TY - JOUR AB - Acanthocephalans, intestinal parasites of vertebrates, are characterised by orders of magnitude higher metal accumulation than free-living organisms, but the mechanism of such effective metal accumulation is still unknown. The aim of our study was to gain new insights into the high-resolution localization of elements in the bodies of acanthocephalans, thus taking an initial step towards elucidating metal uptake and accumulation in organisms under real environmental conditions. For the first time, nanoscale secondary ion mass spectrometry (NanoSIMS) was used for high-resolution mapping of 12 elements (C, Ca, Cu, Fe, N, Na, O, P, Pb, S, Se, and Tl) in three selected body parts (trunk spines, inner part of the proboscis receptacle and inner surface of the tegument) of Dentitruncus truttae, a parasite of brown trout (Salmo trutta) from the Krka River in Croatia. In addition, the same body parts were examined using transmission electron microscopy (TEM) and correlated with NanoSIMS images. Metal concentrations determined using HR ICP-MS confirmed higher accumulation in D. truttae than in the fish intestine. The chemical composition of the acanthocephalan body showed the highest density of C, Ca, N, Na, O, S, as important and constitutive elements in living cells in all studied structures, while Fe was predominant among trace elements. In general, higher element density was found in trunk spines and tegument, as body structures responsible for substance absorption in parasites. The results obtained with NanoSIMS and TEM-NanoSIMS correlative imaging represent pilot data for mapping of elements at nanoscale resolution in the ultrastructure of various body parts of acanthocephalans and generally provide a contribution for further application of this technique in all parasite species. AU - Filipović Marijić, Vlatka AU - Subirana, Maria Angels AU - Schaumlöffel, Dirk AU - Barišić, Josip AU - Gontier, Etienne AU - Krasnici, Nesrete AU - Mijošek, Tatjana AU - Hernández-Orts, Jesús S. AU - Scholz, Tomáš AU - Erk, Marijana ID - 14786 JF - Science of The Total Environment KW - Pollution KW - Waste Management and Disposal KW - Environmental Chemistry KW - Environmental Engineering SN - 0048-9697 TI - First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS VL - 887 ER - TY - JOUR AB - Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes ofMimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system. AU - Stankowski, Sean AU - Chase, Madeline A. AU - McIntosh, Hanna AU - Streisfeld, Matthew A. ID - 14787 IS - 8 JF - Molecular Ecology KW - Genetics KW - Ecology KW - Evolution KW - Behavior and Systematics SN - 0962-1083 TI - Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone VL - 32 ER - TY - JOUR AB - Homeostatic balance in the intestinal epithelium relies on a fast cellular turnover, which is coordinated by an intricate interplay between biochemical signalling, mechanical forces and organ geometry. We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues. AU - Corominas-Murtra, Bernat AU - Hannezo, Edouard B ID - 12162 JF - Seminars in Cell & Developmental Biology KW - Cell Biology KW - Developmental Biology SN - 1084-9521 TI - Modelling the dynamics of mammalian gut homeostasis VL - 150-151 ER - TY - JOUR AB - We give a simple argument to prove Nagai’s conjecture for type II degenerations of compact hyperkähler manifolds and cohomology classes of middle degree. Under an additional assumption, the techniques yield the conjecture in arbitrary degree. This would complete the proof of Nagai’s conjecture in general, as it was proved already for type I degenerations by Kollár, Laza, Saccà, and Voisin [10] and independently by Soldatenkov [18], while it is immediate for type III degenerations. Our arguments are close in spirit to a recent paper by Harder [8] proving similar results for the restrictive class of good degenerations. AU - Huybrechts, D. AU - Mauri, Mirko ID - 13268 IS - 1 JF - Mathematical Research Letters SN - 1073-2780 TI - On type II degenerations of hyperkähler manifolds VL - 30 ER - TY - JOUR AB - This paper is concerned with equilibrium configurations of one-dimensional particle systems with non-convex nearest-neighbour and next-to-nearest-neighbour interactions and its passage to the continuum. The goal is to derive compactness results for a Γ-development of the energy with the novelty that external forces are allowed. In particular, the forces may depend on Lagrangian or Eulerian coordinates and thus may model dead as well as live loads. Our result is based on a new technique for deriving compactness results which are required for calculating the first-order Γ-limit in the presence of external forces: instead of comparing a configuration of n atoms to a global minimizer of the Γ-limit, we compare the configuration to a minimizer in some subclass of functions which in some sense are "close to" the configuration. The paper is complemented with the study of the minimizers of the Γ-limit. AU - Carioni, Marcello AU - Fischer, Julian L AU - Schlömerkemper, Anja ID - 14661 IS - 1 JF - Journal of Convex Analysis SN - 0944-6532 TI - External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development VL - 30 ER - TY - JOUR AB - A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population mean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed. AU - Pauw, Brian R. AU - Smales, Glen J. AU - Anker, Andy S. AU - Annadurai, Venkatasamy AU - Balazs, Daniel AU - Bienert, Ralf AU - Bouwman, Wim G. AU - Breßler, Ingo AU - Breternitz, Joachim AU - Brok, Erik S. AU - Bryant, Gary AU - Clulow, Andrew J. AU - Crater, Erin R. AU - De Geuser, Frédéric AU - Giudice, Alessandra Del AU - Deumer, Jérôme AU - Disch, Sabrina AU - Dutt, Shankar AU - Frank, Kilian AU - Fratini, Emiliano AU - Garcia, Paulo R.A.F. AU - Gilbert, Elliot P. AU - Hahn, Marc B. AU - Hallett, James AU - Hohenschutz, Max AU - Hollamby, Martin AU - Huband, Steven AU - Ilavsky, Jan AU - Jochum, Johanna K. AU - Juelsholt, Mikkel AU - Mansel, Bradley W. AU - Penttilä, Paavo AU - Pittkowski, Rebecca K. AU - Portale, Giuseppe AU - Pozzo, Lilo D. AU - Rochels, Leonhard AU - Rosalie, Julian M. AU - Saloga, Patrick E.J. AU - Seibt, Susanne AU - Smith, Andrew J. AU - Smith, Gregory N. AU - Spiering, Glenn A. AU - Stawski, Tomasz M. AU - Taché, Olivier AU - Thünemann, Andreas F. AU - Toth, Kristof AU - Whitten, Andrew E. AU - Wuttke, Joachim ID - 14799 IS - 6 JF - Journal of Applied Crystallography SN - 0021-8898 TI - The human factor: Results of a small-angle scattering data analysis round robin VL - 56 ER - TY - JOUR AB - We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in a LexRSM not existing even for simple terminating programs. Our contributions are twofold. First, we introduce a generalization of LexRSMs that allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs. AU - Chatterjee, Krishnendu AU - Kafshdar Goharshady, Ehsan AU - Novotný, Petr AU - Zárevúcky, Jiří AU - Zikelic, Dorde ID - 14778 IS - 2 JF - Formal Aspects of Computing KW - Theoretical Computer Science KW - Software SN - 0934-5043 TI - On lexicographic proof rules for probabilistic termination VL - 35 ER - TY - CONF AB - A faithful reproduction of gloss is inherently difficult because of the limited dynamic range, peak luminance, and 3D capabilities of display devices. This work investigates how the display capabilities affect gloss appearance with respect to a real-world reference object. To this end, we employ an accurate imaging pipeline to achieve a perceptual gloss match between a virtual and real object presented side-by-side on an augmented-reality high-dynamic-range (HDR) stereoscopic display, which has not been previously attained to this extent. Based on this precise gloss reproduction, we conduct a series of gloss matching experiments to study how gloss perception degrades based on individual factors: object albedo, display luminance, dynamic range, stereopsis, and tone mapping. We support the study with a detailed analysis of individual factors, followed by an in-depth discussion on the observed perceptual effects. Our experiments demonstrate that stereoscopic presentation has a limited effect on the gloss matching task on our HDR display. However, both reduced luminance and dynamic range of the display reduce the perceived gloss. This means that the visual system cannot compensate for the changes in gloss appearance across luminance (lack of gloss constancy), and the tone mapping operator should be carefully selected when reproducing gloss on a low dynamic range (LDR) display. AU - Chen, Bin AU - Jindal, Akshay AU - Piovarci, Michael AU - Wang, Chao AU - Seidel, Hans Peter AU - Didyk, Piotr AU - Myszkowski, Karol AU - Serrano, Ana AU - Mantiuk, Rafał K. ID - 14798 SN - 9798400703157 T2 - Proceedings of the SIGGRAPH Asia 2023 Conference TI - The effect of display capabilities on the gloss consistency between real and virtual objects ER - TY - JOUR AB - In the last few years, various communication compression techniques have emerged as an indispensable tool helping to alleviate the communication bottleneck in distributed learning. However, despite the fact biased compressors often show superior performance in practice when compared to the much more studied and understood unbiased compressors, very little is known about them. In this work we study three classes of biased compression operators, two of which are new, and their performance when applied to (stochastic) gradient descent and distributed (stochastic) gradient descent. We show for the first time that biased compressors can lead to linear convergence rates both in the single node and distributed settings. We prove that distributed compressed SGD method, employed with error feedback mechanism, enjoys the ergodic rate O(δLexp[−μKδL]+(C+δD)Kμ), where δ≥1 is a compression parameter which grows when more compression is applied, L and μ are the smoothness and strong convexity constants, C captures stochastic gradient noise (C=0 if full gradients are computed on each node) and D captures the variance of the gradients at the optimum (D=0 for over-parameterized models). Further, via a theoretical study of several synthetic and empirical distributions of communicated gradients, we shed light on why and by how much biased compressors outperform their unbiased variants. Finally, we propose several new biased compressors with promising theoretical guarantees and practical performance. AU - Beznosikov, Aleksandr AU - Horvath, Samuel AU - Richtarik, Peter AU - Safaryan, Mher ID - 14815 JF - Journal of Machine Learning Research TI - On biased compression for distributed learning VL - 24 ER - TY - CONF AB - In this paper, we present novel algorithms that efficiently compute a shortest reconfiguration sequence between two given dominating sets in trees and interval graphs under the TOKEN SLIDING model. In this problem, a graph is provided along with its two dominating sets, which can be imagined as tokens placed on vertices. The objective is to find a shortest sequence of dominating sets that transforms one set into the other, with each set in the sequence resulting from sliding a single token in the previous set. While identifying any sequence has been well studied, our work presents the first polynomial algorithms for this optimization variant in the context of dominating sets. AU - Křišťan, Jan Matyáš AU - Svoboda, Jakub ID - 14456 SN - 0302-9743 T2 - 24th International Symposium on Fundamentals of Computation Theory TI - Shortest dominating set reconfiguration under token sliding VL - 14292 ER - TY - CONF AB - This paper explores a modular design architecture aimed at helping blockchains (and other SMR implementation) to scale to a very large number of processes. This comes in contrast to existing monolithic architectures that interleave transaction dissemination, ordering, and execution in a single functionality. To achieve this we first split the monolith to multiple layers which can use existing distributed computing primitives. The exact specifications of the data dissemination part are formally defined by the Proof of Availability & Retrieval (PoA &R) abstraction. Solutions to the PoA &R problem contain two related sub-protocols: one that “pushes” information into the network and another that “pulls” this information. Regarding the latter, there is a dearth of research literature which is rectified in this paper. We present a family of pulling sub-protocols and rigorously analyze them. Extensive simulations support the theoretical claims of efficiency and robustness in case of a very large number of players. Finally, actual implementation and deployment on a small number of machines (roughly the size of several industrial systems) demonstrates the viability of the architecture’s paradigm. AU - Cohen, Shir AU - Goren, Guy AU - Kokoris Kogias, Eleftherios AU - Sonnino, Alberto AU - Spiegelman, Alexander ID - 14829 SN - 0302-9743 T2 - 27th International Conference on Financial Cryptography and Data Security TI - Proof of availability and retrieval in a modular blockchain architecture VL - 13951 ER - TY - JOUR AB - Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems. AU - Schwayer, Cornelia AU - Brückner, David ID - 14827 IS - 24 JF - Journal of Cell Science KW - Cell Biology SN - 0021-9533 TI - Connecting theory and experiment in cell and tissue mechanics VL - 136 ER - TY - CONF AB - We study the problem of learning controllers for discrete-time non-linear stochastic dynamical systems with formal reach-avoid guarantees. This work presents the first method for providing formal reach-avoid guarantees, which combine and generalize stability and safety guarantees, with a tolerable probability threshold p in [0,1] over the infinite time horizon. Our method leverages advances in machine learning literature and it represents formal certificates as neural networks. In particular, we learn a certificate in the form of a reach-avoid supermartingale (RASM), a novel notion that we introduce in this work. Our RASMs provide reachability and avoidance guarantees by imposing constraints on what can be viewed as a stochastic extension of level sets of Lyapunov functions for deterministic systems. Our approach solves several important problems -- it can be used to learn a control policy from scratch, to verify a reach-avoid specification for a fixed control policy, or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification. We validate our approach on 3 stochastic non-linear reinforcement learning tasks. AU - Zikelic, Dorde AU - Lechner, Mathias AU - Henzinger, Thomas A AU - Chatterjee, Krishnendu ID - 14830 IS - 10 KW - General Medicine SN - 2159-5399 T2 - Proceedings of the 37th AAAI Conference on Artificial Intelligence TI - Learning control policies for stochastic systems with reach-avoid guarantees VL - 37 ER - TY - JOUR AB - Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies. AU - Stankowski, Sean AU - Zagrodzka, Zuzanna B AU - Galindo, Juan AU - Montaño-Rendón, Mauricio AU - Faria, Rui AU - Mikhailova, Natalia AU - Blakeslee, April M H AU - Arnason, Einar AU - Broquet, Thomas AU - Morales, Hernán E AU - Grahame, John W AU - Westram, Anja M AU - Johannesson, Kerstin AU - Butlin, Roger K ID - 14833 IS - 1 JF - Evolutionary Journal of the Linnean Society TI - Whole-genome phylogeography of the intertidal snail Littorina saxatilis VL - 2 ER - TY - JOUR AB - Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the products. While efforts to design catalysts are often focused on accelerating the chemical reaction on the catalyst, catalysis is a global property of the catalytic cycle that involves all processes. These are controlled by both intrinsic parameters such as the composition and shape of the catalyst and extrinsic parameters such as the concentration of the chemical species at play. We examine here the conditions that catalysis imposes on the different steps of a reaction cycle and the respective role of intrinsic and extrinsic parameters of the system on the emergence of catalysis by using an approach based on first-passage times. We illustrate this approach for various decompositions of a catalytic cycle into elementary steps, including non-Markovian decompositions, which are useful when the presence and nature of intermediate states are a priori unknown. Our examples cover different types of reactions and clarify the constraints on elementary steps and the impact of species concentrations on catalysis. AU - Sakref, Yann AU - Muñoz Basagoiti, Maitane AU - Zeravcic, Zorana AU - Rivoire, Olivier ID - 14831 IS - 51 JF - The Journal of Physical Chemistry B KW - Materials Chemistry KW - Surfaces KW - Coatings and Films KW - Physical and Theoretical Chemistry SN - 1520-6106 TI - On kinetic constraints that catalysis imposes on elementary processes VL - 127 ER - TY - JOUR AB - Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that these proteins induce. While the pairwise interaction potential of two membrane-deforming spheres has recently been measured, membrane-deformation-induced interactions have been predicted to be nonadditive, and hence their collective behavior cannot be deduced from this measurement. We here employ a colloidal model system consisting of adhesive spheres and giant unilamellar vesicles to test these predictions by measuring the interaction potential of the simplest case of three membrane-deforming, spherical particles. We quantify their interactions and arrangements and, for the first time, experimentally confirm and quantify the nonadditive nature of membrane-deformation-induced interactions. We furthermore conclude that there exist two favorable configurations on the membrane: (1) a linear and (2) a triangular arrangement of the three spheres. Using Monte Carlo simulations, we corroborate the experimentally observed energy minima and identify a lowering of the membrane deformation as the cause for the observed configurations. The high symmetry of the preferred arrangements for three particles suggests that arrangements of many membrane-deforming objects might follow simple rules. AU - Azadbakht, Ali AU - Meadowcroft, Billie AU - Majek, Juraj AU - Šarić, Anđela AU - Kraft, Daniela J. ID - 14844 JF - Biophysical Journal SN - 0006-3495 TI - Nonadditivity in interactions between three membrane-wrapped colloidal spheres ER - TY - GEN AB - Cover Page AU - Becker, Lea Marie AU - Berbon, Mélanie AU - Vallet, Alicia AU - Grelard, Axelle AU - Morvan, Estelle AU - Bardiaux, Benjamin AU - Lichtenecker, Roman AU - Ernst, Matthias AU - Loquet, Antoine AU - Schanda, Paul ID - 14861 IS - 19 KW - General Chemistry KW - Catalysis SN - 1433-7851 T2 - Angewandte Chemie International Edition TI - Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues VL - 62 ER - TY - JOUR AB - We establish a precise three-term asymptotic expansion, with an optimal estimate of the error term, for the rightmost eigenvalue of an n×n random matrix with independent identically distributed complex entries as n tends to infinity. All terms in the expansion are universal. AU - Cipolloni, Giorgio AU - Erdös, László AU - Schröder, Dominik J AU - Xu, Yuanyuan ID - 14849 IS - 6 JF - The Annals of Probability KW - Statistics KW - Probability and Uncertainty KW - Statistics and Probability SN - 0091-1798 TI - On the rightmost eigenvalue of non-Hermitian random matrices VL - 51 ER - TY - JOUR AB - Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen. Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen Cross‐β‐Amyloidstruktur hervorgeht. AU - Becker, Lea Marie AU - Berbon, Mélanie AU - Vallet, Alicia AU - Grelard, Axelle AU - Morvan, Estelle AU - Bardiaux, Benjamin AU - Lichtenecker, Roman AU - Ernst, Matthias AU - Loquet, Antoine AU - Schanda, Paul ID - 14835 IS - 19 JF - Angewandte Chemie KW - General Medicine SN - 0044-8249 TI - Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten VL - 135 ER - TY - CHAP AB - Organization – or departure from a random pattern – in tropical deep convection is heavily studied due to its immediate relevance to climate sensitivity and extremes. Low-latitude convection has motivated numerical model idealizations, where the Coriolis force is removed and boundary conditions are simplified spatially and temporally. One of the most stunning aspects of such idealized simulated cloud organization is the spontaneous clumping of convection that can occur without any predetermining external perturbation, such as inhomogeneous surface boundary conditions or large-scale waves. Whereas individual convective rain cells measure only few kilometers in horizontal diameter, the clusters they form can often span hundreds or even thousands of kilometers. Hence, organization may emerge from the very small scales but can show effects at the synoptic scale. We refer to such emergent organization as convective self-organization. Convective self-organization thus features characteristics of emergence, such as non-trivial system-scale pattern formation or hysteresis. We summarize observational evidence for large-scale organization and briefly recap classical idealized modeling studies that yield convective self-aggregation – emergent organization under strongly idealized boundary conditions. We then focus on developing research, where temporal variation, such as the diurnal cycle, or two-way interactive surface properties yield distinct organizational modes. Convectively generated cold pools and mesoscale convective systems, both ubiquitous in nature, are thereby found to potentially play key roles in promoting – rather than suppressing – sustained system-scale organization. AU - Haerter, Jan O. AU - Muller, Caroline J ED - Sullivan, Sylvia ED - Hoose, Corinna ID - 14853 SN - 2328-8779 T2 - Clouds and Their Climatic Impacts TI - Mechanisms for the Self‐Organization of Tropical Deep Convection ER - TY - CHAP AB - Understanding the mechanisms of chaperones at the atomic level generally requires producing chaperone–client complexes in vitro. This task comes with significant challenges, because one needs to find conditions in which the client protein is presented to the chaperone in a state that binds and at the same time avoid the pitfalls of protein aggregation that are often inherent to such states. The strategy differs significantly for different client proteins and chaperones, but there are common underlying principles. Here, we discuss these principles and deduce the strategies that can be successfully applied for different chaperone–client complexes. We review successful biochemical strategies applied to making the client protein “binding competent” and illustrate the different strategies with examples of recent biophysical and biochemical studies. AU - Sučec, I. AU - Schanda, Paul ED - Hiller, Sebastian ED - Liu, Maili ED - He, Lichun ID - 14847 SN - 9781839162824 T2 - Biophysics of Molecular Chaperones TI - Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies VL - 29 ER - TY - CHAP AB - Regulating protein states is considered the core function of chaperones. However, despite their importance to all major cellular processes, the conformational changes that chaperones impart on polypeptide chains are difficult to study directly due to their heterogeneous, dynamic, and multi-step nature. Here, we review recent advances towards this aim using single-molecule manipulation methods, which are rapidly revealing new mechanisms of conformational control and helping to define a different perspective on the chaperone function. AU - Wruck, F. AU - Avellaneda Sarrió, Mario AU - Naqvi, M. M. AU - Koers, E. J. AU - Till, K. AU - Gross, L. AU - Moayed, F. AU - Roland, A. AU - Heling, L. W. H. J. AU - Mashaghi, A. AU - Tans, S. J. ED - Hiller, Sebastian ED - Liu, Maili ED - He, Lichun ID - 14848 SN - 9781839162824 T2 - Biophysics of Molecular Chaperones TI - Probing Single Chaperone Substrates VL - 29 ER - TY - JOUR AB - Abstract We study the spectrum of the Fröhlich Hamiltonian for the polaron at fixed total momentum. We prove the existence of excited eigenvalues between the ground state energy and the essential spectrum at strong coupling. In fact, our main result shows that the number of excited energy bands diverges in the strong coupling limit. To prove this we derive upper bounds for the min-max values of the corresponding fiber Hamiltonians and compare them with the bottom of the essential spectrum, a lower bound on which was recently obtained by Brooks and Seiringer (Comm. Math. Phys. 404:1 (2023), 287–337). The upper bounds are given in terms of the ground state energy band shifted by momentum-independent excitation energies determined by an effective Hamiltonian of Bogoliubov type. AU - Mitrouskas, David Johannes AU - Seiringer, Robert ID - 14854 IS - 4 JF - Pure and Applied Analysis KW - General Medicine SN - 2578-5885 TI - Ubiquity of bound states for the strongly coupled polaron VL - 5 ER - TY - CONF AB - We entangled microwave and optical photons for the first time as verified by a measured two-mode vacuum squeezing of 0.7 dB. This electro-optic entanglement is the key resource needed to connect cryogenic quantum circuits. AU - Sahu, Rishabh AU - Qiu, Liu AU - Hease, William J AU - Arnold, Georg M AU - Minoguchi, Yuri AU - Rabl, Peter AU - Fink, Johannes M ID - 14872 SN - 9781957171296 T2 - Frontiers in Optics + Laser Science 2023 TI - Entangling microwaves and telecom wavelength light ER - TY - CONF AB - Starting with the empty graph on $[n]$, at each round, a set of $K=K(n)$ edges is presented chosen uniformly at random from the ones that have not been presented yet. We are then asked to choose at most one of the presented edges and add it to the current graph. Our goal is to construct a Hamiltonian graph with $(1+o(1))n$ edges within as few rounds as possible. We show that in this process, one can build a Hamiltonian graph of size $(1+o(1))n$ in $(1+o(1))(1+(\log n)/2K) n$ rounds w.h.p. The case $K=1$ implies that w.h.p. one can build a Hamiltonian graph by choosing $(1+o(1))n$ edges in an online fashion as they appear along the first $(0.5+o(1))n\log n$ rounds of the random graph process. This answers a question of Frieze, Krivelevich and Michaeli. Observe that the number of rounds is asymptotically optimal as the first $0.5n\log n$ edges do not span a Hamilton cycle w.h.p. The case $K=\Theta(\log n)$ implies that the Hamiltonicity threshold of the corresponding Achlioptas process is at most $(1+o(1))(1+(\log n)/2K) n$. This matches the $(1-o(1))(1+(\log n)/2K) n$ lower bound due to Krivelevich, Lubetzky and Sudakov and resolves the problem of determining the Hamiltonicity threshold of the Achlioptas process with $K=\Theta(\log n)$. We also show that in the above process one can construct a graph $G$ that spans a matching of size $\lfloor V(G)/2) \rfloor$ and $(0.5+o(1))n$ edges within $(1+o(1))(0.5+(\log n)/2K) n$ rounds w.h.p. Our proof relies on a robust Hamiltonicity property of the strong $4$-core of the binomial random graph which we use as a black-box. This property allows it to absorb paths covering vertices outside the strong $4$-core into a cycle. AU - Anastos, Michael ID - 14867 T2 - Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications TI - Constructing Hamilton cycles and perfect matchings efficiently ER - TY - GEN AU - Stöllner, Andrea AU - Lenton, Isaac C AU - Muller, Caroline J AU - Waitukaitis, Scott R ID - 14864 T2 - EGU General Assembly 2023 TI - Measuring spontaneous charging of single aerosol particles ER - TY - GEN AU - Rella, Simon AU - Kulikova, Y AU - Minnegalieva, Aygul AU - Kondrashov, Fyodor ID - 14862 IS - Supplement_2 KW - Public Health KW - Environmental and Occupational Health SN - 1101-1262 T2 - European Journal of Public Health TI - Complex vaccination strategies prevent the emergence of vaccine resistance VL - 33 ER - TY - GEN AU - Polesello, Andrea AU - Muller, Caroline J AU - Pasquero, Claudia AU - Meroni, Agostino N. ID - 14863 T2 - EGU General Assembly 2023 TI - Intensification mechanisms of tropical cyclones ER - TY - GEN AB - Fragmented landscapes pose a significant threat to the persistence of species as they are highly susceptible to heightened risk of extinction due to the combined effects of genetic and demographic factors such as genetic drift and demographic stochasticity. This paper explores the intricate interplay between genetic load and extinction risk within metapopulations with a focus on understanding the impact of eco-evolutionary feedback mechanisms. We distinguish between two models of selection: soft selection, characterised by subpopulations maintaining carrying capacity despite load, and hard selection, where load can significantly affect population size. Within the soft selection framework, we investigate the impact of gene flow on genetic load at a single locus, while also considering the effect of selection strength and dominance coefficient. We subsequently build on this to examine how gene flow influences both population size and load under hard selection as well as identify critical thresholds for metapopulation persistence. Our analysis employs the diffusion, semi-deterministic and effective migration approximations. Our findings reveal that under soft selection, even modest levels of migration can significantly alleviate the burden of load. In sharp contrast, with hard selection, a much higher degree of gene flow is required to mitigate load and prevent the collapse of the metapopulation. Overall, this study sheds light into the crucial role migration plays in shaping the dynamics of genetic load and extinction risk in fragmented landscapes, offering valuable insights for conservation strategies and the preservation of diversity in a changing world. AU - Olusanya, Oluwafunmilola O AU - Khudiakova, Kseniia AU - Sachdeva, Himani ID - 14732 T2 - bioRxiv TI - Genetic load, eco-evolutionary feedback and extinction in a metapopulation ER - TY - JOUR AB - We propose a computational design approach for covering a surface with individually addressable RGB LEDs, effectively forming a low-resolution surface screen. To achieve a low-cost and scalable approach, we propose creating designs from flat PCB panels bent in-place along the surface of a 3D printed core. Working with standard rigid PCBs enables the use of established PCB manufacturing services, allowing the fabrication of designs with several hundred LEDs. Our approach optimizes the PCB geometry for folding, and then jointly optimizes the LED packing, circuit and routing, solving a challenging layout problem under strict manufacturing requirements. Unlike paper, PCBs cannot bend beyond a certain point without breaking. Therefore, we introduce parametric cut patterns acting as hinges, designed to allow bending while remaining compact. To tackle the joint optimization of placement, circuit and routing, we propose a specialized algorithm that splits the global problem into one sub-problem per triangle, which is then individually solved. Our technique generates PCB blueprints in a completely automated way. After being fabricated by a PCB manufacturing service, the boards are bent and glued by the user onto the 3D printed support. We demonstrate our technique on a range of physical models and virtual examples, creating intricate surface light patterns from hundreds of LEDs. AU - Freire, Marco AU - Bhargava, Manas AU - Schreck, Camille AU - Hugron, Pierre-Alexandre AU - Bickel, Bernd AU - Lefebvre, Sylvain ID - 13049 IS - 4 JF - Transactions on Graphics KW - PCB design and layout KW - Mesh geometry models SN - 0730-0301 TI - PCBend: Light up your 3D shapes with foldable circuit boards VL - 42 ER - TY - JOUR AB - Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast. AU - Chen, Huihuang AU - Li, Lanxin AU - Zou, Minxia AU - Qi, Linlin AU - Friml, Jiří ID - 13212 IS - 7 JF - Molecular Plant SN - 1752-9867 TI - Distinct functions of TIR1 and AFB1 receptors in auxin signalling. VL - 16 ER - TY - JOUR AB - Tattoos are a highly popular medium, with both artistic and medical applications. Although the mechanical process of tattoo application has evolved historically, the results are reliant on the artisanal skill of the artist. This can be especially challenging for some skin tones, or in cases where artists lack experience. We provide the first systematic overview of tattooing as a computational fabrication technique. We built an automated tattooing rig and a recipe for the creation of silicone sheets mimicking realistic skin tones, which allowed us to create an accurate model predicting tattoo appearance. This enables several exciting applications including tattoo previewing, color retargeting, novel ink spectra optimization, color-accurate prosthetics, and more. AU - Piovarci, Michael AU - Chapiro, Alexandre AU - Bickel, Bernd ID - 12984 IS - 4 JF - Transactions on Graphics KW - appearance KW - modeling KW - reproduction KW - tattoo KW - skin color KW - gamut mapping KW - ink-optimization KW - prosthetic SN - 0730-0301 TI - Skin-Screen: A computational fabrication framework for color tattoos VL - 42 ER - TY - GEN AB - Code and data necessary to reproduce the simulations and data analyses reported in our manuscript: Tomé, D.F., Zhang, Y., Aida, T., Mosto, O., Lu, Y., Chen, M., Sadeh, S., Roy, D. S., Clopath, C. Dynamic and selective engrams emerge with memory consolidation. 2023. AU - Feitosa Tomé, Douglas ID - 14892 TI - douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation ER - TY - JOUR AB - Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator. AU - Mukhopadhyay, Soham AU - Senior, Jorden L AU - Saez Mollejo, Jaime AU - Puglia, Denise AU - Zemlicka, Martin AU - Fink, Johannes M AU - Higginbotham, Andrew P ID - 14032 JF - Nature Physics KW - General Physics and Astronomy SN - 1745-2473 TI - Superconductivity from a melted insulator in Josephson junction arrays VL - 19 ER - TY - JOUR AB - The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general. AU - Qi, Linlin AU - Friml, Jiří ID - 13266 IS - 2 JF - New Phytologist SN - 0028-646X TI - Tale of cAMP as a second messenger in auxin signaling and beyond VL - 240 ER - TY - JOUR AB - Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question. AU - Minchington, Thomas AU - Rus, Stefanie AU - Kicheva, Anna ID - 13136 JF - Current Opinion in Systems Biology TI - Control of tissue dimensions in the developing neural tube and somites VL - 35 ER - TY - JOUR AB - In this paper we consider a class of stochastic reaction-diffusion equations. We provide local well-posedness, regularity, blow-up criteria and positivity of solutions. The key novelties of this work are related to the use transport noise, critical spaces and the proof of higher order regularity of solutions – even in case of non-smooth initial data. Crucial tools are Lp(Lp)-theory, maximal regularity estimates and sharp blow-up criteria. We view the results of this paper as a general toolbox for establishing global well-posedness for a large class of reaction-diffusion systems of practical interest, of which many are completely open. In our follow-up work [8], the results of this paper are applied in the specific cases of the Lotka-Volterra equations and the Brusselator model. AU - Agresti, Antonio AU - Veraar, Mark ID - 13135 IS - 9 JF - Journal of Differential Equations SN - 0022-0396 TI - Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity VL - 368 ER - TY - JOUR AB - Consider a geodesic triangle on a surface of constant curvature and subdivide it recursively into four triangles by joining the midpoints of its edges. We show the existence of a uniform δ>0 such that, at any step of the subdivision, all the triangle angles lie in the interval (δ,π−δ) . Additionally, we exhibit stabilising behaviours for both angles and lengths as this subdivision progresses. AU - Brunck, Florestan R ID - 13270 IS - 3 JF - Discrete and Computational Geometry SN - 0179-5376 TI - Iterated medial triangle subdivision in surfaces of constant curvature VL - 70 ER - TY - JOUR AB - This paper is a collection of results on combinatorial properties of codes for the Z-channel . A Z-channel with error fraction τ takes as input a length- n binary codeword and injects in an adversarial manner up to n τ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest ( L - 1)-list-decodable code for the Z-channel with error fraction τ has exponential size (in n ) if τ is less than a critical value that we call the ( L - 1)- list-decoding Plotkin point and has constant size if τ is larger than the threshold. The ( L -1)-list-decoding Plotkin point is known to be L -1/L-1 – L -L/ L-1 , which equals 1/4 for unique-decoding with L -1 = 1. In this paper, we derive various results for the size of the largest codes above and below the list-decoding Plotkin point. In particular, we show that the largest ( L -1)-list-decodable code ε-above the Plotkin point, for any given sufficiently small positive constant ε > 0, has size Θ L (ε -3/2 ) for any L - 1 ≥ 1. We also devise upper and lower bounds on the exponential size of codes below the list-decoding Plotkin point. AU - Polyanskii, Nikita AU - Zhang, Yihan ID - 13269 IS - 10 JF - IEEE Transactions on Information Theory SN - 0018-9448 TI - Codes for the Z-channel VL - 69 ER - TY - JOUR AB - Given A⊆GL2(Fq), we prove that there exist disjoint subsets B,C⊆A such that A=B⊔C and their additive and multiplicative energies satisfying max{E+(B),E×(C)}≪|A|3/M(|A|), where M(|A|)=min{q4/3/|A|1/3(log|A|)2/3,|A|4/5/q13/5(log|A|)27/10}. We also study some related questions on moderate expanders over matrix rings, namely, for A,B,C⊆GL2(Fq), we have |AB+C|, |(A+B)C|≫q4, whenever |A||B||C|≫q10+1/2. These improve earlier results due to Karabulut, Koh, Pham, Shen, and Vinh ([2019], Expanding phenomena over matrix rings, ForumMath., 31, 951–970). AU - Mohammadi, Ali AU - Pham, Thang AU - Wang, Yiting ID - 13128 IS - 4 JF - Canadian Mathematical Bulletin SN - 0008-4395 TI - An energy decomposition theorem for matrices and related questions VL - 66 ER - TY - JOUR AB - The phytohormone auxin plays central roles in many growth and developmental processes in plants. Development of chemical tools targeting the auxin pathway is useful for both plant biology and agriculture. Here we reveal that naproxen, a synthetic compound with anti-inflammatory activity in humans, acts as an auxin transport inhibitor targeting PIN-FORMED (PIN) transporters in plants. Physiological experiments indicate that exogenous naproxen treatment affects pleiotropic auxin-regulated developmental processes. Additional cellular and biochemical evidence indicates that naproxen suppresses auxin transport, specifically PIN-mediated auxin efflux. Moreover, biochemical and structural analyses confirm that naproxen binds directly to PIN1 protein via the same binding cavity as the indole-3-acetic acid substrate. Thus, by combining cellular, biochemical, and structural approaches, this study clearly establishes that naproxen is a PIN inhibitor and elucidates the underlying mechanisms. Further use of this compound may advance our understanding of the molecular mechanisms of PIN-mediated auxin transport and expand our toolkit in auxin biology and agriculture. AU - Xia, Jing AU - Kong, Mengjuan AU - Yang, Zhisen AU - Sun, Lianghanxiao AU - Peng, Yakun AU - Mao, Yanbo AU - Wei, Hong AU - Ying, Wei AU - Gao, Yongxiao AU - Friml, Jiří AU - Weng, Jianping AU - Liu, Xin AU - Sun, Linfeng AU - Tan, Shutang ID - 13209 IS - 6 JF - Plant Communications TI - Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen VL - 4 ER - TY - JOUR AB - When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases. AU - Grober, Daniel AU - Palaia, Ivan AU - Ucar, Mehmet C AU - Hannezo, Edouard B AU - Šarić, Anđela AU - Palacci, Jérémie A ID - 13971 JF - Nature Physics SN - 1745-2473 TI - Unconventional colloidal aggregation in chiral bacterial baths VL - 19 ER - TY - JOUR AB - The Dean–Kawasaki equation—a strongly singular SPDE—is a basic equation of fluctuating hydrodynamics; it has been proposed in the physics literature to describe the fluctuations of the density of N independent diffusing particles in the regime of large particle numbers N≫1. The singular nature of the Dean–Kawasaki equation presents a substantial challenge for both its analysis and its rigorous mathematical justification. Besides being non-renormalisable by the theory of regularity structures by Hairer et al., it has recently been shown to not even admit nontrivial martingale solutions. In the present work, we give a rigorous and fully quantitative justification of the Dean–Kawasaki equation by considering the natural regularisation provided by standard numerical discretisations: We show that structure-preserving discretisations of the Dean–Kawasaki equation may approximate the density fluctuations of N non-interacting diffusing particles to arbitrary order in N−1 (in suitable weak metrics). In other words, the Dean–Kawasaki equation may be interpreted as a “recipe” for accurate and efficient numerical simulations of the density fluctuations of independent diffusing particles. AU - Cornalba, Federico AU - Fischer, Julian L ID - 10551 IS - 5 JF - Archive for Rational Mechanics and Analysis SN - 0003-9527 TI - The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles VL - 247 ER - TY - JOUR AB - Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. We consider the problem of monitoring the classification decisions of neural networks in the presence of novel classes. For this purpose, we generalize our recently proposed abstraction-based monitor from binary output to real-valued quantitative output. This quantitative output enables new applications, two of which we investigate in the paper. As our first application, we introduce an algorithmic framework for active monitoring of a neural network, which allows us to learn new classes dynamically and yet maintain high monitoring performance. As our second application, we present an offline procedure to retrain the neural network to improve the monitor’s detection performance without deteriorating the network’s classification accuracy. Our experimental evaluation demonstrates both the benefits of our active monitoring framework in dynamic scenarios and the effectiveness of the retraining procedure. AU - Kueffner, Konstantin AU - Lukina, Anna AU - Schilling, Christian AU - Henzinger, Thomas A ID - 13234 JF - International Journal on Software Tools for Technology Transfer SN - 1433-2779 TI - Into the unknown: Active monitoring of neural networks (extended version) VL - 25 ER - TY - JOUR AB - Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing itself as a powerful method for the characterization of protein dynamics at the atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling, and pulse sequence design has paved the way for quantitative analyses of even rare structural fluctuations. In addition to isotropic chemical-shift fluctuations exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has a wider arsenal of observables, allowing to see motions even if the exchanging states do not differ in their chemical shifts. We demonstrate the potential of the technique for probing motions in challenging large enzymes, membrane proteins, and protein assemblies. AU - Napoli, Federico AU - Becker, Lea Marie AU - Schanda, Paul ID - 14036 IS - 10 JF - Current Opinion in Structural Biology SN - 0959-440X TI - Protein dynamics detected by magic-angle spinning relaxation dispersion NMR VL - 82 ER - TY - JOUR AB - Over the last two decades, a significant line of work in theoretical algorithms has made progress in solving linear systems of the form Lx=b, where L is the Laplacian matrix of a weighted graph with weights w(i,j)>0 on the edges. The solution x of the linear system can be interpreted as the potentials of an electrical flow in which the resistance on edge (i, j) is 1/w(i, j). Kelner et al. (in: Proceedings of the 45th Annual ACM Symposium on the Theory of Computing, pp 911–920, 2013. https://doi.org/10.1145/2488608.2488724) give a combinatorial, near-linear time algorithm that maintains the Kirchoff Current Law, and gradually enforces the Kirchoff Potential Law by updating flows around cycles (cycle toggling). In this paper, we consider a dual version of the algorithm that maintains the Kirchoff Potential Law, and gradually enforces the Kirchoff Current Law by cut toggling: each iteration updates all potentials on one side of a fundamental cut of a spanning tree by the same amount. We prove that this dual algorithm also runs in a near-linear number of iterations. We show, however, that if we abstract cut toggling as a natural data structure problem, this problem can be reduced to the online vector–matrix-vector problem, which has been conjectured to be difficult for dynamic algorithms (Henzinger et al., in: Proceedings of the 47th Annual ACM Symposium on the Theory of Computing, pp 21–30, 2015. https://doi.org/10.1145/2746539.2746609). The conjecture implies that the data structure does not have an O(n1−ϵ) time algorithm for any ϵ>0, and thus a straightforward implementation of the cut-toggling algorithm requires essentially linear time per iteration. To circumvent the lower bound, we batch update steps, and perform them simultaneously instead of sequentially. An appropriate choice of batching leads to an O˜(m1.5) time cut-toggling algorithm for solving Laplacian systems. Furthermore, we show that if we sparsify the graph and call our algorithm recursively on the Laplacian system implied by batching and sparsifying, we can reduce the running time to O(m1+ϵ) for any ϵ>0. Thus, the dual cut-toggling algorithm can achieve (almost) the same running time as its primal cycle-toggling counterpart. AU - Henzinger, Monika H AU - Jin, Billy AU - Peng, Richard AU - Williamson, David P. ID - 14043 JF - Algorithmica SN - 0178-4617 TI - A combinatorial cut-toggling algorithm for solving Laplacian linear systems VL - 85 ER - TY - JOUR AB - Polar active matter of self-propelled particles sustain spontaneous flows through the full-integer topological defects. We study theoretically the incompressible flow profiles around ±1 defects induced by polar and dipolar active forces. We show that dipolar forces induce vortical flows around the +1 defect, while the flow around the −1 defect has an 8-fold rotational symmetry. The vortical flow changes its chirality near the +1 defect core in the absence of the friction with a substrate. We show analytically that the flow induced by polar active forces is vortical near the +1 defect and is 4-fold symmetric near the −1 defect, while it becomes uniform in the far-field. For a pair of oppositely charged defects, this polar flow contributes to a mutual interaction force that depends only on the orientation of the defect pair relative to the background polarization, and that enhances defect pair annihilation. This is in contradiction with the effect of dipolar active forces which decay inversely proportional with the defect separation distance. As such, our analyses reveals a long-ranged mechanism for the pairwise interaction between topological defects in polar active matter. AU - Rønning, Jonas AU - Renaud, Julian B AU - Doostmohammadi, Amin AU - Angheluta, Luiza ID - 14087 JF - Soft Matter SN - 1744-683X TI - Spontaneous flows and dynamics of full-integer topological defects in polar active matter VL - 39 ER - TY - JOUR AB - We prove that the generator of the L2 implementation of a KMS-symmetric quantum Markov semigroup can be expressed as the square of a derivation with values in a Hilbert bimodule, extending earlier results by Cipriani and Sauvageot for tracially symmetric semigroups and the second-named author for GNS-symmetric semigroups. This result hinges on the introduction of a new completely positive map on the algebra of bounded operators on the GNS Hilbert space. This transformation maps symmetric Markov operators to symmetric Markov operators and is essential to obtain the required inner product on the Hilbert bimodule. AU - Vernooij, Matthijs AU - Wirth, Melchior ID - 13319 JF - Communications in Mathematical Physics SN - 0010-3616 TI - Derivations and KMS-symmetric quantum Markov semigroups VL - 403 ER - TY - JOUR AB - Alpha oscillations are a distinctive feature of the awake resting state of the human brain. However, their functional role in resting-state neuronal dynamics remains poorly understood. Here we show that, during resting wakefulness, alpha oscillations drive an alternation of attenuation and amplification bouts in neural activity. Our analysis indicates that inhibition is activated in pulses that last for a single alpha cycle and gradually suppress neural activity, while excitation is successively enhanced over a few alpha cycles to amplify neural activity. Furthermore, we show that long-term alpha amplitude fluctuations—the “waxing and waning” phenomenon—are an attenuation-amplification mechanism described by a power-law decay of the activity rate in the “waning” phase. Importantly, we do not observe such dynamics during non-rapid eye movement (NREM) sleep with marginal alpha oscillations. The results suggest that alpha oscillations modulate neural activity not only through pulses of inhibition (pulsed inhibition hypothesis) but also by timely enhancement of excitation (or disinhibition). AU - Lombardi, Fabrizio AU - Herrmann, Hans J. AU - Parrino, Liborio AU - Plenz, Dietmar AU - Scarpetta, Silvia AU - Vaudano, Anna Elisabetta AU - De Arcangelis, Lucilla AU - Shriki, Oren ID - 14402 IS - 10 JF - Cell Reports TI - Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state VL - 42 ER - TY - JOUR AB - There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modeling framework, which determines the time dependency of DNA-variant age-at-onset associations without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the signs of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modeling of large-scale biobank data. AU - Ojavee, Sven E. AU - Darrous, Liza AU - Patxot, Marion AU - Läll, Kristi AU - Fischer, Krista AU - Mägi, Reedik AU - Kutalik, Zoltan AU - Robinson, Matthew Richard ID - 14258 IS - 9 JF - American Journal of Human Genetics SN - 0002-9297 TI - Genetic insights into the age-specific biological mechanisms governing human ovarian aging VL - 110 ER -