationally impractical, we also present an extension which leverages easy-to-use cubic lattices, and is loose only up to a logarithmic factor ind. We show experimentally that our method yields practical improvements for common applications, relative to prior approaches.},
author = {Davies, Peter and Gurunanthan, Vijaykrishna and Moshrefi, Niusha and Ashkboos, Saleh and Alistarh, Dan-Adrian},
booktitle = {9th International Conference on Learning Representations},
location = {Online},
title = {{New bounds for distributed mean estimation and variance reduction}},
year = {2021},
}
@inproceedings{9416,
abstract = {We study the inductive bias of two-layer ReLU networks trained by gradient flow. We identify a class of easy-to-learn (`orthogonally separable') datasets, and characterise the solution that ReLU networks trained on such datasets converge to. Irrespective of network width, the solution turns out to be a combination of two max-margin classifiers: one corresponding to the positive data subset and one corresponding to the negative data subset. The proof is based on the recently introduced concept of extremal sectors, for which we prove a number of properties in the context of orthogonal separability. In particular, we prove stationarity of activation patterns from some time onwards, which enables a reduction of the ReLU network to an ensemble of linear subnetworks.},
author = {Bui Thi Mai, Phuong and Lampert, Christoph},
booktitle = {9th International Conference on Learning Representations},
location = {Online},
title = {{The inductive bias of ReLU networks on orthogonally separable data}},
year = {2021},
}
@article{9449,
abstract = {Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits are particularly interesting owing to their ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor–semiconductor integration. Here, we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled g-factor difference-driven and exchange-driven rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1 μs, which we extend beyond 150 μs using echo techniques. These results demonstrate that Ge hole singlet-triplet qubits are competing with state-of-the-art GaAs and Si singlet-triplet qubits. In addition, their rotation frequencies and coherence are comparable with those of Ge single spin qubits, but singlet-triplet qubits can be operated at much lower fields, emphasizing their potential for on-chip integration with superconducting technologies.},
author = {Jirovec, Daniel and Hofmann, Andrea C and Ballabio, Andrea and Mutter, Philipp M. and Tavani, Giulio and Botifoll, Marc and Crippa, Alessandro and Kukucka, Josip and Sagi, Oliver and Martins, Frederico and Saez Mollejo, Jaime and Prieto Gonzalez, Ivan and Borovkov, Maksim and Arbio, Jordi and Chrastina, Daniel and Isella, Giovanni and Katsaros, Georgios},
issn = {1476-4660},
journal = {Nature Materials},
publisher = {Springer Nature},
title = {{A singlet-triplet hole spin qubit in planar Ge}},
doi = {10.1038/s41563-021-01022-2},
year = {2021},
}
@article{9571,
abstract = {As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes gradients to reduce communication costs. The baseline variant of QSGD provides strong theoretical guarantees, however, for practical purposes, the authors proposed a heuristic variant which we call QSGDinf, which demonstrated impressive empirical gains for distributed training of large neural networks. In this paper, we build on this work to propose a new gradient quantization scheme, and show that it has both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical performance of the QSGDinf heuristic and of other compression methods.},
author = {Ramezani-Kebrya, Ali and Faghri, Fartash and Markov, Ilya and Aksenov, Vitalii and Alistarh, Dan-Adrian and Roy, Daniel M.},
issn = {15337928},
journal = {Journal of Machine Learning Research},
number = {114},
pages = {1−43},
publisher = {Journal of Machine Learning Research},
title = {{NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization}},
volume = {22},
year = {2021},
}
@article{9558,
abstract = {We show that turbulent dynamics that arise in simulations of the three-dimensional Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing can be described as transient visits to the neighborhoods of unstable time-periodic solutions. Based on this description, we reduce the original system with more than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds to the neighborhood of a periodic orbit. The model accurately reproduces long-term averages of the system's observables as weighted sums over the periodic orbits.
},
author = {Yalniz, Gökhan and Hof, Björn and Budanur, Nazmi B},
issn = {1079-7114},
journal = {Physical Review Letters},
number = {24},
publisher = {American Physical Society},
title = {{Coarse graining the state space of a turbulent flow using periodic orbits}},
doi = {10.1103/PhysRevLett.126.244502},
volume = {126},
year = {2021},
}
@article{9570,
abstract = {We present conductance-matrix measurements in long, three-terminal hybrid superconductor-semiconductor nanowires, and compare with theoretical predictions of a magnetic-field-driven, topological quantum phase transition. By examining the nonlocal conductance, we identify the closure of the excitation gap in the bulk of the semiconductor before the emergence of zero-bias peaks, ruling out spurious gap-closure signatures from localized states. We observe that after the gap closes, nonlocal signals and zero-bias peaks fluctuate strongly at both ends, inconsistent with a simple picture of clean topological superconductivity.},
author = {Puglia, Denise and Martinez, E. A. and Ménard, G. C. and Pöschl, A. and Gronin, S. and Gardner, G. C. and Kallaher, R. and Manfra, M. J. and Marcus, C. M. and Higginbotham, Andrew P and Casparis, L.},
issn = {24699969},
journal = {Physical Review B},
number = {23},
publisher = {American Physical Society},
title = {{Closing of the induced gap in a hybrid superconductor-semiconductor nanowire}},
doi = {10.1103/PhysRevB.103.235201},
volume = {103},
year = {2021},
}
@phdthesis{8934,
abstract = {In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.
We use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.},
author = {Goharshady, Amir Kafshdar},
issn = {2663-337X},
pages = {278},
publisher = {IST Austria},
title = {{Parameterized and algebro-geometric advances in static program analysis}},
doi = {10.15479/AT:ISTA:8934},
year = {2021},
}
@article{7956,
abstract = {When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles.},
author = {Pȩkalski, J. and Rzadkowski, Wojciech and Panagiotopoulos, A. Z.},
issn = {10897690},
journal = {The Journal of chemical physics},
number = {20},
publisher = {AIP},
title = {{Shear-induced ordering in systems with competing interactions: A machine learning study}},
doi = {10.1063/5.0005194},
volume = {152},
year = {2020},
}
@article{7957,
abstract = {Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of
mutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches.},
author = {Parenti, Ilaria and Garcia Rabaneda, Luis E and Schön, Hanna and Novarino, Gaia},
issn = {1878108X},
journal = {Trends in Neurosciences},
number = {8},
pages = {608--621},
publisher = {Elsevier},
title = {{Neurodevelopmental disorders: From genetics to functional pathways}},
doi = {10.1016/j.tins.2020.05.004},
volume = {43},
year = {2020},
}
@article{7960,
abstract = {Let A={A1,…,An} be a family of sets in the plane. For 0≤i