@article{9287, abstract = {The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the auxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its polarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. }, author = {Narasimhan, Madhumitha and Gallei, Michelle C and Tan, Shutang and Johnson, Alexander J and Verstraeten, Inge and Li, Lanxin and Rodriguez Solovey, Lesia and Han, Huibin and Himschoot, E and Wang, R and Vanneste, S and Sánchez-Simarro, J and Aniento, F and Adamowski, Maciek and Friml, Jiří}, issn = {1532-2548}, journal = {Plant Physiology}, number = {2}, pages = {1122–1142}, publisher = {Oxford University Press}, title = {{Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking}}, doi = {10.1093/plphys/kiab134}, volume = {186}, year = {2021}, } @phdthesis{10083, abstract = {Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we combined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast alkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins. Besides, transgenic analysis combined with genetic engineering and biochemistry showed that vi they do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell growth, novel auxin signaling pathway as well as auxin-peptide crosstalk. }, author = {Li, Lanxin}, issn = {2663-337X}, publisher = {Institute of Science and Technology Austria}, title = {{Rapid cell growth regulation in Arabidopsis}}, doi = {10.15479/at:ista:10083}, year = {2021}, } @article{10015, abstract = {Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2 Thr31 phosphorylation site for growth regulation in the Arabidopsis root tip.}, author = {Nikonorova, N and Murphy, E and Fonseca de Lima, CF and Zhu, S and van de Cotte, B and Vu, LD and Balcerowicz, D and Li, Lanxin and Kong, X and De Rop, G and Beeckman, T and Friml, Jiří and Vissenberg, K and Morris, PC and Ding, Z and De Smet, I}, issn = {2073-4409}, journal = {Cells}, keywords = {primary root, (phospho)proteomics, auxin, (receptor) kinase}, publisher = {MDPI}, title = {{The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators}}, doi = {10.3390/cells10071665}, volume = {10}, year = {2021}, } @unpublished{10095, abstract = {Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment.}, author = {Li, Lanxin and Verstraeten, Inge and Roosjen, Mark and Takahashi, Koji and Rodriguez Solovey, Lesia and Merrin, Jack and Chen, Jian and Shabala, Lana and Smet, Wouter and Ren, Hong and Vanneste, Steffen and Shabala, Sergey and De Rybel, Bert and Weijers, Dolf and Kinoshita, Toshinori and Gray, William M. and Friml, Jiří}, booktitle = {Research Square}, issn = {2693-5015}, title = {{Cell surface and intracellular auxin signalling for H+-fluxes in root growth}}, doi = {10.21203/rs.3.rs-266395/v3}, year = {2021}, } @phdthesis{10293, abstract = {Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more than their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations are more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient.}, author = {Schmid, Laura}, issn = {2663-337X}, pages = {171}, publisher = {Institute of Science and Technology Austria}, title = {{Evolution of cooperation via (in)direct reciprocity under imperfect information}}, doi = {10.15479/at:ista:10293}, year = {2021}, } @article{9997, abstract = {Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms.}, author = {Schmid, Laura and Shati, Pouya and Hilbe, Christian and Chatterjee, Krishnendu}, issn = {2045-2322}, journal = {Scientific Reports}, keywords = {Multidisciplinary}, number = {1}, publisher = {Springer Nature}, title = {{The evolution of indirect reciprocity under action and assessment generosity}}, doi = {10.1038/s41598-021-96932-1}, volume = {11}, year = {2021}, } @article{9402, abstract = {Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability.}, author = {Schmid, Laura and Chatterjee, Krishnendu and Hilbe, Christian and Nowak, Martin A.}, issn = {2397-3374}, journal = {Nature Human Behaviour}, number = {10}, pages = {1292–1302}, publisher = {Springer Nature}, title = {{A unified framework of direct and indirect reciprocity}}, doi = {10.1038/s41562-021-01114-8}, volume = {5}, year = {2021}, } @article{9817, abstract = {Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements.}, author = {Hafner, Christian and Bickel, Bernd}, issn = {1557-7368}, journal = {ACM Transactions on Graphics}, keywords = {Computing methodologies, shape modeling, modeling and simulation, theory of computation, computational geometry, mathematics of computing, mathematical optimization}, location = {Virtual}, number = {4}, publisher = {Association for Computing Machinery}, title = {{The design space of plane elastic curves}}, doi = {10.1145/3450626.3459800}, volume = {40}, year = {2021}, } @phdthesis{10135, abstract = {Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and cytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and translation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using chemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to cytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects.}, author = {Semerádová, Hana}, isbn = {978-3-99078-014-5}, issn = {2663-337X}, publisher = {Institute of Science and Technology Austria}, title = {{Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis}}, doi = {10.15479/at:ista:10135}, year = {2021}, } @phdthesis{9728, abstract = {Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows. For particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations. The effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.}, author = {Agrawal, Nishchal}, issn = {2663-337X}, keywords = {Drag Reduction, Transition to Turbulence, Multiphase Flows, particle Laden Flows, Complex Flows, Experiments, Fluid Dynamics}, pages = {118}, publisher = {Institute of Science and Technology Austria}, title = {{Transition to turbulence and drag reduction in particle-laden pipe flows}}, doi = {10.15479/at:ista:9728}, year = {2021}, } @inproceedings{10673, abstract = {We propose a neural information processing system obtained by re-purposing the function of a biological neural circuit model to govern simulated and real-world control tasks. Inspired by the structure of the nervous system of the soil-worm, C. elegans, we introduce ordinary neural circuits (ONCs), defined as the model of biological neural circuits reparameterized for the control of alternative tasks. We first demonstrate that ONCs realize networks with higher maximum flow compared to arbitrary wired networks. We then learn instances of ONCs to control a series of robotic tasks, including the autonomous parking of a real-world rover robot. For reconfiguration of the purpose of the neural circuit, we adopt a search-based optimization algorithm. Ordinary neural circuits perform on par and, in some cases, significantly surpass the performance of contemporary deep learning models. ONC networks are compact, 77% sparser than their counterpart neural controllers, and their neural dynamics are fully interpretable at the cell-level.}, author = {Hasani, Ramin and Lechner, Mathias and Amini, Alexander and Rus, Daniela and Grosu, Radu}, booktitle = {Proceedings of the 37th International Conference on Machine Learning}, issn = {2640-3498}, location = {Virtual}, pages = {4082--4093}, title = {{A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits}}, year = {2020}, } @inproceedings{7272, abstract = {Many systems rely on optimistic concurrent search trees for multi-core scalability. In principle, optimistic trees have a simple performance story: searches are read-only and so run in parallel, with writes to shared memory occurring only when modifying the data structure. However, this paper shows that in practice, obtaining the full performance benefits of optimistic search trees is not so simple. We focus on optimistic binary search trees (BSTs) and perform a detailed performance analysis of 10 state-of-the-art BSTs on large scale x86-64 hardware, using both microbenchmarks and an in-memory database system. We find and explain significant unexpected performance differences between BSTs with similar tree structure and search implementations, which we trace to subtle performance-degrading interactions of BSTs with systems software and hardware subsystems. We further derive a prescriptive approach to avoid this performance degradation, as well as algorithmic insights on optimistic BST design. Our work underlines the gap between the theory and practice of multi-core performance, and calls for further research to help bridge this gap.}, author = {Arbel-Raviv, Maya and Brown, Trevor A and Morrison, Adam}, booktitle = {Proceedings of the 2018 USENIX Annual Technical Conference}, isbn = {9781939133021}, location = {Boston, MA, United States}, pages = {295--306}, publisher = {USENIX Association}, title = {{Getting to the root of concurrent binary search tree performance}}, year = {2020}, } @inproceedings{7346, abstract = {The Price of Anarchy (PoA) is a well-established game-theoretic concept to shed light on coordination issues arising in open distributed systems. Leaving agents to selfishly optimize comes with the risk of ending up in sub-optimal states (in terms of performance and/or costs), compared to a centralized system design. However, the PoA relies on strong assumptions about agents' rationality (e.g., resources and information) and interactions, whereas in many distributed systems agents interact locally with bounded resources. They do so repeatedly over time (in contrast to "one-shot games"), and their strategies may evolve. Using a more realistic evolutionary game model, this paper introduces a realized evolutionary Price of Anarchy (ePoA). The ePoA allows an exploration of equilibrium selection in dynamic distributed systems with multiple equilibria, based on local interactions of simple memoryless agents. Considering a fundamental game related to virus propagation on networks, we present analytical bounds on the ePoA in basic network topologies and for different strategy update dynamics. In particular, deriving stationary distributions of the stochastic evolutionary process, we find that the Nash equilibria are not always the most abundant states, and that different processes can feature significant off-equilibrium behavior, leading to a significantly higher ePoA compared to the PoA studied traditionally in the literature. }, author = {Schmid, Laura and Chatterjee, Krishnendu and Schmid, Stefan}, booktitle = {Proceedings of the 23rd International Conference on Principles of Distributed Systems}, location = {Neuchâtel, Switzerland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game}}, doi = {10.4230/LIPIcs.OPODIS.2019.21}, volume = {153}, year = {2020}, } @inproceedings{7348, abstract = {The monitoring of event frequencies can be used to recognize behavioral anomalies, to identify trends, and to deduce or discard hypotheses about the underlying system. For example, the performance of a web server may be monitored based on the ratio of the total count of requests from the least and most active clients. Exact frequency monitoring, however, can be prohibitively expensive; in the above example it would require as many counters as there are clients. In this paper, we propose the efficient probabilistic monitoring of common frequency properties, including the mode (i.e., the most common event) and the median of an event sequence. We define a logic to express composite frequency properties as a combination of atomic frequency properties. Our main contribution is an algorithm that, under suitable probabilistic assumptions, can be used to monitor these important frequency properties with four counters, independent of the number of different events. Our algorithm samples longer and longer subwords of an infinite event sequence. We prove the almost-sure convergence of our algorithm by generalizing ergodic theory from increasing-length prefixes to increasing-length subwords of an infinite sequence. A similar algorithm could be used to learn a connected Markov chain of a given structure from observing its outputs, to arbitrary precision, for a given confidence. }, author = {Ferrere, Thomas and Henzinger, Thomas A and Kragl, Bernhard}, booktitle = {28th EACSL Annual Conference on Computer Science Logic}, isbn = {9783959771320}, issn = {1868-8969}, location = {Barcelona, Spain}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Monitoring event frequencies}}, doi = {10.4230/LIPIcs.CSL.2020.20}, volume = {152}, year = {2020}, } @article{7567, abstract = {Coxeter triangulations are triangulations of Euclidean space based on a single simplex. By this we mean that given an individual simplex we can recover the entire triangulation of Euclidean space by inductively reflecting in the faces of the simplex. In this paper we establish that the quality of the simplices in all Coxeter triangulations is O(1/d−−√) of the quality of regular simplex. We further investigate the Delaunay property for these triangulations. Moreover, we consider an extension of the Delaunay property, namely protection, which is a measure of non-degeneracy of a Delaunay triangulation. In particular, one family of Coxeter triangulations achieves the protection O(1/d2). We conjecture that both bounds are optimal for triangulations in Euclidean space.}, author = {Choudhary, Aruni and Kachanovich, Siargey and Wintraecken, Mathijs}, issn = {1661-8289}, journal = {Mathematics in Computer Science}, pages = {141--176}, publisher = {Springer Nature}, title = {{Coxeter triangulations have good quality}}, doi = {10.1007/s11786-020-00461-5}, volume = {14}, year = {2020}, } @article{7594, abstract = {The concept of the entanglement between spin and orbital degrees of freedom plays a crucial role in our understanding of various phases and exotic ground states in a broad class of materials, including orbitally ordered materials and spin liquids. We investigate how the spin-orbital entanglement in a Mott insulator depends on the value of the spin-orbit coupling of the relativistic origin. To this end, we numerically diagonalize a one-dimensional spin-orbital model with Kugel-Khomskii exchange interactions between spins and orbitals on different sites supplemented by the on-site spin-orbit coupling. In the regime of small spin-orbit coupling with regard to the spin-orbital exchange, the ground state to a large extent resembles the one obtained in the limit of vanishing spin-orbit coupling. On the other hand, for large spin-orbit coupling the ground state can, depending on the model parameters, either still show negligible spin-orbital entanglement or evolve to a highly spin-orbitally-entangled phase with completely distinct properties that are described by an effective XXZ model. The presented results suggest that (i) the spin-orbital entanglement may be induced by large on-site spin-orbit coupling, as found in the 5d transition metal oxides, such as the iridates; (ii) for Mott insulators with weak spin-orbit coupling of Ising type, such as, e.g., the alkali hyperoxides, the effects of the spin-orbit coupling on the ground state can, in the first order of perturbation theory, be neglected.}, author = {Gotfryd, Dorota and Paerschke, Ekaterina and Chaloupka, Jiri and Oles, Andrzej M. and Wohlfeld, Krzysztof}, journal = {Physical Review Research}, number = {1}, publisher = {American Physical Society}, title = {{How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator}}, doi = {10.1103/PhysRevResearch.2.013353}, volume = {2}, year = {2020}, } @inproceedings{7605, abstract = {Union-Find (or Disjoint-Set Union) is one of the fundamental problems in computer science; it has been well-studied from both theoretical and practical perspectives in the sequential case. Recently, there has been mounting interest in analyzing this problem in the concurrent scenario, and several asymptotically-efficient algorithms have been proposed. Yet, to date, there is very little known about the practical performance of concurrent Union-Find. This work addresses this gap. We evaluate and analyze the performance of several concurrent Union-Find algorithms and optimization strategies across a wide range of platforms (Intel, AMD, and ARM) and workloads (social, random, and road networks, as well as integrations into more complex algorithms). We first observe that, due to the limited computational cost, the number of induced cache misses is the critical determining factor for the performance of existing algorithms. We introduce new techniques to reduce this cost by storing node priorities implicitly and by using plain reads and writes in a way that does not affect the correctness of the algorithms. Finally, we show that Union-Find implementations are an interesting application for Transactional Memory (TM): one of the fastest algorithm variants we discovered is a sequential one that uses coarse-grained locking with the lock elision optimization to reduce synchronization cost and increase scalability. }, author = {Alistarh, Dan-Adrian and Fedorov, Alexander and Koval, Nikita}, booktitle = {23rd International Conference on Principles of Distributed Systems}, isbn = {9783959771337}, issn = {18688969}, location = {Neuchatal, Switzerland}, pages = {15:1--15:16}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{In search of the fastest concurrent union-find algorithm}}, doi = {10.4230/LIPIcs.OPODIS.2019.15}, volume = {153}, year = {2020}, } @unpublished{7601, abstract = {Plasmodesmata (PD) are crucial structures for intercellular communication in multicellular plants with remorins being their crucial plant-specific structural and functional constituents. The PD biogenesis is an intriguing but poorly understood process. By expressing an Arabidopsis remorin protein in mammalian cells, we have reconstituted a PD-like filamentous structure, termed remorin filament (RF), connecting neighboring cells physically and physiologically. Notably, RFs are capable of transporting macromolecules intercellularly, in a way similar to plant PD. With further super-resolution microscopic analysis and biochemical characterization, we found that RFs are also composed of actin filaments, forming the core skeleton structure, aligned with the remorin protein. This unique heterologous filamentous structure might explain the molecular mechanism for remorin function as well as PD construction. Furthermore, remorin protein exhibits a specific distribution manner in the plasma membrane in mammalian cells, representing a lipid nanodomain, depending on its lipid modification status. Our studies not only provide crucial insights into the mechanism of PD biogenesis, but also uncovers unsuspected fundamental mechanistic and evolutionary links between intercellular communication systems of plants and animals.}, author = {Wei, Zhuang and Tan, Shutang and Liu, Tao and Wu, Yuan and Lei, Ji-Gang and Chen, ZhengJun and Friml, Jiří and Xue, Hong-Wei and Liao, Kan}, booktitle = {bioRxiv}, pages = {22}, publisher = {Cold Spring Harbor Laboratory}, title = {{Plasmodesmata-like intercellular connections by plant remorin in animal cells}}, doi = {10.1101/791137}, year = {2020}, } @article{7651, abstract = {The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.}, author = {Larsson, J. and Westram, Anja M and Bengmark, S. and Lundh, T. and Butlin, R. K.}, issn = {1742-5662}, journal = {Journal of The Royal Society Interface}, number = {163}, publisher = {The Royal Society}, title = {{A developmentally descriptive method for quantifying shape in gastropod shells}}, doi = {10.1098/rsif.2019.0721}, volume = {17}, year = {2020}, } @inproceedings{7803, abstract = {We settle the complexity of the (Δ+1)-coloring and (Δ+1)-list coloring problems in the CONGESTED CLIQUE model by presenting a simple deterministic algorithm for both problems running in a constant number of rounds. This matches the complexity of the recent breakthrough randomized constant-round (Δ+1)-list coloring algorithm due to Chang et al. (PODC'19), and significantly improves upon the state-of-the-art O(logΔ)-round deterministic (Δ+1)-coloring bound of Parter (ICALP'18). A remarkable property of our algorithm is its simplicity. Whereas the state-of-the-art randomized algorithms for this problem are based on the quite involved local coloring algorithm of Chang et al. (STOC'18), our algorithm can be described in just a few lines. At a high level, it applies a careful derandomization of a recursive procedure which partitions the nodes and their respective palettes into separate bins. We show that after O(1) recursion steps, the remaining uncolored subgraph within each bin has linear size, and thus can be solved locally by collecting it to a single node. This algorithm can also be implemented in the Massively Parallel Computation (MPC) model provided that each machine has linear (in n, the number of nodes in the input graph) space. We also show an extension of our algorithm to the MPC regime in which machines have sublinear space: we present the first deterministic (Δ+1)-list coloring algorithm designed for sublinear-space MPC, which runs in O(logΔ+loglogn) rounds.}, author = {Czumaj, Artur and Davies, Peter and Parter, Merav}, booktitle = {Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing}, location = {Salerno, Italy}, pages = {309--318}, publisher = {Association for Computing Machinery}, title = {{Simple, deterministic, constant-round coloring in the congested clique}}, doi = {10.1145/3382734.3405751}, year = {2020}, } @inproceedings{7806, abstract = {We consider the following decision problem EMBEDk→d in computational topology (where k ≤ d are fixed positive integers): Given a finite simplicial complex K of dimension k, does there exist a (piecewise-linear) embedding of K into ℝd? The special case EMBED1→2 is graph planarity, which is decidable in linear time, as shown by Hopcroft and Tarjan. In higher dimensions, EMBED2→3 and EMBED3→3 are known to be decidable (as well as NP-hard), and recent results of Čadek et al. in computational homotopy theory, in combination with the classical Haefliger–Weber theorem in geometric topology, imply that EMBEDk→d can be solved in polynomial time for any fixed pair (k, d) of dimensions in the so-called metastable range . Here, by contrast, we prove that EMBEDk→d is algorithmically undecidable for almost all pairs of dimensions outside the metastable range, namely for . This almost completely resolves the decidability vs. undecidability of EMBEDk→d in higher dimensions and establishes a sharp dichotomy between polynomial-time solvability and undecidability. Our result complements (and in a wide range of dimensions strengthens) earlier results of Matoušek, Tancer, and the second author, who showed that EMBEDk→d is undecidable for 4 ≤ k ϵ {d – 1, d}, and NP-hard for all remaining pairs (k, d) outside the metastable range and satisfying d ≥ 4.}, author = {Filakovský, Marek and Wagner, Uli and Zhechev, Stephan Y}, booktitle = {Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms}, isbn = {9781611975994}, location = {Salt Lake City, UT, United States}, pages = {767--785}, publisher = {SIAM}, title = {{Embeddability of simplicial complexes is undecidable}}, doi = {10.1137/1.9781611975994.47}, volume = {2020-January}, year = {2020}, } @article{7814, abstract = {Scientific research is to date largely restricted to wealthy laboratories in developed nations due to the necessity of complex and expensive equipment. This inequality limits the capacity of science to be used as a diplomatic channel. Maker movements use open-source technologies including additive manufacturing (3D printing) and laser cutting, together with low-cost computers for developing novel products. This movement is setting the groundwork for a revolution, allowing scientific equipment to be sourced at a fraction of the cost and has the potential to increase the availability of equipment for scientists around the world. Science education is increasingly recognized as another channel for science diplomacy. In this perspective, we introduce the idea that the Maker movement and open-source technologies have the potential to revolutionize science, technology, engineering and mathematics (STEM) education worldwide. We present an open-source STEM didactic tool called SCOPES (Sparking Curiosity through Open-source Platforms in Education and Science). SCOPES is self-contained, independent of local resources, and cost-effective. SCOPES can be adapted to communicate complex subjects from genetics to neurobiology, perform real-world biological experiments and explore digitized scientific samples. We envision such platforms will enhance science diplomacy by providing a means for scientists to share their findings with classrooms and for educators to incorporate didactic concepts into STEM lessons. By providing students the opportunity to design, perform, and share scientific experiments, students also experience firsthand the benefits of a multinational scientific community. We provide instructions on how to build and use SCOPES on our webpage: http://scopeseducation.org.}, author = {Beattie, Robert J and Hippenmeyer, Simon and Pauler, Florian}, issn = {2504-284X}, journal = {Frontiers in Education}, publisher = {Frontiers Media}, title = {{SCOPES: Sparking curiosity through Open-Source platforms in education and science}}, doi = {10.3389/feduc.2020.00048}, volume = {5}, year = {2020}, } @article{7866, abstract = {In this paper, we establish convergence to equilibrium for a drift–diffusion–recombination system modelling the charge transport within certain semiconductor devices. More precisely, we consider a two-level system for electrons and holes which is augmented by an intermediate energy level for electrons in so-called trapped states. The recombination dynamics use the mass action principle by taking into account this additional trap level. The main part of the paper is concerned with the derivation of an entropy–entropy production inequality, which entails exponential convergence to the equilibrium via the so-called entropy method. The novelty of our approach lies in the fact that the entropy method is applied uniformly in a fast-reaction parameter which governs the lifetime of electrons on the trap level. Thus, the resulting decay estimate for the densities of electrons and holes extends to the corresponding quasi-steady-state approximation.}, author = {Fellner, Klemens and Kniely, Michael}, issn = {22969039}, journal = {Journal of Elliptic and Parabolic Equations}, pages = {529--598}, publisher = {Springer Nature}, title = {{Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model}}, doi = {10.1007/s41808-020-00068-8}, volume = {6}, year = {2020}, } @article{7919, abstract = {We explore the time evolution of two impurities in a trapped one-dimensional Bose gas that follows a change of the boson-impurity interaction. We study the induced impurity-impurity interactions and their effect on the quench dynamics. In particular, we report on the size of the impurity cloud, the impurity-impurity entanglement, and the impurity-impurity correlation function. The presented numerical simulations are based upon the variational multilayer multiconfiguration time-dependent Hartree method for bosons. To analyze and quantify induced impurity-impurity correlations, we employ an effective two-body Hamiltonian with a contact interaction. We show that the effective model consistent with the mean-field attraction of two heavy impurities explains qualitatively our results for weak interactions. Our findings suggest that the quench dynamics in cold-atom systems can be a tool for studying impurity-impurity correlations.}, author = {Mistakidis, S. I. and Volosniev, Artem and Schmelcher, P.}, issn = {2643-1564}, journal = {Physical Review Research}, publisher = {American Physical Society}, title = {{Induced correlations between impurities in a one-dimensional quenched Bose gas}}, doi = {10.1103/physrevresearch.2.023154}, volume = {2}, year = {2020}, } @inproceedings{7991, abstract = {We define and study a discrete process that generalizes the convex-layer decomposition of a planar point set. Our process, which we call homotopic curve shortening (HCS), starts with a closed curve (which might self-intersect) in the presence of a set P⊂ ℝ² of point obstacles, and evolves in discrete steps, where each step consists of (1) taking shortcuts around the obstacles, and (2) reducing the curve to its shortest homotopic equivalent. We find experimentally that, if the initial curve is held fixed and P is chosen to be either a very fine regular grid or a uniformly random point set, then HCS behaves at the limit like the affine curve-shortening flow (ACSF). This connection between HCS and ACSF generalizes the link between "grid peeling" and the ACSF observed by Eppstein et al. (2017), which applied only to convex curves, and which was studied only for regular grids. We prove that HCS satisfies some properties analogous to those of ACSF: HCS is invariant under affine transformations, preserves convexity, and does not increase the total absolute curvature. Furthermore, the number of self-intersections of a curve, or intersections between two curves (appropriately defined), does not increase. Finally, if the initial curve is simple, then the number of inflection points (appropriately defined) does not increase.}, author = {Avvakumov, Sergey and Nivasch, Gabriel}, booktitle = {36th International Symposium on Computational Geometry}, isbn = {9783959771436}, issn = {18688969}, location = {Zürich, Switzerland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Homotopic curve shortening and the affine curve-shortening flow}}, doi = {10.4230/LIPIcs.SoCG.2020.12}, volume = {164}, year = {2020}, } @inproceedings{7989, abstract = {We prove general topological Radon-type theorems for sets in ℝ^d, smooth real manifolds or finite dimensional simplicial complexes. Combined with a recent result of Holmsen and Lee, it gives fractional Helly theorem, and consequently the existence of weak ε-nets as well as a (p,q)-theorem. More precisely: Let X be either ℝ^d, smooth real d-manifold, or a finite d-dimensional simplicial complex. Then if F is a finite, intersection-closed family of sets in X such that the ith reduced Betti number (with ℤ₂ coefficients) of any set in F is at most b for every non-negative integer i less or equal to k, then the Radon number of F is bounded in terms of b and X. Here k is the smallest integer larger or equal to d/2 - 1 if X = ℝ^d; k=d-1 if X is a smooth real d-manifold and not a surface, k=0 if X is a surface and k=d if X is a d-dimensional simplicial complex. Using the recent result of the author and Kalai, we manage to prove the following optimal bound on fractional Helly number for families of open sets in a surface: Let F be a finite family of open sets in a surface S such that the intersection of any subfamily of F is either empty, or path-connected. Then the fractional Helly number of F is at most three. This also settles a conjecture of Holmsen, Kim, and Lee about an existence of a (p,q)-theorem for open subsets of a surface.}, author = {Patakova, Zuzana}, booktitle = {36th International Symposium on Computational Geometry}, isbn = {9783959771436}, issn = {18688969}, location = {Zürich, Switzerland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Bounding radon number via Betti numbers}}, doi = {10.4230/LIPIcs.SoCG.2020.61}, volume = {164}, year = {2020}, } @inproceedings{7992, abstract = {Let K be a convex body in ℝⁿ (i.e., a compact convex set with nonempty interior). Given a point p in the interior of K, a hyperplane h passing through p is called barycentric if p is the barycenter of K ∩ h. In 1961, Grünbaum raised the question whether, for every K, there exists an interior point p through which there are at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly resolved affirmatively by showing that this is the case if p=p₀ is the point of maximal depth in K. However, while working on a related question, we noticed that one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample; this re-opens Grünbaum’s question. It follows from known results that for n ≥ 2, there are always at least three distinct barycentric cuts through the point p₀ ∈ K of maximal depth. Using tools related to Morse theory we are able to improve this bound: four distinct barycentric cuts through p₀ are guaranteed if n ≥ 3.}, author = {Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, booktitle = {36th International Symposium on Computational Geometry}, isbn = {9783959771436}, issn = {18688969}, location = {Zürich, Switzerland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Barycentric cuts through a convex body}}, doi = {10.4230/LIPIcs.SoCG.2020.62}, volume = {164}, year = {2020}, } @inproceedings{7994, abstract = {In the recent study of crossing numbers, drawings of graphs that can be extended to an arrangement of pseudolines (pseudolinear drawings) have played an important role as they are a natural combinatorial extension of rectilinear (or straight-line) drawings. A characterization of the pseudolinear drawings of K_n was found recently. We extend this characterization to all graphs, by describing the set of minimal forbidden subdrawings for pseudolinear drawings. Our characterization also leads to a polynomial-time algorithm to recognize pseudolinear drawings and construct the pseudolines when it is possible.}, author = {Arroyo Guevara, Alan M and Bensmail, Julien and Bruce Richter, R.}, booktitle = {36th International Symposium on Computational Geometry}, isbn = {9783959771436}, issn = {18688969}, location = {Zürich, Switzerland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Extending drawings of graphs to arrangements of pseudolines}}, doi = {10.4230/LIPIcs.SoCG.2020.9}, volume = {164}, year = {2020}, } @article{8011, abstract = {Relaxation to a thermal state is the inevitable fate of nonequilibrium interacting quantum systems without special conservation laws. While thermalization in one-dimensional systems can often be suppressed by integrability mechanisms, in two spatial dimensions thermalization is expected to be far more effective due to the increased phase space. In this work we propose a general framework for escaping or delaying the emergence of the thermal state in two-dimensional arrays of Rydberg atoms via the mechanism of quantum scars, i.e., initial states that fail to thermalize. The suppression of thermalization is achieved in two complementary ways: by adding local perturbations or by adjusting the driving Rabi frequency according to the local connectivity of the lattice. We demonstrate that these mechanisms allow us to realize robust quantum scars in various two-dimensional lattices, including decorated lattices with nonconstant connectivity. In particular, we show that a small decrease of the Rabi frequency at the corners of the lattice is crucial for mitigating the strong boundary effects in two-dimensional systems. Our results identify synchronization as an important tool for future experiments on two-dimensional quantum scars.}, author = {Michailidis, Alexios and Turner, C. J. and Papić, Z. and Abanin, D. A. and Serbyn, Maksym}, issn = {2643-1564}, journal = {Physical Review Research}, number = {2}, publisher = {American Physical Society}, title = {{Stabilizing two-dimensional quantum scars by deformation and synchronization}}, doi = {10.1103/physrevresearch.2.022065}, volume = {2}, year = {2020}, } @unpublished{8063, abstract = {We present a generative model of images that explicitly reasons over the set of objects they show. Our model learns a structured latent representation that separates objects from each other and from the background; unlike prior works, it explicitly represents the 2D position and depth of each object, as well as an embedding of its segmentation mask and appearance. The model can be trained from images alone in a purely unsupervised fashion without the need for object masks or depth information. Moreover, it always generates complete objects, even though a significant fraction of training images contain occlusions. Finally, we show that our model can infer decompositions of novel images into their constituent objects, including accurate prediction of depth ordering and segmentation of occluded parts.}, author = {Anciukevicius, Titas and Lampert, Christoph and Henderson, Paul M}, booktitle = {arXiv}, title = {{Object-centric image generation with factored depths, locations, and appearances}}, year = {2020}, } @unpublished{8081, abstract = {Here, we employ micro- and nanosized cellulose particles, namely paper fines and cellulose nanocrystals, to induce hierarchical organization over a wide length scale. After processing them into carbonaceous materials, we demonstrate that these hierarchically organized materials outperform the best materials for supercapacitors operating with organic electrolytes reported in literature in terms of specific energy/power (Ragone plot) while showing hardly any capacity fade over 4,000 cycles. The highly porous materials feature a specific surface area as high as 2500 m2ˑg-1 and exhibit pore sizes in the range of 0.5 to 200 nm as proven by scanning electron microscopy and N2 physisorption. The carbonaceous materials have been further investigated by X-ray photoelectron spectroscopy and RAMAN spectroscopy. Since paper fines are an underutilized side stream in any paper production process, they are a cheap and highly available feedstock to prepare carbonaceous materials with outstanding performance in electrochemical applications. }, author = {Hobisch, Mathias A. and Mourad, Eléonore and Fischer, Wolfgang J. and Prehal, Christian and Eyley, Samuel and Childress, Anthony and Zankel, Armin and Mautner, Andreas and Breitenbach, Stefan and Rao, Apparao M. and Thielemans, Wim and Freunberger, Stefan Alexander and Eckhart, Rene and Bauer, Wolfgang and Spirk, Stefan }, title = {{High specific capacitance supercapacitors from hierarchically organized all-cellulose composites}}, year = {2020}, } @article{8105, abstract = {Physical and biological systems often exhibit intermittent dynamics with bursts or avalanches (active states) characterized by power-law size and duration distributions. These emergent features are typical of systems at the critical point of continuous phase transitions, and have led to the hypothesis that such systems may self-organize at criticality, i.e. without any fine tuning of parameters. Since the introduction of the Bak-Tang-Wiesenfeld (BTW) model, the paradigm of self-organized criticality (SOC) has been very fruitful for the analysis of emergent collective behaviors in a number of systems, including the brain. Although considerable effort has been devoted in identifying and modeling scaling features of burst and avalanche statistics, dynamical aspects related to the temporal organization of bursts remain often poorly understood or controversial. Of crucial importance to understand the mechanisms responsible for emergent behaviors is the relationship between active and quiet periods, and the nature of the correlations. Here we investigate the dynamics of active (θ-bursts) and quiet states (δ-bursts) in brain activity during the sleep-wake cycle. We show the duality of power-law (θ, active phase) and exponential-like (δ, quiescent phase) duration distributions, typical of SOC, jointly emerge with power-law temporal correlations and anti-correlated coupling between active and quiet states. Importantly, we demonstrate that such temporal organization shares important similarities with earthquake dynamics, and propose that specific power-law correlations and coupling between active and quiet states are distinctive characteristics of a class of systems with self-organization at criticality.}, author = {Lombardi, Fabrizio and Wang, Jilin W.J.L. and Zhang, Xiyun and Ivanov, Plamen Ch}, issn = {2100-014X}, journal = {EPJ Web of Conferences}, publisher = {EDP Sciences}, title = {{Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality}}, doi = {10.1051/epjconf/202023000005}, volume = {230}, year = {2020}, } @inproceedings{8135, abstract = {Discrete Morse theory has recently lead to new developments in the theory of random geometric complexes. This article surveys the methods and results obtained with this new approach, and discusses some of its shortcomings. It uses simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics.}, author = {Edelsbrunner, Herbert and Nikitenko, Anton and Ölsböck, Katharina and Synak, Peter}, booktitle = {Topological Data Analysis}, isbn = {9783030434076}, issn = {21978549}, pages = {181--218}, publisher = {Springer Nature}, title = {{Radius functions on Poisson–Delaunay mosaics and related complexes experimentally}}, doi = {10.1007/978-3-030-43408-3_8}, volume = {15}, year = {2020}, } @inbook{8173, abstract = {Understanding how the activity of membrane receptors and cellular signaling pathways shapes cell behavior is of fundamental interest in basic and applied research. Reengineering receptors to react to light instead of their cognate ligands allows for generating defined signaling inputs with high spatial and temporal precision and facilitates the dissection of complex signaling networks. Here, we describe fundamental considerations in the design of light-regulated receptor tyrosine kinases (Opto-RTKs) and appropriate control experiments. We also introduce methods for transient receptor expression in HEK293 cells, quantitative assessment of signaling activity in reporter gene assays, semiquantitative assessment of (in)activation time courses through Western blot (WB) analysis, and easy to implement light stimulation hardware.}, author = {Kainrath, Stephanie and Janovjak, Harald L}, booktitle = {Photoswitching Proteins}, editor = {Niopek, Dominik}, issn = {19406029}, pages = {233--246}, publisher = {Springer Nature}, title = {{Design and application of light-regulated receptor tyrosine kinases}}, doi = {10.1007/978-1-0716-0755-8_16}, volume = {2173}, year = {2020}, } @misc{8181, author = {Hauschild, Robert}, publisher = {IST Austria}, title = {{Amplified centrosomes in dendritic cells promote immune cell effector functions}}, doi = {10.15479/AT:ISTA:8181}, year = {2020}, } @misc{8294, abstract = {Automated root growth analysis and tracking of root tips. }, author = {Hauschild, Robert}, publisher = {IST Austria}, title = {{RGtracker}}, doi = {10.15479/AT:ISTA:8294}, year = {2020}, } @inproceedings{8322, abstract = {Reverse firewalls were introduced at Eurocrypt 2015 by Miro-nov and Stephens-Davidowitz, as a method for protecting cryptographic protocols against attacks on the devices of the honest parties. In a nutshell: a reverse firewall is placed outside of a device and its goal is to “sanitize” the messages sent by it, in such a way that a malicious device cannot leak its secrets to the outside world. It is typically assumed that the cryptographic devices are attacked in a “functionality-preserving way” (i.e. informally speaking, the functionality of the protocol remains unchanged under this attacks). In their paper, Mironov and Stephens-Davidowitz construct a protocol for passively-secure two-party computations with firewalls, leaving extension of this result to stronger models as an open question. In this paper, we address this problem by constructing a protocol for secure computation with firewalls that has two main advantages over the original protocol from Eurocrypt 2015. Firstly, it is a multiparty computation protocol (i.e. it works for an arbitrary number n of the parties, and not just for 2). Secondly, it is secure in much stronger corruption settings, namely in the active corruption model. More precisely: we consider an adversary that can fully corrupt up to 𝑛−1 parties, while the remaining parties are corrupt in a functionality-preserving way. Our core techniques are: malleable commitments and malleable non-interactive zero-knowledge, which in particular allow us to create a novel protocol for multiparty augmented coin-tossing into the well with reverse firewalls (that is based on a protocol of Lindell from Crypto 2001).}, author = {Chakraborty, Suvradip and Dziembowski, Stefan and Nielsen, Jesper Buus}, booktitle = {Advances in Cryptology – CRYPTO 2020}, isbn = {9783030568795}, issn = {16113349}, location = {Santa Barbara, CA, United States}, pages = {732--762}, publisher = {Springer Nature}, title = {{Reverse firewalls for actively secure MPCs}}, doi = {10.1007/978-3-030-56880-1_26}, volume = {12171}, year = {2020}, } @inproceedings{8339, abstract = {Discrete Gaussian distributions over lattices are central to lattice-based cryptography, and to the computational and mathematical aspects of lattices more broadly. The literature contains a wealth of useful theorems about the behavior of discrete Gaussians under convolutions and related operations. Yet despite their structural similarities, most of these theorems are formally incomparable, and their proofs tend to be monolithic and written nearly “from scratch,” making them unnecessarily hard to verify, understand, and extend. In this work we present a modular framework for analyzing linear operations on discrete Gaussian distributions. The framework abstracts away the particulars of Gaussians, and usually reduces proofs to the choice of appropriate linear transformations and elementary linear algebra. To showcase the approach, we establish several general properties of discrete Gaussians, and show how to obtain all prior convolution theorems (along with some new ones) as straightforward corollaries. As another application, we describe a self-reduction for Learning With Errors (LWE) that uses a fixed number of samples to generate an unlimited number of additional ones (having somewhat larger error). The distinguishing features of our reduction are its simple analysis in our framework, and its exclusive use of discrete Gaussians without any loss in parameters relative to a prior mixed discrete-and-continuous approach. As a contribution of independent interest, for subgaussian random matrices we prove a singular value concentration bound with explicitly stated constants, and we give tighter heuristics for specific distributions that are commonly used for generating lattice trapdoors. These bounds yield improvements in the concrete bit-security estimates for trapdoor lattice cryptosystems.}, author = {Genise, Nicholas and Micciancio, Daniele and Peikert, Chris and Walter, Michael}, booktitle = {23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography}, isbn = {9783030453732}, issn = {16113349}, location = {Edinburgh, United Kingdom}, pages = {623--651}, publisher = {Springer Nature}, title = {{Improved discrete Gaussian and subgaussian analysis for lattice cryptography}}, doi = {10.1007/978-3-030-45374-9_21}, volume = {12110}, year = {2020}, } @inproceedings{8572, abstract = {We present the results of the ARCH 2020 friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. In its fourth edition, eight tools have been applied to solve eight different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, C2E2, HyDRA, Hylaa, Hylaa-Continuous, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.}, author = {Althoff, Matthias and Bak, Stanley and Bao, Zongnan and Forets, Marcelo and Frehse, Goran and Freire, Daniel and Kochdumper, Niklas and Li, Yangge and Mitra, Sayan and Ray, Rajarshi and Schilling, Christian and Schupp, Stefan and Wetzlinger, Mark}, booktitle = {EPiC Series in Computing}, pages = {16--48}, publisher = {EasyChair}, title = {{ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics}}, doi = {10.29007/7dt2}, volume = {74}, year = {2020}, } @inproceedings{8571, abstract = {We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2020. This year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. These tools are applied to solve reachability analysis problems on six benchmark problems, two of them featuring hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.}, author = {Geretti, Luca and Alexandre Dit Sandretto, Julien and Althoff, Matthias and Benet, Luis and Chapoutot, Alexandre and Chen, Xin and Collins, Pieter and Forets, Marcelo and Freire, Daniel and Immler, Fabian and Kochdumper, Niklas and Sanders, David and Schilling, Christian}, booktitle = {EPiC Series in Computing}, pages = {49--75}, publisher = {EasyChair}, title = {{ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics}}, doi = {10.29007/zkf6}, volume = {74}, year = {2020}, } @inproceedings{8600, abstract = {A vector addition system with states (VASS) consists of a finite set of states and counters. A transition changes the current state to the next state, and every counter is either incremented, or decremented, or left unchanged. A state and value for each counter is a configuration; and a computation is an infinite sequence of configurations with transitions between successive configurations. A probabilistic VASS consists of a VASS along with a probability distribution over the transitions for each state. Qualitative properties such as state and configuration reachability have been widely studied for VASS. In this work we consider multi-dimensional long-run average objectives for VASS and probabilistic VASS. For a counter, the cost of a configuration is the value of the counter; and the long-run average value of a computation for the counter is the long-run average of the costs of the configurations in the computation. The multi-dimensional long-run average problem given a VASS and a threshold value for each counter, asks whether there is a computation such that for each counter the long-run average value for the counter does not exceed the respective threshold. For probabilistic VASS, instead of the existence of a computation, we consider whether the expected long-run average value for each counter does not exceed the respective threshold. Our main results are as follows: we show that the multi-dimensional long-run average problem (a) is NP-complete for integer-valued VASS; (b) is undecidable for natural-valued VASS (i.e., nonnegative counters); and (c) can be solved in polynomial time for probabilistic integer-valued VASS, and probabilistic natural-valued VASS when all computations are non-terminating.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan}, booktitle = {31st International Conference on Concurrency Theory}, isbn = {9783959771603}, issn = {18688969}, location = {Virtual}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Multi-dimensional long-run average problems for vector addition systems with states}}, doi = {10.4230/LIPIcs.CONCUR.2020.23}, volume = {171}, year = {2020}, } @inproceedings{8599, abstract = {A graph game is a two-player zero-sum game in which the players move a token throughout a graph to produce an infinite path, which determines the winner or payoff of the game. In bidding games, both players have budgets, and in each turn, we hold an "auction" (bidding) to determine which player moves the token. In this survey, we consider several bidding mechanisms and study their effect on the properties of the game. Specifically, bidding games, and in particular bidding games of infinite duration, have an intriguing equivalence with random-turn games in which in each turn, the player who moves is chosen randomly. We show how minor changes in the bidding mechanism lead to unexpected differences in the equivalence with random-turn games.}, author = {Avni, Guy and Henzinger, Thomas A}, booktitle = {31st International Conference on Concurrency Theory}, isbn = {9783959771603}, issn = {18688969}, location = {Virtual}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{A survey of bidding games on graphs}}, doi = {10.4230/LIPIcs.CONCUR.2020.2}, volume = {171}, year = {2020}, } @inproceedings{8725, abstract = {The design and implementation of efficient concurrent data structures have seen significant attention. However, most of this work has focused on concurrent data structures providing good \emph{worst-case} guarantees. In real workloads, objects are often accessed at different rates, since access distributions may be non-uniform. Efficient distribution-adaptive data structures are known in the sequential case, e.g. the splay-trees; however, they often are hard to translate efficiently in the concurrent case. In this paper, we investigate distribution-adaptive concurrent data structures and propose a new design called the splay-list. At a high level, the splay-list is similar to a standard skip-list, with the key distinction that the height of each element adapts dynamically to its access rate: popular elements ``move up,'' whereas rarely-accessed elements decrease in height. We show that the splay-list provides order-optimal amortized complexity bounds for a subset of operations while being amenable to efficient concurrent implementation. Experimental results show that the splay-list can leverage distribution-adaptivity to improve on the performance of classic concurrent designs, and can outperform the only previously-known distribution-adaptive design in certain settings.}, author = {Aksenov, Vitaly and Alistarh, Dan-Adrian and Drozdova, Alexandra and Mohtashami, Amirkeivan}, booktitle = {34th International Symposium on Distributed Computing}, isbn = {9783959771689}, issn = {1868-8969}, location = {Freiburg, Germany}, pages = {3:1--3:18}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{The splay-list: A distribution-adaptive concurrent skip-list}}, doi = {10.4230/LIPIcs.DISC.2020.3}, volume = {179}, year = {2020}, } @article{8726, abstract = {Several realistic spin-orbital models for transition metal oxides go beyond the classical expectations and could be understood only by employing the quantum entanglement. Experiments on these materials confirm that spin-orbital entanglement has measurable consequences. Here, we capture the essential features of spin-orbital entanglement in complex quantum matter utilizing 1D spin-orbital model which accommodates SU(2)⊗SU(2) symmetric Kugel-Khomskii superexchange as well as the Ising on-site spin-orbit coupling. Building on the results obtained for full and effective models in the regime of strong spin-orbit coupling, we address the question whether the entanglement found on superexchange bonds always increases when the Ising spin-orbit coupling is added. We show that (i) quantum entanglement is amplified by strong spin-orbit coupling and, surprisingly, (ii) almost classical disentangled states are possible. We complete the latter case by analyzing how the entanglement existing for intermediate values of spin-orbit coupling can disappear for higher values of this coupling.}, author = {Gotfryd, Dorota and Paerschke, Ekaterina and Wohlfeld, Krzysztof and Oleś, Andrzej M.}, issn = {2410-3896}, journal = {Condensed Matter}, number = {3}, publisher = {MDPI}, title = {{Evolution of spin-orbital entanglement with increasing ising spin-orbit coupling}}, doi = {10.3390/condmat5030053}, volume = {5}, year = {2020}, } @inproceedings{9040, abstract = {Machine learning and formal methods have complimentary benefits and drawbacks. In this work, we address the controller-design problem with a combination of techniques from both fields. The use of black-box neural networks in deep reinforcement learning (deep RL) poses a challenge for such a combination. Instead of reasoning formally about the output of deep RL, which we call the wizard, we extract from it a decision-tree based model, which we refer to as the magic book. Using the extracted model as an intermediary, we are able to handle problems that are infeasible for either deep RL or formal methods by themselves. First, we suggest, for the first time, a synthesis procedure that is based on a magic book. We synthesize a stand-alone correct-by-design controller that enjoys the favorable performance of RL. Second, we incorporate a magic book in a bounded model checking (BMC) procedure. BMC allows us to find numerous traces of the plant under the control of the wizard, which a user can use to increase the trustworthiness of the wizard and direct further training.}, author = {Alamdari, Par Alizadeh and Avni, Guy and Henzinger, Thomas A and Lukina, Anna}, booktitle = {Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design}, isbn = {9783854480426}, issn = {2708-7824}, location = {Online Conference}, pages = {138--147}, publisher = {TU Wien Academic Press}, title = {{Formal methods with a touch of magic}}, doi = {10.34727/2020/isbn.978-3-85448-042-6_21}, year = {2020}, } @inbook{9096, author = {Schmid-Hempel, Paul and Cremer, Sylvia M}, booktitle = {Encyclopedia of Social Insects}, editor = {Starr, C}, isbn = {9783319903064}, publisher = {Springer Nature}, title = {{Parasites and Pathogens}}, doi = {10.1007/978-3-319-90306-4_94-1}, year = {2020}, } @inbook{9123, abstract = {Inversions are chromosomal rearrangements where the order of genes is reversed. Inversions originate by mutation and can be under positive, negative or balancing selection. Selective effects result from potential disruptive effects on meiosis, gene disruption at inversion breakpoints and, importantly, the effects of inversions as modifiers of recombination rate: Recombination is strongly reduced in individuals heterozygous for an inversion, allowing for alleles at different loci to be inherited as a ‘block’. This may lead to a selective advantage whenever it is favourable to keep certain combinations of alleles associated, for example under local adaptation with gene flow. Inversions can cover a considerable part of a chromosome and contain numerous loci under different selection pressures, so that the resulting overall effects may be complex. Empirical data from various systems show that inversions may have a prominent role in local adaptation, speciation, parallel evolution, the maintenance of polymorphism and sex chromosome evolution.}, author = {Westram, Anja M and Faria, Rui and Butlin, Roger and Johannesson, Kerstin}, booktitle = {eLS}, isbn = {9780470016176}, publisher = {Wiley}, title = {{Inversions and Evolution}}, doi = {10.1002/9780470015902.a0029007}, year = {2020}, } @article{9249, abstract = {Rhombic dodecahedron is a space filling polyhedron which represents the close packing of spheres in 3D space and the Voronoi structures of the face centered cubic (FCC) lattice. In this paper, we describe a new coordinate system where every 3-integer coordinates grid point corresponds to a rhombic dodecahedron centroid. In order to illustrate the interest of the new coordinate system, we propose the characterization of 3D digital plane with its topological features, such as the interrelation between the thickness of the digital plane and the separability constraint we aim to obtain. We also present the characterization of 3D digital lines and study it as the intersection of multiple digital planes. Characterization of 3D digital sphere with relevant topological features is proposed as well along with the 48-symmetry appearing in the new coordinate system.}, author = {Biswas, Ranita and Largeteau-Skapin, Gaëlle and Zrour, Rita and Andres, Eric}, issn = {2353-3390}, journal = {Mathematical Morphology - Theory and Applications}, number = {1}, pages = {143--158}, publisher = {De Gruyter}, title = {{Digital objects in rhombic dodecahedron grid}}, doi = {10.1515/mathm-2020-0106}, volume = {4}, year = {2020}, } @inproceedings{9299, abstract = {We call a multigraph non-homotopic if it can be drawn in the plane in such a way that no two edges connecting the same pair of vertices can be continuously transformed into each other without passing through a vertex, and no loop can be shrunk to its end-vertex in the same way. It is easy to see that a non-homotopic multigraph on n>1 vertices can have arbitrarily many edges. We prove that the number of crossings between the edges of a non-homotopic multigraph with n vertices and m>4n edges is larger than cm2n for some constant c>0 , and that this bound is tight up to a polylogarithmic factor. We also show that the lower bound is not asymptotically sharp as n is fixed and m⟶∞ .}, author = {Pach, János and Tardos, Gábor and Tóth, Géza}, booktitle = {28th International Symposium on Graph Drawing and Network Visualization}, isbn = {9783030687656}, issn = {1611-3349}, location = {Virtual, Online}, pages = {359--371}, publisher = {Springer Nature}, title = {{Crossings between non-homotopic edges}}, doi = {10.1007/978-3-030-68766-3_28}, volume = {12590}, year = {2020}, } @inproceedings{9632, abstract = {Second-order information, in the form of Hessian- or Inverse-Hessian-vector products, is a fundamental tool for solving optimization problems. Recently, there has been significant interest in utilizing this information in the context of deep neural networks; however, relatively little is known about the quality of existing approximations in this context. Our work examines this question, identifies issues with existing approaches, and proposes a method called WoodFisher to compute a faithful and efficient estimate of the inverse Hessian. Our main application is to neural network compression, where we build on the classic Optimal Brain Damage/Surgeon framework. We demonstrate that WoodFisher significantly outperforms popular state-of-the-art methods for oneshot pruning. Further, even when iterative, gradual pruning is allowed, our method results in a gain in test accuracy over the state-of-the-art approaches, for standard image classification datasets such as ImageNet ILSVRC. We examine how our method can be extended to take into account first-order information, as well as illustrate its ability to automatically set layer-wise pruning thresholds and perform compression in the limited-data regime. The code is available at the following link, https://github.com/IST-DASLab/WoodFisher.}, author = {Singh, Sidak Pal and Alistarh, Dan-Adrian}, booktitle = {Advances in Neural Information Processing Systems}, isbn = {9781713829546}, issn = {10495258}, location = {Vancouver, Canada}, pages = {18098--18109}, publisher = {Curran Associates}, title = {{WoodFisher: Efficient second-order approximation for neural network compression}}, volume = {33}, year = {2020}, } @article{9630, abstract = {Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory needed for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context.}, author = {Edelsbrunner, Herbert and Virk, Ziga and Wagner, Hubert}, issn = {1920180X}, journal = {Journal of Computational Geometry}, number = {2}, pages = {162--182}, publisher = {Carleton University}, title = {{Topological data analysis in information space}}, doi = {10.20382/jocg.v11i2a7}, volume = {11}, year = {2020}, } @inproceedings{9631, abstract = {The ability to leverage large-scale hardware parallelism has been one of the key enablers of the accelerated recent progress in machine learning. Consequently, there has been considerable effort invested into developing efficient parallel variants of classic machine learning algorithms. However, despite the wealth of knowledge on parallelization, some classic machine learning algorithms often prove hard to parallelize efficiently while maintaining convergence. In this paper, we focus on efficient parallel algorithms for the key machine learning task of inference on graphical models, in particular on the fundamental belief propagation algorithm. We address the challenge of efficiently parallelizing this classic paradigm by showing how to leverage scalable relaxed schedulers in this context. We present an extensive empirical study, showing that our approach outperforms previous parallel belief propagation implementations both in terms of scalability and in terms of wall-clock convergence time, on a range of practical applications.}, author = {Aksenov, Vitaly and Alistarh, Dan-Adrian and Korhonen, Janne}, booktitle = {Advances in Neural Information Processing Systems}, isbn = {9781713829546}, issn = {10495258}, location = {Vancouver, Canada}, pages = {22361--22372}, publisher = {Curran Associates}, title = {{Scalable belief propagation via relaxed scheduling}}, volume = {33}, year = {2020}, } @inproceedings{8533, abstract = {Game of Life is a simple and elegant model to study dynamical system over networks. The model consists of a graph where every vertex has one of two types, namely, dead or alive. A configuration is a mapping of the vertices to the types. An update rule describes how the type of a vertex is updated given the types of its neighbors. In every round, all vertices are updated synchronously, which leads to a configuration update. While in general, Game of Life allows a broad range of update rules, we focus on two simple families of update rules, namely, underpopulation and overpopulation, that model several interesting dynamics studied in the literature. In both settings, a dead vertex requires at least a desired number of live neighbors to become alive. For underpopulation (resp., overpopulation), a live vertex requires at least (resp. at most) a desired number of live neighbors to remain alive. We study the basic computation problems, e.g., configuration reachability, for these two families of rules. For underpopulation rules, we show that these problems can be solved in polynomial time, whereas for overpopulation rules they are PSPACE-complete.}, author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Jecker, Ismael R and Svoboda, Jakub}, booktitle = {45th International Symposium on Mathematical Foundations of Computer Science}, isbn = {9783959771597}, issn = {18688969}, location = {Prague, Czech Republic}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Simplified game of life: Algorithms and complexity}}, doi = {10.4230/LIPIcs.MFCS.2020.22}, volume = {170}, year = {2020}, } @inproceedings{8534, abstract = {A regular language L of finite words is composite if there are regular languages L₁,L₂,…,L_t such that L = ⋂_{i = 1}^t L_i and the index (number of states in a minimal DFA) of every language L_i is strictly smaller than the index of L. Otherwise, L is prime. Primality of regular languages was introduced and studied in [O. Kupferman and J. Mosheiff, 2015], where the complexity of deciding the primality of the language of a given DFA was left open, with a doubly-exponential gap between the upper and lower bounds. We study primality for unary regular languages, namely regular languages with a singleton alphabet. A unary language corresponds to a subset of ℕ, making the study of unary prime languages closer to that of primality in number theory. We show that the setting of languages is richer. In particular, while every composite number is the product of two smaller numbers, the number t of languages necessary to decompose a composite unary language induces a strict hierarchy. In addition, a primality witness for a unary language L, namely a word that is not in L but is in all products of languages that contain L and have an index smaller than L’s, may be of exponential length. Still, we are able to characterize compositionality by structural properties of a DFA for L, leading to a LogSpace algorithm for primality checking of unary DFAs.}, author = {Jecker, Ismael R and Kupferman, Orna and Mazzocchi, Nicolas}, booktitle = {45th International Symposium on Mathematical Foundations of Computer Science}, isbn = {9783959771597}, issn = {18688969}, location = {Prague, Czech Republic}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Unary prime languages}}, doi = {10.4230/LIPIcs.MFCS.2020.51}, volume = {170}, year = {2020}, } @article{8538, abstract = {We prove some recent experimental observations of Dan Reznik concerning periodic billiard orbits in ellipses. For example, the sum of cosines of the angles of a periodic billiard polygon remains constant in the 1-parameter family of such polygons (that exist due to the Poncelet porism). In our proofs, we use geometric and complex analytic methods.}, author = {Akopyan, Arseniy and Schwartz, Richard and Tabachnikov, Serge}, issn = {2199-6768}, journal = {European Journal of Mathematics}, publisher = {Springer Nature}, title = {{Billiards in ellipses revisited}}, doi = {10.1007/s40879-020-00426-9}, year = {2020}, } @unpublished{8616, abstract = {The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal in vivo imaging, we reported that a substantial proportion of blood vessels in the adult brain sporadically occluded and regressed. Their regression proceeded through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels were found to be widespread in mouse, monkey and human brains. Both brief occlusions of the middle cerebral artery and lipopolysaccharide-mediated inflammation induced an increase of vessel regression. Blockage of leukocyte adhesion to endothelial cells alleviated LPS-induced vessel regression. We further revealed that blood vessel regression caused a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain.}, author = {Gao, Xiaofei and Li, Jun-Liszt and Chen, Xingjun and Ci, Bo and Chen, Fei and Lu, Nannan and Shen, Bo and Zheng, Lijun and Jia, Jie-Min and Yi, Yating and Zhang, Shiwen and Shi, Ying-Chao and Shi, Kaibin and Propson, Nicholas E and Huang, Yubin and Poinsatte, Katherine and Zhang, Zhaohuan and Yue, Yuanlei and Bosco, Dale B and Lu, Ying-mei and Yang, Shi-bing and Adams, Ralf H. and Lindner, Volkhard and Huang, Fen and Wu, Long-Jun and Zheng, Hui and Han, Feng and Hippenmeyer, Simon and Stowe, Ann M. and Peng, Bo and Margeta, Marta and Wang, Xiaoqun and Liu, Qiang and Körbelin, Jakob and Trepel, Martin and Lu, Hui and Zhou, Bo O. and Zhao, Hu and Su, Wenzhi and Bachoo, Robert M. and Ge, Woo-ping}, booktitle = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, title = {{Reduction of neuronal activity mediated by blood-vessel regression in the brain}}, doi = {10.1101/2020.09.15.262782}, year = {2020}, } @techreport{8695, abstract = {A look at international activities on Open Science reveals a broad spectrum from individual institutional policies to national action plans. The present Recommendations for a National Open Science Strategy in Austria are based on these international initiatives and present practical considerations for their coordinated implementation with regard to strategic developments in research, technology and innovation (RTI) in Austria until 2030. They are addressed to all relevant actors in the RTI system, in particular to Research Performing Organisations, Research Funding Organisations, Research Policy, memory institutions such as Libraries and Researchers. The recommendation paper was developed from 2018 to 2020 by the OANA working group "Open Science Strategy" and published for the first time in spring 2020 for a public consultation. The now available final version of the recommendation document, which contains feedback and comments from the consultation, is intended to provide an impetus for further discussion and implementation of Open Science in Austria and serves as a contribution and basis for a potential national Open Science Strategy in Austria. The document builds on the diverse expertise of the authors (academia, administration, library and archive, information technology, science policy, funding system, etc.) and reflects their personal experiences and opinions.}, author = {Mayer, Katja and Rieck, Katharina and Reichmann, Stefan and Danowski, Patrick and Graschopf, Anton and König, Thomas and Kraker, Peter and Lehner, Patrick and Reckling, Falk and Ross-Hellauer, Tony and Spichtinger, Daniel and Tzatzanis, Michalis and Schürz, Stefanie}, pages = {36}, publisher = {OANA}, title = {{Empfehlungen für eine nationale Open Science Strategie in Österreich / Recommendations for a National Open Science Strategy in Austria}}, doi = {10.5281/ZENODO.4109242}, year = {2020}, } @article{8706, abstract = {As part of the Austrian Transition to Open Access (AT2OA) project, subproject TP1-B is working on designing a monitoring solution for the output of Open Access publications in Austria. This report on a potential Open Access monitoring approach in Austria is one of the results of these efforts and can serve as a basis for discussion on an international level.}, author = {Danowski, Patrick and Ferus, Andreas and Hikl, Anna-Laetitia and McNeill, Gerda and Miniberger, Clemens and Reding, Steve and Zarka, Tobias and Zojer, Michael}, issn = {10222588}, journal = {Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare}, number = {2}, pages = {278--284}, publisher = {Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare}, title = {{„Recommendation“ for the further procedure for open access monitoring. Deliverable of the AT2OA subproject TP1-B}}, doi = {10.31263/voebm.v73i2.3941}, volume = {73}, year = {2020}, } @article{8978, abstract = {Mosaic analysis with double markers (MADM) technology enables concomitant fluorescent cell labeling and induction of uniparental chromosome disomy (UPD) with single-cell resolution. In UPD, imprinted genes are either overexpressed 2-fold or are not expressed. Here, the MADM platform is utilized to probe imprinting phenotypes at the transcriptional level. This protocol highlights major steps for the generation and isolation of projection neurons and astrocytes with MADM-induced UPD from mouse cerebral cortex for downstream single-cell and low-input sample RNA-sequencing experiments. For complete details on the use and execution of this protocol, please refer to Laukoter et al. (2020b).}, author = {Laukoter, Susanne and Amberg, Nicole and Pauler, Florian and Hippenmeyer, Simon}, issn = {2666-1667}, journal = {STAR Protocols}, number = {3}, publisher = {Elsevier}, title = {{Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy}}, doi = {10.1016/j.xpro.2020.100215}, volume = {1}, year = {2020}, } @inproceedings{9103, abstract = {We introduce LRT-NG, a set of techniques and an associated toolset that computes a reachtube (an over-approximation of the set of reachable states over a given time horizon) of a nonlinear dynamical system. LRT-NG significantly advances the state-of-the-art Langrangian Reachability and its associated tool LRT. From a theoretical perspective, LRT-NG is superior to LRT in three ways. First, it uses for the first time an analytically computed metric for the propagated ball which is proven to minimize the ball’s volume. We emphasize that the metric computation is the centerpiece of all bloating-based techniques. Secondly, it computes the next reachset as the intersection of two balls: one based on the Cartesian metric and the other on the new metric. While the two metrics were previously considered opposing approaches, their joint use considerably tightens the reachtubes. Thirdly, it avoids the "wrapping effect" associated with the validated integration of the center of the reachset, by optimally absorbing the interval approximation in the radius of the next ball. From a tool-development perspective, LRT-NG is superior to LRT in two ways. First, it is a standalone tool that no longer relies on CAPD. This required the implementation of the Lohner method and a Runge-Kutta time-propagation method. Secondly, it has an improved interface, allowing the input model and initial conditions to be provided as external input files. Our experiments on a comprehensive set of benchmarks, including two Neural ODEs, demonstrates LRT-NG’s superior performance compared to LRT, CAPD, and Flow*.}, author = {Gruenbacher, Sophie and Cyranka, Jacek and Lechner, Mathias and Islam, Md Ariful and Smolka, Scott A. and Grosu, Radu}, booktitle = {Proceedings of the 59th IEEE Conference on Decision and Control}, isbn = {9781728174471}, issn = {07431546}, location = {Jeju Islang, Korea (South)}, pages = {1556--1563}, publisher = {IEEE}, title = {{Lagrangian reachtubes: The next generation}}, doi = {10.1109/CDC42340.2020.9304042}, volume = {2020}, year = {2020}, } @article{9208, abstract = {Bending-active structures are able to efficiently produce complex curved shapes from flat panels. The desired deformation of the panels derives from the proper selection of their elastic properties. Optimized panels, called FlexMaps, are designed such that, once they are bent and assembled, the resulting static equilibrium configuration matches a desired input 3D shape. The FlexMaps elastic properties are controlled by locally varying spiraling geometric mesostructures, which are optimized in size and shape to match specific bending requests, namely the global curvature of the target shape. The design pipeline starts from a quad mesh representing the input 3D shape, which defines the edge size and the total amount of spirals: every quad will embed one spiral. Then, an optimization algorithm tunes the geometry of the spirals by using a simplified pre-computed rod model. This rod model is derived from a non-linear regression algorithm which approximates the non-linear behavior of solid FEM spiral models subject to hundreds of load combinations. This innovative pipeline has been applied to the project of a lightweight plywood pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted arch that fits a bounding box of 3.90x3.96x3.25 meters. This case study serves to test the applicability of this methodology at the architectural scale. The structure is validated via FE analyses and the fabrication of the full scale prototype.}, author = {Laccone, Francesco and Malomo, Luigi and Perez Rodriguez, Jesus and Pietroni, Nico and Ponchio, Federico and Bickel, Bernd and Cignoni, Paolo}, issn = {25233971}, journal = {SN Applied Sciences}, number = {9}, publisher = {Springer Nature}, title = {{A bending-active twisted-arch plywood structure: Computational design and fabrication of the FlexMaps Pavilion}}, doi = {10.1007/s42452-020-03305-w}, volume = {2}, year = {2020}, } @inproceedings{9221, abstract = {Recent works have shown that gradient descent can find a global minimum for over-parameterized neural networks where the widths of all the hidden layers scale polynomially with N (N being the number of training samples). In this paper, we prove that, for deep networks, a single layer of width N following the input layer suffices to ensure a similar guarantee. In particular, all the remaining layers are allowed to have constant widths, and form a pyramidal topology. We show an application of our result to the widely used LeCun’s initialization and obtain an over-parameterization requirement for the single wide layer of order N2. }, author = {Nguyen, Quynh and Mondelli, Marco}, booktitle = {34th Conference on Neural Information Processing Systems}, location = {Vancouver, Canada}, pages = {11961–11972}, publisher = {Curran Associates}, title = {{Global convergence of deep networks with one wide layer followed by pyramidal topology}}, volume = {33}, year = {2020}, } @inproceedings{9415, abstract = {Optimizing convolutional neural networks for fast inference has recently become an extremely active area of research. One of the go-to solutions in this context is weight pruning, which aims to reduce computational and memory footprint by removing large subsets of the connections in a neural network. Surprisingly, much less attention has been given to exploiting sparsity in the activation maps, which tend to be naturally sparse in many settings thanks to the structure of rectified linear (ReLU) activation functions. In this paper, we present an in-depth analysis of methods for maximizing the sparsity of the activations in a trained neural network, and show that, when coupled with an efficient sparse-input convolution algorithm, we can leverage this sparsity for significant performance gains. To induce highly sparse activation maps without accuracy loss, we introduce a new regularization technique, coupled with a new threshold-based sparsification method based on a parameterized activation function called Forced-Activation-Threshold Rectified Linear Unit (FATReLU). We examine the impact of our methods on popular image classification models, showing that most architectures can adapt to significantly sparser activation maps without any accuracy loss. Our second contribution is showing that these these compression gains can be translated into inference speedups: we provide a new algorithm to enable fast convolution operations over networks with sparse activations, and show that it can enable significant speedups for end-to-end inference on a range of popular models on the large-scale ImageNet image classification task on modern Intel CPUs, with little or no retraining cost. }, author = {Kurtz, Mark and Kopinsky, Justin and Gelashvili, Rati and Matveev, Alexander and Carr, John and Goin, Michael and Leiserson, William and Moore, Sage and Nell, Bill and Shavit, Nir and Alistarh, Dan-Adrian}, booktitle = {37th International Conference on Machine Learning, ICML 2020}, issn = {2640-3498}, location = {Online}, pages = {5533--5543}, title = {{Inducing and exploiting activation sparsity for fast neural network inference}}, volume = {119}, year = {2020}, } @inproceedings{10672, abstract = {The family of feedback alignment (FA) algorithms aims to provide a more biologically motivated alternative to backpropagation (BP), by substituting the computations that are unrealistic to be implemented in physical brains. While FA algorithms have been shown to work well in practice, there is a lack of rigorous theory proofing their learning capabilities. Here we introduce the first feedback alignment algorithm with provable learning guarantees. In contrast to existing work, we do not require any assumption about the size or depth of the network except that it has a single output neuron, i.e., such as for binary classification tasks. We show that our FA algorithm can deliver its theoretical promises in practice, surpassing the learning performance of existing FA methods and matching backpropagation in binary classification tasks. Finally, we demonstrate the limits of our FA variant when the number of output neurons grows beyond a certain quantity.}, author = {Lechner, Mathias}, booktitle = {8th International Conference on Learning Representations}, location = {Virtual ; Addis Ababa, Ethiopia}, publisher = {ICLR}, title = {{Learning representations for binary-classification without backpropagation}}, year = {2020}, } @inproceedings{8188, abstract = {A natural approach to generative modeling of videos is to represent them as a composition of moving objects. Recent works model a set of 2D sprites over a slowly-varying background, but without considering the underlying 3D scene that gives rise to them. We instead propose to model a video as the view seen while moving through a scene with multiple 3D objects and a 3D background. Our model is trained from monocular videos without any supervision, yet learns to generate coherent 3D scenes containing several moving objects. We conduct detailed experiments on two datasets, going beyond the visual complexity supported by state-of-the-art generative approaches. We evaluate our method on depth-prediction and 3D object detection---tasks which cannot be addressed by those earlier works---and show it out-performs them even on 2D instance segmentation and tracking.}, author = {Henderson, Paul M and Lampert, Christoph}, booktitle = {34th Conference on Neural Information Processing Systems}, isbn = {9781713829546}, location = {Vancouver, Canada}, pages = {3106–3117}, publisher = {Curran Associates}, title = {{Unsupervised object-centric video generation and decomposition in 3D}}, volume = {33}, year = {2020}, } @book{7474, abstract = {This booklet is a collection of abstracts presented at the AHPC conference.}, editor = {Schlögl, Alois and Kiss, Janos and Elefante, Stefano}, isbn = {978-3-99078-004-6}, location = {Klosterneuburg, Austria}, pages = {72}, publisher = {IST Austria}, title = {{Austrian High-Performance-Computing meeting (AHPC2020)}}, doi = {10.15479/AT:ISTA:7474}, year = {2020}, } @inproceedings{7808, abstract = {Quantization converts neural networks into low-bit fixed-point computations which can be carried out by efficient integer-only hardware, and is standard practice for the deployment of neural networks on real-time embedded devices. However, like their real-numbered counterpart, quantized networks are not immune to malicious misclassification caused by adversarial attacks. We investigate how quantization affects a network’s robustness to adversarial attacks, which is a formal verification question. We show that neither robustness nor non-robustness are monotonic with changing the number of bits for the representation and, also, neither are preserved by quantization from a real-numbered network. For this reason, we introduce a verification method for quantized neural networks which, using SMT solving over bit-vectors, accounts for their exact, bit-precise semantics. We built a tool and analyzed the effect of quantization on a classifier for the MNIST dataset. We demonstrate that, compared to our method, existing methods for the analysis of real-numbered networks often derive false conclusions about their quantizations, both when determining robustness and when detecting attacks, and that existing methods for quantized networks often miss attacks. Furthermore, we applied our method beyond robustness, showing how the number of bits in quantization enlarges the gender bias of a predictor for students’ grades.}, author = {Giacobbe, Mirco and Henzinger, Thomas A and Lechner, Mathias}, booktitle = {International Conference on Tools and Algorithms for the Construction and Analysis of Systems}, isbn = {9783030452360}, issn = {16113349}, location = {Dublin, Ireland}, pages = {79--97}, publisher = {Springer Nature}, title = {{How many bits does it take to quantize your neural network?}}, doi = {10.1007/978-3-030-45237-7_5}, volume = {12079}, year = {2020}, } @inproceedings{7952, abstract = {Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. manifolds defined as the zero set of some multivariate vector-valued smooth function f: ℝ^d → ℝ^(d-n). A natural (and efficient) way to approximate an isomanifold is to consider its Piecewise-Linear (PL) approximation based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we give conditions under which the PL-approximation of an isomanifold is topologically equivalent to the isomanifold. The conditions are easy to satisfy in the sense that they can always be met by taking a sufficiently fine triangulation 𝒯. This contrasts with previous results on the triangulation of manifolds where, in arbitrary dimensions, delicate perturbations are needed to guarantee topological correctness, which leads to strong limitations in practice. We further give a bound on the Fréchet distance between the original isomanifold and its PL-approximation. Finally we show analogous results for the PL-approximation of an isomanifold with boundary. }, author = {Boissonnat, Jean-Daniel and Wintraecken, Mathijs}, booktitle = {36th International Symposium on Computational Geometry}, isbn = {978-3-95977-143-6}, issn = {1868-8969}, location = {Zürich, Switzerland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{The topological correctness of PL-approximations of isomanifolds}}, doi = {10.4230/LIPIcs.SoCG.2020.20}, volume = {164}, year = {2020}, } @inproceedings{7990, abstract = {Given a finite point set P in general position in the plane, a full triangulation is a maximal straight-line embedded plane graph on P. A partial triangulation on P is a full triangulation of some subset P' of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge, removes a non-extreme point of degree 3, or adds a point in P ⧵ P' as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The goal of this paper is to investigate the structure of this graph, with emphasis on its connectivity. For sets P of n points in general position, we show that the bistellar flip graph is (n-3)-connected, thereby answering, for sets in general position, an open questions raised in a book (by De Loera, Rambau, and Santos) and a survey (by Lee and Santos) on triangulations. This matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points and projecting the lower convex hull), where (n-3)-connectivity has been known since the late 1980s through the secondary polytope (Gelfand, Kapranov, Zelevinsky) and Balinski’s Theorem. Our methods also yield the following results (see the full version [Wagner and Welzl, 2020]): (i) The bistellar flip graph can be covered by graphs of polytopes of dimension n-3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n-3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations are regular iff the trivial subdivision has height n-3 in the partial order of partial subdivisions. (iv) There are arbitrarily large sets P with non-regular partial triangulations, while every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular partial triangulations (answering a question by F. Santos in the unexpected direction).}, author = {Wagner, Uli and Welzl, Emo}, booktitle = {36th International Symposium on Computational Geometry}, isbn = {9783959771436}, issn = {18688969}, location = {Zürich, Switzerland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips)}}, doi = {10.4230/LIPIcs.SoCG.2020.67}, volume = {164}, year = {2020}, } @inproceedings{7807, abstract = {In a straight-line embedded triangulation of a point set P in the plane, removing an inner edge and—provided the resulting quadrilateral is convex—adding the other diagonal is called an edge flip. The (edge) flip graph has all triangulations as vertices, and a pair of triangulations is adjacent if they can be obtained from each other by an edge flip. The goal of this paper is to contribute to a better understanding of the flip graph, with an emphasis on its connectivity. For sets in general position, it is known that every triangulation allows at least edge flips (a tight bound) which gives the minimum degree of any flip graph for n points. We show that for every point set P in general position, the flip graph is at least -vertex connected. Somewhat more strongly, we show that the vertex connectivity equals the minimum degree occurring in the flip graph, i.e. the minimum number of flippable edges in any triangulation of P, provided P is large enough. Finally, we exhibit some of the geometry of the flip graph by showing that the flip graph can be covered by 1-skeletons of polytopes of dimension (products of associahedra). A corresponding result ((n – 3)-vertex connectedness) can be shown for the bistellar flip graph of partial triangulations, i.e. the set of all triangulations of subsets of P which contain all extreme points of P. This will be treated separately in a second part.}, author = {Wagner, Uli and Welzl, Emo}, booktitle = {Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms}, isbn = {9781611975994}, location = {Salt Lake City, UT, United States}, pages = {2823--2841}, publisher = {SIAM}, title = {{Connectivity of triangulation flip graphs in the plane (Part I: Edge flips)}}, doi = {10.1137/1.9781611975994.172}, volume = {2020-January}, year = {2020}, } @misc{13073, abstract = {The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.}, author = {Simon, Alexis and Fraisse, Christelle and El Ayari, Tahani and Liautard-Haag, Cathy and Strelkov, Petr and Welch, John and Bierne, Nicolas}, publisher = {Dryad}, title = {{How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels}}, doi = {10.5061/DRYAD.R4XGXD29N}, year = {2020}, } @misc{13065, abstract = {Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.}, author = {Arnoux, Stephanie and Fraisse, Christelle and Sauvage, Christopher}, publisher = {Dryad}, title = {{VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species}}, doi = {10.5061/DRYAD.Q2BVQ83HD}, year = {2020}, } @inproceedings{8536, abstract = {This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N 1−1/µ ), where N is the block length and µ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 and 1.}, author = {Mondelli, Marco and Hashemi, Seyyed Ali and Cioffi, John and Goldsmith, Andrea}, booktitle = {IEEE International Symposium on Information Theory - Proceedings}, isbn = {9781728164328}, issn = {21578095}, location = {Los Angeles, CA, United States}, publisher = {IEEE}, title = {{Simplified successive cancellation decoding of polar codes has sublinear latency}}, doi = {10.1109/ISIT44484.2020.9174141}, volume = {2020-June}, year = {2020}, } @article{9308, author = {Avvakumov, Sergey and Wagner, Uli and Mabillard, Isaac and Skopenkov, A. B.}, issn = {0036-0279}, journal = {Russian Mathematical Surveys}, number = {6}, pages = {1156--1158}, publisher = {IOP Publishing}, title = {{Eliminating higher-multiplicity intersections, III. Codimension 2}}, doi = {10.1070/RM9943}, volume = {75}, year = {2020}, } @article{6358, abstract = {We study dynamical optimal transport metrics between density matricesassociated to symmetric Dirichlet forms on finite-dimensional C∗-algebras. Our settingcovers arbitrary skew-derivations and it provides a unified framework that simultaneously generalizes recently constructed transport metrics for Markov chains, Lindblad equations, and the Fermi Ornstein–Uhlenbeck semigroup. We develop a non-nommutative differential calculus that allows us to obtain non-commutative Ricci curvature bounds, logarithmic Sobolev inequalities, transport-entropy inequalities, andspectral gap estimates.}, author = {Carlen, Eric A. and Maas, Jan}, issn = {15729613}, journal = {Journal of Statistical Physics}, number = {2}, pages = {319--378}, publisher = {Springer Nature}, title = {{Non-commutative calculus, optimal transport and functional inequalities in dissipative quantum systems}}, doi = {10.1007/s10955-019-02434-w}, volume = {178}, year = {2020}, } @inbook{74, abstract = {We study the Gromov waist in the sense of t-neighborhoods for measures in the Euclidean space, motivated by the famous theorem of Gromov about the waist of radially symmetric Gaussian measures. In particular, it turns our possible to extend Gromov’s original result to the case of not necessarily radially symmetric Gaussian measure. We also provide examples of measures having no t-neighborhood waist property, including a rather wide class of compactly supported radially symmetric measures and their maps into the Euclidean space of dimension at least 2. We use a simpler form of Gromov’s pancake argument to produce some estimates of t-neighborhoods of (weighted) volume-critical submanifolds in the spirit of the waist theorems, including neighborhoods of algebraic manifolds in the complex projective space. In the appendix of this paper we provide for reader’s convenience a more detailed explanation of the Caffarelli theorem that we use to handle not necessarily radially symmetric Gaussian measures.}, author = {Akopyan, Arseniy and Karasev, Roman}, booktitle = {Geometric Aspects of Functional Analysis}, editor = {Klartag, Bo'az and Milman, Emanuel}, isbn = {9783030360191}, issn = {16179692}, pages = {1--27}, publisher = {Springer Nature}, title = {{Gromov's waist of non-radial Gaussian measures and radial non-Gaussian measures}}, doi = {10.1007/978-3-030-36020-7_1}, volume = {2256}, year = {2020}, } @article{177, abstract = {We develop a geometric version of the circle method and use it to compute the compactly supported cohomology of the space of rational curves through a point on a smooth affine hypersurface of sufficiently low degree.}, author = {Browning, Timothy D and Sawin, Will}, journal = {Annals of Mathematics}, number = {3}, pages = {893--948}, publisher = {Princeton University}, title = {{A geometric version of the circle method}}, doi = {10.4007/annals.2020.191.3.4}, volume = {191}, year = {2020}, } @article{6649, abstract = {While Hartree–Fock theory is well established as a fundamental approximation for interacting fermions, it has been unclear how to describe corrections to it due to many-body correlations. In this paper we start from the Hartree–Fock state given by plane waves and introduce collective particle–hole pair excitations. These pairs can be approximately described by a bosonic quadratic Hamiltonian. We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type upper bound to the ground state energy. Our result justifies the random-phase approximation in the mean-field scaling regime, for repulsive, regular interaction potentials. }, author = {Benedikter, Niels P and Nam, Phan Thành and Porta, Marcello and Schlein, Benjamin and Seiringer, Robert}, issn = {1432-0916}, journal = {Communications in Mathematical Physics}, pages = {2097–2150}, publisher = {Springer Nature}, title = {{Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime}}, doi = {10.1007/s00220-019-03505-5}, volume = {374}, year = {2020}, } @article{6796, abstract = {Nearby grid cells have been observed to express a remarkable degree of long-rangeorder, which is often idealized as extending potentially to infinity. Yet their strict peri-odic firing and ensemble coherence are theoretically possible only in flat environments, much unlike the burrows which rodents usually live in. Are the symmetrical, coherent grid maps inferred in the lab relevant to chart their way in their natural habitat? We consider spheres as simple models of curved environments and waiting for the appropriate experiments to be performed, we use our adaptation model to predict what grid maps would emerge in a network with the same type of recurrent connections, which on the plane produce coherence among the units. We find that on the sphere such connections distort the maps that single grid units would express on their own, and aggregate them into clusters. When remapping to a different spherical environment, units in each cluster maintain only partial coherence, similar to what is observed in disordered materials, such as spin glasses.}, author = {Stella, Federico and Urdapilleta, Eugenio and Luo, Yifan and Treves, Alessandro}, issn = {10981063}, journal = {Hippocampus}, number = {4}, pages = {302--313}, publisher = {Wiley}, title = {{Partial coherence and frustration in self-organizing spherical grids}}, doi = {10.1002/hipo.23144}, volume = {30}, year = {2020}, } @article{6761, abstract = {In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability.}, author = {Avni, Guy and Henzinger, Thomas A and Kupferman, Orna}, issn = {03043975}, journal = {Theoretical Computer Science}, pages = {42--55}, publisher = {Elsevier}, title = {{Dynamic resource allocation games}}, doi = {10.1016/j.tcs.2019.06.031}, volume = {807}, year = {2020}, } @article{6593, abstract = {We consider the monotone variational inequality problem in a Hilbert space and describe a projection-type method with inertial terms under the following properties: (a) The method generates a strongly convergent iteration sequence; (b) The method requires, at each iteration, only one projection onto the feasible set and two evaluations of the operator; (c) The method is designed for variational inequality for which the underline operator is monotone and uniformly continuous; (d) The method includes an inertial term. The latter is also shown to speed up the convergence in our numerical results. A comparison with some related methods is given and indicates that the new method is promising.}, author = {Shehu, Yekini and Li, Xiao-Huan and Dong, Qiao-Li}, issn = {1572-9265}, journal = {Numerical Algorithms}, pages = {365--388}, publisher = {Springer Nature}, title = {{An efficient projection-type method for monotone variational inequalities in Hilbert spaces}}, doi = {10.1007/s11075-019-00758-y}, volume = {84}, year = {2020}, } @article{6808, abstract = {Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions.}, author = {Jahr, Wiebke and Velicky, Philipp and Danzl, Johann G}, issn = {1046-2023}, journal = {Methods}, number = {3}, pages = {27--41}, publisher = {Elsevier}, title = {{Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens}}, doi = {10.1016/j.ymeth.2019.07.019}, volume = {174}, year = {2020}, } @article{6563, abstract = {This paper presents two algorithms. The first decides the existence of a pointed homotopy between given simplicial maps 𝑓,𝑔:𝑋→𝑌, and the second computes the group [𝛴𝑋,𝑌]∗ of pointed homotopy classes of maps from a suspension; in both cases, the target Y is assumed simply connected. More generally, these algorithms work relative to 𝐴⊆𝑋.}, author = {Filakovský, Marek and Vokřínek, Lukas}, issn = {16153383}, journal = {Foundations of Computational Mathematics}, pages = {311--330}, publisher = {Springer Nature}, title = {{Are two given maps homotopic? An algorithmic viewpoint}}, doi = {10.1007/s10208-019-09419-x}, volume = {20}, year = {2020}, } @article{6952, abstract = {We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, most existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to existing approaches, while also supporting weaker supervision. Importantly, it can be trained purely from 2D images, without pose annotations, and with only a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to reason over lighting parameters and exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach in various settings, showing that: (i) it learns to disentangle shape from pose and lighting; (ii) using shading in the loss improves performance compared to just silhouettes; (iii) when using a standard single white light, our model outperforms state-of-the-art 2D-supervised methods, both with and without pose supervision, thanks to exploiting shading cues; (iv) performance improves further when using multiple coloured lights, even approaching that of state-of-the-art 3D-supervised methods; (v) shapes produced by our model capture smooth surfaces and fine details better than voxel-based approaches; and (vi) our approach supports concave classes such as bathtubs and sofas, which methods based on silhouettes cannot learn.}, author = {Henderson, Paul M and Ferrari, Vittorio}, issn = {1573-1405}, journal = {International Journal of Computer Vision}, pages = {835--854}, publisher = {Springer Nature}, title = {{Learning single-image 3D reconstruction by generative modelling of shape, pose and shading}}, doi = {10.1007/s11263-019-01219-8}, volume = {128}, year = {2020}, } @article{7148, abstract = {In the cerebellum, GluD2 is exclusively expressed in Purkinje cells, where it regulates synapse formation and regeneration, synaptic plasticity, and motor learning. Delayed cognitive development in humans with GluD2 gene mutations suggests extracerebellar functions of GluD2. However, extracerebellar expression of GluD2 and its relationship with that of GluD1 are poorly understood. GluD2 mRNA and protein were widely detected, with relatively high levels observed in the olfactory glomerular layer, medial prefrontal cortex, cingulate cortex, retrosplenial granular cortex, olfactory tubercle, subiculum, striatum, lateral septum, anterodorsal thalamic nucleus, and arcuate hypothalamic nucleus. These regions were also enriched for GluD1, and many individual neurons coexpressed the two GluDs. In the retrosplenial granular cortex, GluD1 and GluD2 were selectively expressed at PSD‐95‐expressing glutamatergic synapses, and their coexpression on the same synapses was shown by SDS‐digested freeze‐fracture replica labeling. Biochemically, GluD1 and GluD2 formed coimmunoprecipitable complex formation in HEK293T cells and in the cerebral cortex and hippocampus. We further estimated the relative protein amount by quantitative immunoblotting using GluA2/GluD2 and GluA2/GluD1 chimeric proteins as standards for titration of GluD1 and GluD2 antibodies. Intriguingly, the relative amount of GluD2 was almost comparable to that of GluD1 in the postsynaptic density fraction prepared from the cerebral cortex and hippocampus. In contrast, GluD2 was overwhelmingly predominant in the cerebellum. Thus, we have determined the relative extracerebellar expression of GluD1 and GluD2 at regional, neuronal, and synaptic levels. These data provide a molecular–anatomical basis for possible competitive and cooperative interactions of GluD family members at synapses in various brain regions.}, author = {Nakamoto, Chihiro and Konno, Kohtarou and Miyazaki, Taisuke and Nakatsukasa, Ena and Natsume, Rie and Abe, Manabu and Kawamura, Meiko and Fukazawa, Yugo and Shigemoto, Ryuichi and Yamasaki, Miwako and Sakimura, Kenji and Watanabe, Masahiko}, issn = {1096-9861}, journal = {Journal of Comparative Neurology}, number = {6}, pages = {1003--1027}, publisher = {Wiley}, title = {{Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain}}, doi = {10.1002/cne.24792}, volume = {528}, year = {2020}, } @article{7033, abstract = {Removal of the Bax gene from mice completely protects the somas of retinal ganglion cells (RGCs) from apoptosis following optic nerve injury. This makes BAX a promising therapeutic target to prevent neurodegeneration. In this study, Bax+/− mice were used to test the hypothesis that lowering the quantity of BAX in RGCs would delay apoptosis following optic nerve injury. RGCs were damaged by performing optic nerve crush (ONC) and then immunostaining for phospho-cJUN, and quantitative PCR were used to monitor the status of the BAX activation mechanism in the months following injury. The apoptotic susceptibility of injured cells was directly tested by virally introducing GFP-BAX into Bax−/− RGCs after injury. The competency of quiescent RGCs to reactivate their BAX activation mechanism was tested by intravitreal injection of the JNK pathway agonist, anisomycin. Twenty-four weeks after ONC, Bax+/− mice had significantly less cell loss in their RGC layer than Bax+/+ mice 3 weeks after ONC. Bax+/− and Bax+/+ RGCs exhibited similar patterns of nuclear phospho-cJUN accumulation immediately after ONC, which persisted in Bax+/− RGCs for up to 7 weeks before abating. The transcriptional activation of BAX-activating genes was similar in Bax+/− and Bax+/+ RGCs following ONC. Intriguingly, cells deactivated their BAX activation mechanism between 7 and 12 weeks after crush. Introduction of GFP-BAX into Bax−/− cells at 4 weeks after ONC showed that these cells had a nearly normal capacity to activate this protein, but this capacity was lost 8 weeks after crush. Collectively, these data suggest that 8–12 weeks after crush, damaged cells no longer displayed increased susceptibility to BAX activation relative to their naïve counterparts. In this same timeframe, retinal glial activation and the signaling of the pro-apoptotic JNK pathway also abated. Quiescent RGCs did not show a timely reactivation of their JNK pathway following intravitreal injection with anisomycin. These findings demonstrate that lowering the quantity of BAX in RGCs is neuroprotective after acute injury. Damaged RGCs enter a quiescent state months after injury and are no longer responsive to an apoptotic stimulus. Quiescent RGCs will require rejuvenation to reacquire functionality.}, author = {Donahue, RJ and Maes, Margaret E and Grosser, JA and Nickells, RW}, issn = {1559-1182}, journal = {Molecular Neurobiology}, number = {2}, pages = {1070–1084}, publisher = {Springer Nature}, title = {{BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage}}, doi = {10.1007/s12035-019-01783-7}, volume = {57}, year = {2020}, } @article{6997, author = {Zhang, Yuzhou and Friml, Jiří}, issn = {1469-8137}, journal = {New Phytologist}, number = {3}, pages = {1049--1052}, publisher = {Wiley}, title = {{Auxin guides roots to avoid obstacles during gravitropic growth}}, doi = {10.1111/nph.16203}, volume = {225}, year = {2020}, } @article{7149, abstract = {In recent years, many genes have been associated with chromatinopathies classified as “Cornelia de Lange Syndrome‐like.” It is known that the phenotype of these patients becomes less recognizable, overlapping to features characteristic of other syndromes caused by genetic variants affecting different regulators of chromatin structure and function. Therefore, Cornelia de Lange syndrome diagnosis might be arduous due to the seldom discordance between unexpected molecular diagnosis and clinical evaluation. Here, we review the molecular features of Cornelia de Lange syndrome, supporting the hypothesis that “CdLS‐like syndromes” are part of a larger “rare disease family” sharing multiple clinical features and common disrupted molecular pathways.}, author = {Avagliano, Laura and Parenti, Ilaria and Grazioli, Paolo and Di Fede, Elisabetta and Parodi, Chiara and Mariani, Milena and Kaiser, Frank J. and Selicorni, Angelo and Gervasini, Cristina and Massa, Valentina}, issn = {1399-0004}, journal = {Clinical Genetics}, number = {1}, pages = {3--11}, publisher = {Wiley}, title = {{Chromatinopathies: A focus on Cornelia de Lange syndrome}}, doi = {10.1111/cge.13674}, volume = {97}, year = {2020}, } @article{7004, abstract = {We define an action of the (double of) Cohomological Hall algebra of Kontsevich and Soibelman on the cohomology of the moduli space of spiked instantons of Nekrasov. We identify this action with the one of the affine Yangian of gl(1). Based on that we derive the vertex algebra at the corner Wr1,r2,r3 of Gaiotto and Rapčák. We conjecture that our approach works for a big class of Calabi–Yau categories, including those associated with toric Calabi–Yau 3-folds.}, author = {Rapcak, Miroslav and Soibelman, Yan and Yang, Yaping and Zhao, Gufang}, issn = {1432-0916}, journal = {Communications in Mathematical Physics}, pages = {1803--1873}, publisher = {Springer Nature}, title = {{Cohomological Hall algebras, vertex algebras and instantons}}, doi = {10.1007/s00220-019-03575-5}, volume = {376}, year = {2020}, } @article{7204, abstract = {Plant root architecture dynamically adapts to various environmental conditions, such as salt‐containing soil. The phytohormone abscisic acid (ABA) is involved among others also in these developmental adaptations, but the underlying molecular mechanism remains elusive. Here, a novel branch of the ABA signaling pathway in Arabidopsis involving PYR/PYL/RCAR (abbreviated as PYLs) receptor‐protein phosphatase 2A (PP2A) complex that acts in parallel to the canonical PYLs‐protein phosphatase 2C (PP2C) mechanism is identified. The PYLs‐PP2A signaling modulates root gravitropism and lateral root formation through regulating phytohormone auxin transport. In optimal conditions, PYLs ABA receptor interacts with the catalytic subunits of PP2A, increasing their phosphatase activity and thus counteracting PINOID (PID) kinase‐mediated phosphorylation of PIN‐FORMED (PIN) auxin transporters. By contrast, in salt and osmotic stress conditions, ABA binds to PYLs, inhibiting the PP2A activity, which leads to increased PIN phosphorylation and consequently modulated directional auxin transport leading to adapted root architecture. This work reveals an adaptive mechanism that may flexibly adjust plant root growth to withstand saline and osmotic stresses. It occurs via the cross‐talk between the stress hormone ABA and the versatile developmental regulator auxin.}, author = {Li, Yang and Wang, Yaping and Tan, Shutang and Li, Zhen and Yuan, Zhi and Glanc, Matous and Domjan, David and Wang, Kai and Xuan, Wei and Guo, Yan and Gong, Zhizhong and Friml, Jiří and Zhang, Jing}, issn = {2198-3844}, journal = {Advanced Science}, number = {3}, publisher = {Wiley}, title = {{Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex}}, doi = {10.1002/advs.201901455}, volume = {7}, year = {2020}, } @article{7220, abstract = {BACKGROUND:The introduction of image-guided methods to bypass surgery has resulted in optimized preoperative identification of the recipients and excellent patency rates. However, the recently presented methods have also been resource-consuming. In the present study, we have reported a cost-efficient planning workflow for extracranial-intracranial (EC-IC) revascularization combined with transdural indocyanine green videoangiography (tICG-VA). METHODS:We performed a retrospective review at a single tertiary referral center from 2011 to 2018. A novel software-derived workflow was applied for 25 of 92 bypass procedures during the study period. The precision and accuracy were assessed using tICG-VA identification of the cortical recipients and a comparison of the virtual and actual data. The data from a control group of 25 traditionally planned procedures were also matched. RESULTS:The intraoperative transfer time of the calculated coordinates averaged 0.8 minute (range, 0.4-1.9 minutes). The definitive recipients matched the targeted branches in 80%, and a neighboring branch was used in 16%. Our workflow led to a significant craniotomy size reduction in the study group compared with that in the control group (P = 0.005). tICG-VA was successfully applied in 19 cases. An average of 2 potential recipient arteries were identified transdurally, resulting in tailored durotomy and 3 craniotomy adjustments. Follow-up patency results were available for 49 bypass surgeries, comprising 54 grafts. The overall patency rate was 91% at a median follow-up period of 26 months. No significant difference was found in the patency rate between the study and control groups (P = 0.317). CONCLUSIONS:Our clinical results have validated the presented planning and surgical workflow and support the routine implementation of tICG-VA for recipient identification before durotomy.}, author = {Dodier, Philippe and Auzinger, Thomas and Mistelbauer, Gabriel and Wang, Wei Te and Ferraz-Leite, Heber and Gruber, Andreas and Marik, Wolfgang and Winter, Fabian and Fischer, Gerrit and Frischer, Josa M. and Bavinzski, Gerhard}, issn = {1878-8769}, journal = {World Neurosurgery}, number = {2}, pages = {e892--e902}, publisher = {Elsevier}, title = {{Novel software-derived workflow in extracranial–intracranial bypass surgery validated by transdural indocyanine green videoangiography}}, doi = {10.1016/j.wneu.2019.11.038}, volume = {134}, year = {2020}, } @article{7142, abstract = {The phytohormone auxin acts as an amazingly versatile coordinator of plant growth and development. With its morphogen-like properties, auxin controls sites and timing of differentiation and/or growth responses both, in quantitative and qualitative terms. Specificity in the auxin response depends largely on distinct modes of signal transmission, by which individual cells perceive and convert auxin signals into a remarkable diversity of responses. The best understood, or so-called canonical mechanism of auxin perception ultimately results in variable adjustments of the cellular transcriptome, via a short, nuclear signal transduction pathway. Additional findings that accumulated over decades implied that an additional, presumably, cell surface-based auxin perception mechanism mediates very rapid cellular responses and decisively contributes to the cell's overall hormonal response. Recent investigations into both, nuclear and cell surface auxin signalling challenged this assumed partition of roles for different auxin signalling pathways and revealed an unexpected complexity in transcriptional and non-transcriptional cellular responses mediated by auxin.}, author = {Gallei, Michelle C and Luschnig, Christian and Friml, Jiří}, issn = {1879-0356}, journal = {Current Opinion in Plant Biology}, number = {2}, pages = {43--49}, publisher = {Elsevier}, title = {{Auxin signalling in growth: Schrödinger's cat out of the bag}}, doi = {10.1016/j.pbi.2019.10.003}, volume = {53}, year = {2020}, } @article{7166, abstract = {In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors.}, author = {Ucar, Mehmet C and Lipowsky, Reinhard}, issn = {1530-6992}, journal = {Nano Letters}, number = {1}, pages = {669--676}, publisher = {American Chemical Society}, title = {{Collective force generation by molecular motors is determined by strain-induced unbinding}}, doi = {10.1021/acs.nanolett.9b04445}, volume = {20}, year = {2020}, } @misc{9885, abstract = {Data obtained from the fine-grained simulations used in Figures 2-5, data obtained from the coarse-grained numerical calculations used in Figure 6, and a sample script for the fine-grained simulation as a Jupyter notebook (ZIP)}, author = {Ucar, Mehmet C and Lipowsky, Reinhard}, publisher = {American Chemical Society }, title = {{MURL_Dataz}}, doi = {10.1021/acs.nanolett.9b04445.s002}, year = {2020}, } @article{7218, abstract = {The combined resection of skull-infiltrating tumours and immediate cranioplastic reconstruction predominantly relies on freehand-moulded solutions. Techniques that enable this procedure to be performed easily in routine clinical practice would be useful. A cadaveric study was developed in which a new software tool was used to perform single-stage reconstructions with prefabricated implants after the resection of skull-infiltrating pathologies. A novel 3D visualization and interaction framework was developed to create 10 virtual craniotomies in five cadaveric specimens. Polyether ether ketone (PEEK) implants were manufactured according to the bone defects. The image-guided craniotomy was reconstructed with PEEK and compared to polymethyl methacrylate (PMMA). Navigational accuracy and surgical precision were assessed. The PEEK workflow resulted in up to 10-fold shorter reconstruction times than the standard technique. Surgical precision was reflected by the mean 1.1 ± 0.29 mm distance between the virtual and real craniotomy, with submillimetre precision in 50%. Assessment of the global offset between virtual and actual craniotomy revealed an average shift of 4.5 ± 3.6 mm. The results validated the ‘elective single-stage cranioplasty’ technique as a state-of-the-art virtual planning method and surgical workflow. This patient-tailored workflow could significantly reduce surgical times compared to the traditional, intraoperative acrylic moulding method and may be an option for the reconstruction of bone defects in the craniofacial region.}, author = {Dodier, Philippe and Winter, Fabian and Auzinger, Thomas and Mistelbauer, Gabriel and Frischer, Josa M. and Wang, Wei Te and Mallouhi, Ammar and Marik, Wolfgang and Wolfsberger, Stefan and Reissig, Lukas and Hammadi, Firas and Matula, Christian and Baumann, Arnulf and Bavinzski, Gerhard}, issn = {1399-0020}, journal = {International Journal of Oral and Maxillofacial Surgery}, number = {8}, pages = {P1007--1015}, publisher = {Elsevier}, title = {{Single-stage bone resection and cranioplastic reconstruction: Comparison of a novel software-derived PEEK workflow with the standard reconstructive method}}, doi = {10.1016/j.ijom.2019.11.011}, volume = {49}, year = {2020}, } @article{7219, abstract = {Root system architecture (RSA), governed by the phytohormone auxin, endows plants with an adaptive advantage in particular environments. Using geographically representative arabidopsis (Arabidopsis thaliana) accessions as a resource for GWA mapping, Waidmann et al. and Ogura et al. recently identified two novel components involved in modulating auxin-mediated RSA and conferring plant fitness in particular habitats.}, author = {Xiao, Guanghui and Zhang, Yuzhou}, issn = {13601385}, journal = {Trends in Plant Science}, number = {2}, pages = {P121--123}, publisher = {Elsevier}, title = {{Adaptive growth: Shaping auxin-mediated root system architecture}}, doi = {10.1016/j.tplants.2019.12.001}, volume = {25}, year = {2020}, } @article{7234, abstract = {T lymphocytes utilize amoeboid migration to navigate effectively within complex microenvironments. The precise rearrangement of the actin cytoskeleton required for cellular forward propulsion is mediated by actin regulators, including the actin‐related protein 2/3 (Arp2/3) complex, a macromolecular machine that nucleates branched actin filaments at the leading edge. The consequences of modulating Arp2/3 activity on the biophysical properties of the actomyosin cortex and downstream T cell function are incompletely understood. We report that even a moderate decrease of Arp3 levels in T cells profoundly affects actin cortex integrity. Reduction in total F‐actin content leads to reduced cortical tension and disrupted lamellipodia formation. Instead, in Arp3‐knockdown cells, the motility mode is dominated by blebbing migration characterized by transient, balloon‐like protrusions at the leading edge. Although this migration mode seems to be compatible with interstitial migration in three‐dimensional environments, diminished locomotion kinetics and impaired cytotoxicity interfere with optimal T cell function. These findings define the importance of finely tuned, Arp2/3‐dependent mechanophysical membrane integrity in cytotoxic effector T lymphocyte activities.}, author = {Obeidy, Peyman and Ju, Lining A. and Oehlers, Stefan H. and Zulkhernain, Nursafwana S. and Lee, Quintin and Galeano Niño, Jorge L. and Kwan, Rain Y.Q. and Tikoo, Shweta and Cavanagh, Lois L. and Mrass, Paulus and Cook, Adam J.L. and Jackson, Shaun P. and Biro, Maté and Roediger, Ben and Sixt, Michael K and Weninger, Wolfgang}, issn = {14401711}, journal = {Immunology and Cell Biology}, number = {2}, pages = {93--113}, publisher = {Wiley}, title = {{Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes}}, doi = {10.1111/imcb.12304}, volume = {98}, year = {2020}, } @article{7253, abstract = {The cyclin-dependent kinase inhibitor p57KIP2 is encoded by the imprinted Cdkn1c locus, exhibits maternal expression, and is essential for cerebral cortex development. How Cdkn1c regulates corticogenesis is however not clear. To this end we employ Mosaic Analysis with Double Markers (MADM) technology to genetically dissect Cdkn1c gene function in corticogenesis at single cell resolution. We find that the previously described growth-inhibitory Cdkn1c function is a non-cell-autonomous one, acting on the whole organism. In contrast we reveal a growth-promoting cell-autonomous Cdkn1c function which at the mechanistic level mediates radial glial progenitor cell and nascent projection neuron survival. Strikingly, the growth-promoting function of Cdkn1c is highly dosage sensitive but not subject to genomic imprinting. Collectively, our results suggest that the Cdkn1c locus regulates cortical development through distinct cell-autonomous and non-cell-autonomous mechanisms. More generally, our study highlights the importance to probe the relative contributions of cell intrinsic gene function and tissue-wide mechanisms to the overall phenotype.}, author = {Laukoter, Susanne and Beattie, Robert J and Pauler, Florian and Amberg, Nicole and Nakayama, Keiichi I. and Hippenmeyer, Simon}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development}}, doi = {10.1038/s41467-019-14077-2}, volume = {11}, year = {2020}, } @article{7339, abstract = {Cytoskeletal filaments such as microtubules (MTs) and filamentous actin (F-actin) dynamically support cell structure and functions. In central presynaptic terminals, F-actin is expressed along the release edge and reportedly plays diverse functional roles, but whether axonal MTs extend deep into terminals and play any physiological role remains controversial. At the calyx of Held in rats of either sex, confocal and high-resolution microscopy revealed that MTs enter deep into presynaptic terminal swellings and partially colocalize with a subset of synaptic vesicles (SVs). Electrophysiological analysis demonstrated that depolymerization of MTs specifically prolonged the slow-recovery time component of EPSCs from short-term depression induced by a train of high-frequency stimulation, whereas depolymerization of F-actin specifically prolonged the fast-recovery component. In simultaneous presynaptic and postsynaptic action potential recordings, depolymerization of MTs or F-actin significantly impaired the fidelity of high-frequency neurotransmission. We conclude that MTs and F-actin differentially contribute to slow and fast SV replenishment, thereby maintaining high-frequency neurotransmission.}, author = {Piriya Ananda Babu, Lashmi and Wang, Han Ying and Eguchi, Kohgaku and Guillaud, Laurent and Takahashi, Tomoyuki}, issn = {15292401}, journal = {Journal of neuroscience}, number = {1}, pages = {131--142}, publisher = {Society for Neuroscience}, title = {{Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission}}, doi = {10.1523/JNEUROSCI.1571-19.2019}, volume = {40}, year = {2020}, } @article{7350, abstract = {The ability to sense environmental temperature and to coordinate growth and development accordingly, is critical to the reproductive success of plants. Flowering time is regulated at the level of gene expression by a complex network of factors that integrate environmental and developmental cues. One of the main players, involved in modulating flowering time in response to changes in ambient temperature is FLOWERING LOCUS M (FLM). FLM transcripts can undergo extensive alternative splicing producing multiple variants, of which FLM-β and FLM-δ are the most representative. While FLM-β codes for the flowering repressor FLM protein, translation of FLM-δ has the opposite effect on flowering. Here we show that the cyclin-dependent kinase G2 (CDKG2), together with its cognate cyclin, CYCLYN L1 (CYCL1) affects the alternative splicing of FLM, balancing the levels of FLM-β and FLM-δ across the ambient temperature range. In the absence of the CDKG2/CYCL1 complex, FLM-β expression is reduced while FLM-δ is increased in a temperature dependent manner and these changes are associated with an early flowering phenotype in the cdkg2 mutant lines. In addition, we found that transcript variants retaining the full FLM intron 1 are sequestered in the cell nucleus. Strikingly, FLM intron 1 splicing is also regulated by CDKG2/CYCL1. Our results provide evidence that temperature and CDKs regulate the alternative splicing of FLM, contributing to flowering time definition.}, author = {Nibau, Candida and Gallemi, Marçal and Dadarou, Despoina and Doonan, John H. and Cavallari, Nicola}, issn = {1664-462X}, journal = {Frontiers in Plant Science}, publisher = {Frontiers Media}, title = {{Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2}}, doi = {10.3389/fpls.2019.01680}, volume = {10}, year = {2020}, }