@article{14665, abstract = {We derive lower bounds on the maximal rates for multiple packings in high-dimensional Euclidean spaces. For any N > 0 and L ∈ Z ≥2 , a multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L - 1 balls of radius √ nN around points in C . This is a natural generalization of the sphere packing problem. We study the multiple packing problem for both bounded point sets whose points have norm at most √ nP for some constant P > 0, and unbounded point sets whose points are allowed to be anywhere in R n . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied over finite fields. We derive the best known lower bounds on the optimal multiple packing density. This is accomplished by establishing an inequality which relates the list-decoding error exponent for additive white Gaussian noise channels, a quantity of average-case nature, to the list-decoding radius, a quantity of worst-case nature. We also derive novel bounds on the list-decoding error exponent for infinite constellations and closed-form expressions for the list-decoding error exponents for the power-constrained AWGN channel, which may be of independent interest beyond multiple packing.}, author = {Zhang, Yihan and Vatedka, Shashank}, issn = {1557-9654}, journal = {IEEE Transactions on Information Theory}, publisher = {IEEE}, title = {{Multiple packing: Lower bounds via error exponents}}, doi = {10.1109/TIT.2023.3334032}, year = {2023}, } @article{14666, abstract = {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.}, author = {Chintaluri, Chaitanya and Vogels, Tim P}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {48}, publisher = {National Academy of Sciences}, title = {{Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species}}, doi = {10.1073/pnas.2306525120}, volume = {120}, year = {2023}, } @article{14667, abstract = {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. }, author = {Erdös, László and Ji, Hong Chang}, issn = {0246-0203}, journal = {Annales de l'institut Henri Poincare (B) Probability and Statistics}, number = {4}, pages = {2083--2105}, publisher = {Institute of Mathematical Statistics}, title = {{Functional CLT for non-Hermitian random matrices}}, doi = {10.1214/22-AIHP1304}, volume = {59}, year = {2023}, } @article{14683, abstract = {Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1}, author = {Amberg, Nicole and Cheung, Giselle T and Hippenmeyer, Simon}, issn = {2666-1667}, journal = {STAR Protocols}, keywords = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Neuroscience}, number = {1}, publisher = {Elsevier}, title = {{Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry}}, doi = {10.1016/j.xpro.2023.102771}, volume = {5}, year = {2023}, } @article{14687, abstract = {The short history of research on Li-O2 batteries has seen a remarkable number of mechanistic U-turns over the years. From the initial use of carbonate electrolytes, that were then found to be entirely unsuitable, to the belief that (su)peroxide was solely responsible for degradation, before the more reactive singlet oxygen was found to form, to the hypothesis that capacity depends on a competing surface/solution mechanism before a practically exclusive solution mechanism was identified. Herein, we argue for an ever-fresh look at the reported data without bias towards supposedly established explanations. We explain how the latest findings on rate and capacity limits, as well as the origin of side reactions, are connected via the disproportionation (DISP) step in the (dis)charge mechanism. Therefrom, directions emerge for the design of electrolytes and mediators on how to suppress side reactions and to enable high rate and high reversible capacity.}, author = {Jethwa, Rajesh B and Mondal, Soumyadip and Pant, Bhargavi and Freunberger, Stefan Alexander}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, publisher = {Wiley}, title = {{To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries}}, doi = {10.1002/anie.202316476}, year = {2023}, } @article{14689, author = {Ing-Simmons, Elizabeth and Machnik, Nick N and Vaquerizas, Juan M.}, issn = {1546-1718}, journal = {Nature Genetics}, number = {12}, pages = {2053--2055}, publisher = {Springer Nature}, title = {{Reply to: Revisiting the use of structural similarity index in Hi-C}}, doi = {10.1038/s41588-023-01595-5}, volume = {55}, year = {2023}, } @article{14690, abstract = {Generalized multifractality characterizes system size dependence of pure scaling local observables at Anderson transitions in all 10 symmetry classes of disordered systems. Recently, the concept of generalized multifractality has been extended to boundaries of critical disordered noninteracting systems. Here we study the generalized boundary multifractality in the presence of electron-electron interaction, focusing on the spin quantum Hall symmetry class (class C). Employing the two-loop renormalization group analysis within the Finkel'stein nonlinear sigma model, we compute the anomalous dimensions of the pure scaling operators located at the boundary of the system. We find that generalized boundary multifractal exponents are twice larger than their bulk counterparts. Exact symmetry relations between generalized boundary multifractal exponents in the case of noninteracting systems are explicitly broken by the interaction.}, author = {Babkin, Serafim and Burmistrov, I}, issn = {2469-9969}, journal = {Physical Review B}, number = {20}, publisher = {American Physical Society}, title = {{Boundary multifractality in the spin quantum Hall symmetry class with interaction}}, doi = {10.1103/PhysRevB.108.205429}, volume = {108}, year = {2023}, } @inproceedings{14691, abstract = {Continuous Group-Key Agreement (CGKA) allows a group of users to maintain a shared key. It is the fundamental cryptographic primitive underlying group messaging schemes and related protocols, most notably TreeKEM, the underlying key agreement protocol of the Messaging Layer Security (MLS) protocol, a standard for group messaging by the IETF. CKGA works in an asynchronous setting where parties only occasionally must come online, and their messages are relayed by an untrusted server. The most expensive operation provided by CKGA is that which allows for a user to refresh their key material in order to achieve forward secrecy (old messages are secure when a user is compromised) and post-compromise security (users can heal from compromise). One caveat of early CGKA protocols is that these update operations had to be performed sequentially, with any user wanting to update their key material having had to receive and process all previous updates. Late versions of TreeKEM do allow for concurrent updates at the cost of a communication overhead per update message that is linear in the number of updating parties. This was shown to be indeed necessary when achieving PCS in just two rounds of communication by [Bienstock et al. TCC’20]. The recently proposed protocol CoCoA [Alwen et al. Eurocrypt’22], however, shows that this overhead can be reduced if PCS requirements are relaxed, and only a logarithmic number of rounds is required. The natural question, thus, is whether CoCoA is optimal in this setting. In this work we answer this question, providing a lower bound on the cost (concretely, the amount of data to be uploaded to the server) for CGKA protocols that heal in an arbitrary k number of rounds, that shows that CoCoA is very close to optimal. Additionally, we extend CoCoA to heal in an arbitrary number of rounds, and propose a modification of it, with a reduced communication cost for certain k. We prove our bound in a combinatorial setting where the state of the protocol progresses in rounds, and the state of the protocol in each round is captured by a set system, each set specifying a set of users who share a secret key. We show this combinatorial model is equivalent to a symbolic model capturing building blocks including PRFs and public-key encryption, related to the one used by Bienstock et al. Our lower bound is of order k•n1+1/(k-1)/log(k), where 2≤k≤log(n) is the number of updates per user the protocol requires to heal. This generalizes the n2 bound for k=2 from Bienstock et al.. This bound almost matches the k⋅n1+2/(k-1) or k2⋅n1+1/(k-1) efficiency we get for the variants of the CoCoA protocol also introduced in this paper.}, author = {Auerbach, Benedikt and Cueto Noval, Miguel and Pascual Perez, Guillermo and Pietrzak, Krzysztof Z}, booktitle = {21st International Conference on Theory of Cryptography}, isbn = {9783031486203}, issn = {1611-3349}, location = {Taipei, Taiwan}, pages = {271--300}, publisher = {Springer Nature}, title = {{On the cost of post-compromise security in concurrent Continuous Group-Key Agreement}}, doi = {10.1007/978-3-031-48621-0_10}, volume = {14371}, year = {2023}, } @inproceedings{14692, abstract = {The generic-group model (GGM) aims to capture algorithms working over groups of prime order that only rely on the group operation, but do not exploit any additional structure given by the concrete implementation of the group. In it, it is possible to prove information-theoretic lower bounds on the hardness of problems like the discrete logarithm (DL) or computational Diffie-Hellman (CDH). Thus, since its introduction, it has served as a valuable tool to assess the concrete security provided by cryptographic schemes based on such problems. A work on the related algebraic-group model (AGM) introduced a method, used by many subsequent works, to adapt GGM lower bounds for one problem to another, by means of conceptually simple reductions. In this work, we propose an alternative approach to extend GGM bounds from one problem to another. Following an idea by Yun [EC15], we show that, in the GGM, the security of a large class of problems can be reduced to that of geometric search-problems. By reducing the security of the resulting geometric-search problems to variants of the search-by-hypersurface problem, for which information theoretic lower bounds exist, we give alternative proofs of several results that used the AGM approach. The main advantage of our approach is that our reduction from geometric search-problems works, as well, for the GGM with preprocessing (more precisely the bit-fixing GGM introduced by Coretti, Dodis and Guo [Crypto18]). As a consequence, this opens up the possibility of transferring preprocessing GGM bounds from one problem to another, also by means of simple reductions. Concretely, we prove novel preprocessing bounds on the hardness of the d-strong discrete logarithm, the d-strong Diffie-Hellman inversion, and multi-instance CDH problems, as well as a large class of Uber assumptions. Additionally, our approach applies to Shoup’s GGM without additional restrictions on the query behavior of the adversary, while the recent works of Zhang, Zhou, and Katz [AC22] and Zhandry [Crypto22] highlight that this is not the case for the AGM approach.}, author = {Auerbach, Benedikt and Hoffmann, Charlotte and Pascual Perez, Guillermo}, booktitle = {21st International Conference on Theory of Cryptography}, isbn = {9783031486203}, issn = {1611-3349}, pages = {301--330}, publisher = {Springer Nature}, title = {{Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing}}, doi = {10.1007/978-3-031-48621-0_11}, volume = {14371}, year = {2023}, } @inproceedings{14693, abstract = {Lucas sequences are constant-recursive integer sequences with a long history of applications in cryptography, both in the design of cryptographic schemes and cryptanalysis. In this work, we study the sequential hardness of computing Lucas sequences over an RSA modulus. First, we show that modular Lucas sequences are at least as sequentially hard as the classical delay function given by iterated modular squaring proposed by Rivest, Shamir, and Wagner (MIT Tech. Rep. 1996) in the context of time-lock puzzles. Moreover, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring. In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring. Second, we demonstrate the feasibility of constructing practically-efficient verifiable delay functions based on the sequential hardness of modular Lucas sequences. Our construction builds on the work of Pietrzak (ITCS 2019) by leveraging the intrinsic connection between the problem of computing modular Lucas sequences and exponentiation in an appropriate extension field.}, author = {Hoffmann, Charlotte and Hubáček, Pavel and Kamath, Chethan and Krňák, Tomáš}, booktitle = {21st International Conference on Theory of Cryptography}, isbn = {9783031486234}, issn = {1611-3349}, location = {Taipei, Taiwan}, pages = {336--362}, publisher = {Springer Nature}, title = {{(Verifiable) delay functions from Lucas sequences}}, doi = {10.1007/978-3-031-48624-1_13}, volume = {14372}, year = {2023}, } @phdthesis{14697, author = {Stopp, Julian A}, isbn = {978-3-99078-038-1}, issn = {2663 - 337X}, pages = {226}, publisher = {Institute of Science and Technology Austria}, title = {{Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function}}, doi = {10.15479/at:ista:14697}, year = {2023}, } @article{14701, author = {Archer, Lynden A. and Bruce, Peter G. and Calvo, Ernesto J. and Dewar, Daniel and Ellison, James H. J. and Freunberger, Stefan Alexander and Gao, Xiangwen and Hardwick, Laurence J. and Horwitz, Gabriela and Janek, Jürgen and Johnson, Lee R. and Jordan, Jack W. and Matsuda, Shoichi and Menkin, Svetlana and Mondal, Soumyadip and Qiu, Qianyuan and Samarakoon, Thukshan and Temprano, Israel and Uosaki, Kohei and Vailaya, Ganesh and Wachsman, Eric D. and Wu, Yiying and Ye, Shen}, issn = {1364-5498}, journal = {Faraday Discussions}, keywords = {Physical and Theoretical Chemistry}, publisher = {Royal Society of Chemistry}, title = {{Towards practical metal–oxygen batteries: General discussion}}, doi = {10.1039/d3fd90062b}, year = {2023}, } @article{14702, author = {Attard, Gary A. and Calvo, Ernesto J. and Curtiss, Larry A. and Dewar, Daniel and Ellison, James H. J. and Gao, Xiangwen and Grey, Clare P. and Hardwick, Laurence J. and Horwitz, Gabriela and Janek, Juergen and Johnson, Lee R. and Jordan, Jack W. and Matsuda, Shoichi and Mondal, Soumyadip and Neale, Alex R. and Ortiz-Vitoriano, Nagore and Temprano, Israel and Vailaya, Ganesh and Wachsman, Eric D. and Wang, Hsien-Hau and Wu, Yiying and Ye, Shen}, issn = {1364-5498}, journal = {Faraday Discussions}, keywords = {Physical and Theoretical Chemistry}, publisher = {Royal Society of Chemistry}, title = {{Materials for stable metal–oxygen battery cathodes: general discussion}}, doi = {10.1039/d3fd90059b}, year = {2023}, } @unpublished{14703, abstract = {We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation.}, author = {Ishida, Sadashige and Lavenant, Hugo}, booktitle = {arXiv}, keywords = {Optimal transport, Hamilton-Jacobi equation, convex optimization}, title = {{Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation}}, doi = {10.48550/arXiv.2312.12213}, year = {2023}, } @article{14709, abstract = {Amid the delays due to the global pandemic, in early October 2022, the auxin community gathered in the idyllic peninsula of Cavtat, Croatia. More than 170 scientists from across the world converged to discuss the latest advancements in fundamental and applied research in the field. The topics, from signalling and transport to plant architecture and response to the environment, show how auxin research must bridge from the molecular realm to macroscopic developmental responses. This is mirrored in this collection of reviews, contributed by participants of the Auxin 2022 meeting.}, author = {Del Bianco, Marta and Friml, Jiří and Strader, Lucia and Kepinski, Stefan}, issn = {1460-2431}, journal = {Journal of Experimental Botany}, number = {22}, pages = {6889--6892}, publisher = {Oxford University Press}, title = {{Auxin research: Creating tools for a greener future}}, doi = {10.1093/jxb/erad420}, volume = {74}, year = {2023}, } @article{14710, abstract = {The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells.}, author = {Curatolo, Agnese I. and Kimchi, Ofer and Goodrich, Carl Peter and Krueger, Ryan K. and Brenner, Michael P.}, issn = {20411723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{A computational toolbox for the assembly yield of complex and heterogeneous structures}}, doi = {10.1038/s41467-023-43168-4}, volume = {14}, year = {2023}, } @article{14715, abstract = {We consider N trapped bosons in the mean-field limit with coupling constant λN = 1/(N − 1). The ground state of such systems exhibits Bose–Einstein condensation. We prove that the probability of finding ℓ particles outside the condensate wave function decays exponentially in ℓ.}, author = {Mitrouskas, David Johannes and Pickl, Peter}, issn = {1089-7658}, journal = {Journal of Mathematical Physics}, number = {12}, publisher = {AIP Publishing}, title = {{Exponential decay of the number of excitations in the weakly interacting Bose gas}}, doi = {10.1063/5.0172199}, volume = {64}, year = {2023}, } @article{14716, abstract = {Background: Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature. Results: In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models’ performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics. Conclusions: Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers.}, author = {Yurtseven, Alper and Buyanova, Sofia and Agrawal, Amay Ajaykumar A. and Bochkareva, Olga and Kalinina, Olga V V.}, issn = {1471-2180}, journal = {BMC Microbiology}, number = {1}, publisher = {Springer Nature}, title = {{Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis}}, doi = {10.1186/s12866-023-03147-7}, volume = {23}, year = {2023}, } @article{14717, abstract = {We count primitive lattices of rank d inside Zn as their covolume tends to infinity, with respect to certain parameters of such lattices. These parameters include, for example, the subspace that a lattice spans, namely its projection to the Grassmannian; its homothety class and its equivalence class modulo rescaling and rotation, often referred to as a shape. We add to a prior work of Schmidt by allowing sets in the spaces of parameters that are general enough to conclude the joint equidistribution of these parameters. In addition to the primitive d-lattices Λ themselves, we also consider their orthogonal complements in Zn⁠, A1⁠, and show that the equidistribution occurs jointly for Λ and A1⁠. Finally, our asymptotic formulas for the number of primitive lattices include an explicit bound on the error term.}, author = {Horesh, Tal and Karasik, Yakov}, issn = {1464-3847}, journal = {Quarterly Journal of Mathematics}, number = {4}, pages = {1253--1294}, publisher = {Oxford University Press}, title = {{Equidistribution of primitive lattices in ℝn}}, doi = {10.1093/qmath/haad008}, volume = {74}, year = {2023}, } @inproceedings{14718, abstract = {Binary decision diagrams (BDDs) are one of the fundamental data structures in formal methods and computer science in general. However, the performance of BDD-based algorithms greatly depends on memory latency due to the reliance on large hash tables and thus, by extension, on the speed of random memory access. This hinders the full utilisation of resources available on modern CPUs, since the absolute memory latency has not improved significantly for at least a decade. In this paper, we explore several implementation techniques that improve the performance of BDD manipulation either through enhanced memory locality or by partially eliminating random memory access. On a benchmark suite of 600+ BDDs derived from real-world applications, we demonstrate runtime that is comparable or better than parallelising the same operations on eight CPU cores. }, author = {Pastva, Samuel and Henzinger, Thomas A}, booktitle = {Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design}, isbn = {9783854480600}, location = {Ames, IA, United States}, pages = {122--131}, publisher = {TU Vienna Academic Press}, title = {{Binary decision diagrams on modern hardware}}, doi = {10.34727/2023/isbn.978-3-85448-060-0_20}, year = {2023}, }