TY - JOUR
AB - Tissue morphogenesis in multicellular organisms is brought about by spatiotemporal coordination of mechanical and chemical signals. Extensive work on how mechanical forces together with the well‐established morphogen signalling pathways can actively shape living tissues has revealed evolutionary conserved mechanochemical features of embryonic development. More recently, attention has been drawn to the description of tissue material properties and how they can influence certain morphogenetic processes. Interestingly, besides the role of tissue material properties in determining how much tissues deform in response to force application, there is increasing theoretical and experimental evidence, suggesting that tissue material properties can abruptly and drastically change in development. These changes resemble phase transitions, pointing at the intriguing possibility that important morphogenetic processes in development, such as symmetry breaking and self‐organization, might be mediated by tissue phase transitions. In this review, we summarize recent findings on the regulation and role of tissue material properties in the context of the developing embryo. We posit that abrupt changes of tissue rheological properties may have important implications in maintaining the balance between robustness and adaptability during embryonic development.
AU - Petridou, Nicoletta
AU - Heisenberg, Carl-Philipp J
ID - 6980
IS - 20
JF - The EMBO Journal
SN - 0261-4189
TI - Tissue rheology in embryonic organization
VL - 38
ER -
TY - JOUR
AB - We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ϕ : G → M of a graph G into a 2-manifold M maps the vertices in V(G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to the same point or overlapping arcs due to data compression or low resolution. This raises the computational problem of deciding whether a given map ϕ : G → M comes from an embedding. A map ϕ : G → M is a weak embedding if it can be perturbed into an embedding ψ ϵ : G → M with ‖ ϕ − ψ ϵ ‖ < ϵ for every ϵ > 0, where ‖.‖ is the unform norm.
A polynomial-time algorithm for recognizing weak embeddings has recently been found by Fulek and Kynčl. It reduces the problem to solving a system of linear equations over Z2. It runs in O(n2ω)≤ O(n4.75) time, where ω ∈ [2,2.373) is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler: We perform a sequence of local operations that gradually “untangles” the image ϕ(G) into an embedding ψ(G) or reports that ϕ is not a weak embedding. It combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.
AU - Akitaya, Hugo
AU - Fulek, Radoslav
AU - Tóth, Csaba
ID - 6982
IS - 4
JF - ACM Transactions on Algorithms
TI - Recognizing weak embeddings of graphs
VL - 15
ER -
TY - JOUR
AB - Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver.
AU - Kelemen, Réka K
AU - Rajakaruna, H
AU - Cockburn, IA
AU - Ganusov, VV
ID - 6983
JF - Frontiers in Immunology
SN - 1664-3224
TI - Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells
VL - 10
ER -
TY - CONF
AB - In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked contribution of individual cells to the network's output is computed by analyzing a set of interpretable metrics of their decoupled step and sinusoidal responses. As a result, our method is able to uniquely identify neurons with insightful dynamics, quantify relationships between dynamical properties and test accuracy through ablation analysis, and interpret the impact of network capacity on a network's dynamical distribution. Finally, we demonstrate the generalizability and scalability of our method by evaluating a series of different benchmark sequential datasets.
AU - Hasani, Ramin
AU - Amini, Alexander
AU - Lechner, Mathias
AU - Naser, Felix
AU - Grosu, Radu
AU - Rus, Daniela
ID - 6985
SN - 9781728119854
T2 - Proceedings of the International Joint Conference on Neural Networks
TI - Response characterization for auditing cell dynamics in long short-term memory networks
ER -
TY - JOUR
AB - Li-Nadler proposed a conjecture about traces of Hecke categories, which implies the semistable part of the Betti geometric Langlands conjecture of Ben-Zvi-Nadler in genus 1. We prove a Weyl group analogue of this conjecture. Our theorem holds in the natural generality of reflection groups in Euclidean or hyperbolic space. As a corollary, we give an expression of the centralizer of a finite order element in a reflection group using homotopy theory.
AU - Li, Penghui
ID - 6986
IS - 11
JF - Proceedings of the American Mathematical Society
SN - 0002-9939
TI - A colimit of traces of reflection groups
VL - 147
ER -
TY - CHAP
AB - Cells are arranged into species-specific patterns during early embryogenesis. Such cell division patterns are important since they often reflect the distribution of localized cortical factors from eggs/fertilized eggs to specific cells as well as the emergence of organismal form. However, it has proven difficult to reveal the mechanisms that underlie the emergence of cell positioning patterns that underlie embryonic shape, likely because a systems-level approach is required that integrates cell biological, genetic, developmental, and mechanical parameters. The choice of organism to address such questions is also important. Because ascidians display the most extreme form of invariant cleavage pattern among the metazoans, we have been analyzing the cell biological mechanisms that underpin three aspects of cell division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous cell cycles) which affect the overall shape of the blastula-stage ascidian embryo composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell stage that in turn undergo two further successive rounds of UCD. Starting at the 16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages. Perturbing either UCD or the alternate cell division rhythm perturbs cell position. We propose that dynamic cell shape changes propagate throughout the embryo via cell-cell contacts to create the ascidian-specific invariant cleavage pattern.
AU - McDougall, Alex
AU - Chenevert, Janet
AU - Godard, Benoit G
AU - Dumollard, Remi
ED - Tworzydlo, Waclaw
ED - Bilinski, Szczepan M.
ID - 6987
SN - 0080-1844
T2 - Evo-Devo: Non-model species in cell and developmental biology
TI - Emergence of embryo shape during cleavage divisions
VL - 68
ER -
TY - JOUR
AB - Platelets are central players in thrombosis and hemostasis but are increasingly recognized as key components of the immune system. They shape ensuing immune responses by recruiting leukocytes, and support the development of adaptive immunity. Recent data shed new light on the complex role of platelets in immunity. Here, we summarize experimental and clinical data on the role of platelets in host defense against bacteria. Platelets bind, contain, and kill bacteria directly; however, platelet proinflammatory effector functions and cross-talk with the coagulation system, can also result in damage to the host (e.g., acute lung injury and sepsis). Novel clinical insights support this dichotomy: platelet inhibition/thrombocytopenia can be either harmful or protective, depending on pathophysiological context. Clinical studies are currently addressing this aspect in greater depth.
AU - Nicolai, Leo
AU - Gärtner, Florian R
AU - Massberg, Steffen
ID - 6988
IS - 10
JF - Trends in Immunology
SN - 1471-4906
TI - Platelets in host defense: Experimental and clinical insights
VL - 40
ER -
TY - CONF
AB - When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with hole(s) to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special simple holes guarantee foldability.
AU - Aichholzer, Oswin
AU - Akitaya, Hugo A
AU - Cheung, Kenneth C
AU - Demaine, Erik D
AU - Demaine, Martin L
AU - Fekete, Sandor P
AU - Kleist, Linda
AU - Kostitsyna, Irina
AU - Löffler, Maarten
AU - Masárová, Zuzana
AU - Mundilova, Klara
AU - Schmidt, Christiane
ID - 6989
T2 - Proceedings of the 31st Canadian Conference on Computational Geometry
TI - Folding polyominoes with holes into a cube
ER -
TY - JOUR
AB - Plasmodesmata (PD) are plant-specific membrane-lined channels that create cytoplasmic and membrane continuities between adjacent cells, thereby facilitating cell–cell communication and virus movement. Plant cells have evolved diverse mechanisms to regulate PD plasticity in response to numerous environmental stimuli. In particular, during defense against plant pathogens, the defense hormone, salicylic acid (SA), plays a crucial role in the regulation of PD permeability in a callose-dependent manner. Here, we uncover a mechanism by which plants restrict the spreading of virus and PD cargoes using SA signaling by increasing lipid order and closure of PD. We showed that exogenous SA application triggered the compartmentalization of lipid raft nanodomains through a modulation of the lipid raft-regulatory protein, Remorin (REM). Genetic studies, superresolution imaging, and transmission electron microscopy observation together demonstrated that Arabidopsis REM1.2 and REM1.3 are crucial for plasma membrane nanodomain assembly to control PD aperture and functionality. In addition, we also found that a 14-3-3 epsilon protein modulates REM clustering and membrane nanodomain compartmentalization through its direct interaction with REM proteins. This study unveils a molecular mechanism by which the key plant defense hormone, SA, triggers membrane lipid nanodomain reorganization, thereby regulating PD closure to impede virus spreading.
AU - Huang, D
AU - Sun, Y
AU - Ma, Z
AU - Ke, M
AU - Cui, Y
AU - Chen, Z
AU - Chen, C
AU - Ji, C
AU - Tran, TM
AU - Yang, L
AU - Lam, SM
AU - Han, Y
AU - Shu, G
AU - Friml, Jiří
AU - Miao, Y
AU - Jiang, L
AU - Chen, X
ID - 6999
IS - 42
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
TI - Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization
VL - 116
ER -
TY - JOUR
AB - The main contributions of this paper are the proposition and the convergence analysis of a class of inertial projection-type algorithm for solving variational inequality problems in real Hilbert spaces where the underline operator is monotone and uniformly continuous. We carry out a unified analysis of the proposed method under very mild assumptions. In particular, weak convergence of the generated sequence is established and nonasymptotic O(1 / n) rate of convergence is established, where n denotes the iteration counter. We also present some experimental results to illustrate the profits gained by introducing the inertial extrapolation steps.
AU - Shehu, Yekini
AU - Iyiola, Olaniyi S.
AU - Li, Xiao-Huan
AU - Dong, Qiao-Li
ID - 7000
IS - 4
JF - Computational and Applied Mathematics
SN - 2238-3603
TI - Convergence analysis of projection method for variational inequalities
VL - 38
ER -
TY - JOUR
AB - Multiple Importance Sampling (MIS) is a key technique for achieving robustness of Monte Carlo estimators in computer graphics and other fields. We derive optimal weighting functions for MIS that provably minimize the variance of an MIS estimator, given a set of sampling techniques. We show that the resulting variance reduction over the balance heuristic can be higher than predicted by the variance bounds derived by Veach and Guibas, who assumed only non-negative weights in their proof. We theoretically analyze the variance of the optimal MIS weights and show the relation to the variance of the balance heuristic. Furthermore, we establish a connection between the new weighting functions and control variates as previously applied to mixture sampling. We apply the new optimal weights to integration problems in light transport and show that they allow for new design considerations when choosing the appropriate sampling techniques for a given integration problem.
AU - Kondapaneni, Ivo
AU - Vevoda, Petr
AU - Grittmann, Pascal
AU - Skrivan, Tomas
AU - Slusallek, Philipp
AU - Křivánek, Jaroslav
ID - 7002
IS - 4
JF - ACM Transactions on Graphics
SN - 0730-0301
TI - Optimal multiple importance sampling
VL - 38
ER -
TY - JOUR
AB - Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during intense neuronal activity via a two-step process. First, bulk endosomes are formed direct from the plasma membrane from which SVs are then generated. SV generation from bulk endosomes requires the efflux of previously accumulated calcium and activation of the protein phosphatase calcineurin. However, it is still unknown how calcineurin mediates SV generation. We addressed this question using a series of acute interventions that decoupled the generation of SVs from bulk endosomes in rat primary neuronal culture. This was achieved by either disruption of protein–protein interactions via delivery of competitive peptides, or inhibition of enzyme activity by known inhibitors. SV generation was monitored using either a morphological horseradish peroxidase assay or an optical assay that monitors the replenishment of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin I interaction. Peptides that disrupted syndapin I interactions with eps15 homology domain-containing proteins had no effect. This revealed that (i) calcineurin must be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity is essential for SV fission and (iii) the calcineurin-dependent interaction between dynamin I and syndapin I is essential for SV generation. We therefore propose that a calcineurin-dependent dephosphorylation cascade that requires both dynamin I GTPase and syndapin I lipid-deforming activity is essential for SV generation from bulk endosomes.
AU - Cheung, Giselle T
AU - Cousin, Michael A.
ID - 7005
IS - 5
JF - Journal of Neurochemistry
SN - 0022-3042
TI - Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction
VL - 151
ER -
TY - JOUR
AB - We consider the primitive relay channel, where the source sends a message to the relay and to the destination, and the relay helps the communication by transmitting an additional message to the destination via a separate channel. Two well-known coding techniques have been introduced for this setting: decode-and-forward and compress-and-forward. In decode-and-forward, the relay completely decodes the message and sends some information to the destination; in compress-and-forward, the relay does not decode, and it sends a compressed version of the received signal to the destination using Wyner–Ziv coding. In this paper, we present a novel coding paradigm that provides an improved achievable rate for the primitive relay channel. The idea is to combine compress-and-forward and decode-and-forward via a chaining construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward; and, in the second block, we use decode-and-forward. More specifically, in the first block, the relay does not decode, it compresses the received signal via Wyner–Ziv, and it sends only part of the compression to the destination. In the second block, the relay completely decodes the message, it sends some information to the destination, and it also sends the remaining part of the compression coming from the first block. By doing so, we are able to strictly outperform both compress-and-forward and decode-and-forward. Note that the proposed coding scheme can be implemented with polar codes. As such, it has the typical attractive properties of polar coding schemes, namely, quasi-linear encoding and decoding complexity, and error probability that decays at super-polynomial speed. As a running example, we take into account the special case of the erasure relay channel, and we provide a comparison between the rates achievable by our proposed scheme and the existing upper and lower bounds.
AU - Mondelli, Marco
AU - Hassani, S. Hamed
AU - Urbanke, Rüdiger
ID - 7007
IS - 10
JF - Algorithms
SN - 1999-4893
TI - A new coding paradigm for the primitive relay channel
VL - 12
ER -
TY - JOUR
AB - Cell migration is essential for physiological processes as diverse as development, immune defence and wound healing. It is also a hallmark of cancer malignancy. Thousands of publications have elucidated detailed molecular and biophysical mechanisms of cultured cells migrating on flat, 2D substrates of glass and plastic. However, much less is known about how cells successfully navigate the complex 3D environments of living tissues. In these more complex, native environments, cells use multiple modes of migration, including mesenchymal, amoeboid, lobopodial and collective, and these are governed by the local extracellular microenvironment, specific modalities of Rho GTPase signalling and non- muscle myosin contractility. Migration through 3D environments is challenging because it requires the cell to squeeze through complex or dense extracellular structures. Doing so requires specific cellular adaptations to mechanical features of the extracellular matrix (ECM) or its remodelling. In addition, besides navigating through diverse ECM environments and overcoming extracellular barriers, cells often interact with neighbouring cells and tissues through physical and signalling interactions. Accordingly, cells need to call on an impressively wide diversity of mechanisms to meet these challenges. This Review examines how cells use both classical and novel mechanisms of locomotion as they traverse challenging 3D matrices and cellular environments. It focuses on principles rather than details of migratory mechanisms and draws comparisons between 1D, 2D and 3D migration.
AU - Yamada, KM
AU - Sixt, Michael K
ID - 7009
IS - 12
JF - Nature Reviews Molecular Cell Biology
SN - 1471-0072
TI - Mechanisms of 3D cell migration
VL - 20
ER -
TY - CONF
AB - Numerous biophysical questions require the quantification of short-range interactions between (functionalized) surfaces and synthetic or biological objects such as cells. Here, we present an original, custom built setup for reflection interference contrast microscopy that can assess distances between a substrate and a flowing object at high speed with nanometric accuracy. We demonstrate its use to decipher the complex biochemical and mechanical interplay regulating blood cell homing at the vessel wall in the microcirculation using an in vitro approach. We show that in the absence of specific biochemical interactions, flowing cells are repelled from the soft layer lining the vessel wall, contributing to red blood cell repulsion in vivo. In contrast, this so-called glycocalyx stabilizes rolling of cells under flow in the presence of a specific receptor naturally present on activated leucocytes and a number of cancer cell lines.
AU - Davies, Heather S.
AU - Baranova, Natalia S.
AU - El Amri, Nouha
AU - Coche-Guérente, Liliane
AU - Verdier, Claude
AU - Bureau, Lionel
AU - Richter, Ralf P.
AU - Débarre, Delphine
ID - 7010
SN - 1605-7422
T2 - Advances in Microscopic Imaging II
TI - Blood cell-vessel wall interactions probed by reflection interference contrast microscopy
VL - 11076
ER -
TY - JOUR
AB - Chains of superconducting circuit devices provide a natural platform for studies of synthetic bosonic quantum matter. Motivated by the recent experimental progress in realizing disordered and interacting chains of superconducting transmon devices, we study the bosonic many-body localization phase transition using the methods of exact diagonalization as well as matrix product state dynamics. We estimate the location of transition separating the ergodic and the many-body localized phases as a function of the disorder strength and the many-body on-site interaction strength. The main difference between the bosonic model realized by superconducting circuits and similar fermionic model is that the effect of the on-site interaction is stronger due to the possibility of multiple excitations occupying the same site. The phase transition is found to be robust upon including longer-range hopping and interaction terms present in the experiments. Furthermore, we calculate experimentally relevant local observables and show that their temporal fluctuations can be used to distinguish between the dynamics of Anderson insulator, many-body localization, and delocalized phases. While we consider unitary dynamics, neglecting the effects of dissipation, decoherence, and measurement back action, the timescales on which the dynamics is unitary are sufficient for observation of characteristic dynamics in the many-body localized phase. Moreover, the experimentally available disorder strength and interactions allow for tuning the many-body localization phase transition, thus making the arrays of superconducting circuit devices a promising platform for exploring localization physics and phase transition.
AU - Orell, Tuure
AU - Michailidis, Alexios
AU - Serbyn, Maksym
AU - Silveri, Matti
ID - 7013
IS - 13
JF - Physical Review B
SN - 2469-9950
TI - Probing the many-body localization phase transition with superconducting circuits
VL - 100
ER -
TY - JOUR
AB - We modify the "floating crystal" trial state for the classical homogeneous electron gas (also known as jellium), in order to suppress the boundary charge fluctuations that are known to lead to a macroscopic increase of the energy. The argument is to melt a thin layer of the crystal close to the boundary and consequently replace it by an incompressible fluid. With the aid of this trial state we show that three different definitions of the ground-state energy of jellium coincide. In the first point of view the electrons are placed in a neutralizing uniform background. In the second definition there is no background but the electrons are submitted to the constraint that their density is constant, as is appropriate in density functional theory. Finally, in the third system each electron interacts with a periodic image of itself; that is, periodic boundary conditions are imposed on the interaction potential.
AU - Lewin, Mathieu
AU - Lieb, Elliott H.
AU - Seiringer, Robert
ID - 7015
IS - 3
JF - Physical Review B
SN - 2469-9950
TI - Floating Wigner crystal with no boundary charge fluctuations
VL - 100
ER -
TY - DATA
AB - Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.
AU - Tomanek, Isabella
ID - 7016
KW - Escherichia coli
KW - gene amplification
KW - galactose
KW - DOG
KW - experimental evolution
KW - Illumina sequence data
KW - FACS data
KW - microfluidics data
TI - Data for the paper "Gene amplification as a form of population-level gene expression regulation"
ER -
TY - JOUR
AB - Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90% of the variation in cellular response can be decomposed into three principal components (PCs) that have clear biological interpretations. We demonstrate that the third PC captures emergent transcriptional programs that are dependent on both drugs and can predict antagonism with a third drug targeting the emergent pathway. We further show that emergent gene expression patterns are most pronounced at a drug ratio where the drug interaction is strongest, providing a guideline for future measurements. Our results provide a readily applicable recipe for uncovering emergent responses in other systems and for higher-order drug combinations. A record of this paper’s transparent peer review process is included in the Supplemental Information.
AU - Lukacisin, Martin
AU - Bollenbach, Tobias
ID - 7026
IS - 5
JF - Cell Systems
SN - 2405-4712
TI - Emergent gene expression responses to drug combinations predict higher-order drug interactions
VL - 9
ER -
TY - CONF
AB - Optical frequency combs (OFCs) are light sources whose spectra consists of equally spaced frequency lines in the optical domain [1]. They have great potential for improving high-capacity data transfer, all-optical atomic clocks, spectroscopy, and high-precision measurements [2].
AU - Rueda Sanchez, Alfredo R
AU - Sedlmeir, Florian
AU - Leuchs, Gerd
AU - Kuamri, Madhuri
AU - Schwefel, Harald G. L.
ID - 7032
SN - 9781728104690
T2 - 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference
TI - Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators
ER -
TY - JOUR
AB - We find a graph of genus 5 and its drawing on the orientable surface of genus 4 with every pair of independent edges crossing an even number of times. This shows that the strong Hanani–Tutte theorem cannot be extended to the orientable surface of genus 4. As a base step in the construction we use a counterexample to an extension of the unified Hanani–Tutte theorem on the torus.
AU - Fulek, Radoslav
AU - Kynčl, Jan
ID - 7034
IS - 6
JF - Combinatorica
SN - 0209-9683
TI - Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4
VL - 39
ER -
TY - CONF
AB - The aim of this short note is to expound one particular issue that was discussed during the talk [10] given at the symposium ”Researches on isometries as preserver problems and related topics” at Kyoto RIMS. That is, the role of Dirac masses by describing the isometry group of various metric spaces of probability measures. This article is of survey character, and it does not contain any essentially new results.From an isometric point of view, in some cases, metric spaces of measures are similar to C(K)-type function spaces. Similarity means here that their isometries are driven by some nice transformations of the underlying space. Of course, it depends on the particular choice of the metric how nice these transformations should be. Sometimes, as we will see, being a homeomorphism is enough to generate an isometry. But sometimes we need more: the transformation must preserve the underlying distance as well. Statements claiming that isometries in questions are necessarily induced by homeomorphisms are called Banach-Stone-type results, while results asserting that the underlying transformation is necessarily an isometry are termed as isometric rigidity results.As Dirac masses can be considered as building bricks of the set of all Borel measures, a natural question arises:Is it enough to understand how an isometry acts on the set of Dirac masses? Does this action extend uniquely to all measures?In what follows, we will thoroughly investigate this question.
AU - Geher, Gyorgy Pal
AU - Titkos, Tamas
AU - Virosztek, Daniel
ID - 7035
T2 - Kyoto RIMS Kôkyûroku
TI - Dirac masses and isometric rigidity
VL - 2125
ER -
TY - JOUR
AB - A recent class of topological nodal-line semimetals with the general formula MSiX (M = Zr, Hf and X = S, Se, Te) has attracted much experimental and theoretical interest due to their properties, particularly their large magnetoresistances and high carrier mobilities. The plateletlike nature of the MSiX crystals and their extremely low residual resistivities make measurements of the resistivity along the [001] direction extremely challenging. To accomplish such measurements, microstructures of single crystals were prepared using focused ion beam techniques. Microstructures prepared in this manner have very well-defined geometries and maintain their high crystal quality, verified by the observations of quantum oscillations. We present magnetoresistance and quantum oscillation data for currents applied along both [001] and [100] in ZrSiS and ZrSiSe, which are consistent with the nontrivial topology of the Dirac line-node, as determined by a measured π Berry phase. Surprisingly, we find that, despite the three dimensional nature of both the Fermi surfaces of ZrSiS and ZrSiSe, both the resistivity anisotropy under applied magnetic fields and the in-plane angular dependent magnetoresistance differ considerably between the two compounds. Finally, we discuss the role microstructuring can play in the study of these materials and our ability to make these microstructures free-standing.
AU - Shirer, Kent R.
AU - Modic, Kimberly A
AU - Zimmerling, Tino
AU - Bachmann, Maja D.
AU - König, Markus
AU - Moll, Philip J. W.
AU - Schoop, Leslie
AU - Mackenzie, Andrew P.
ID - 7055
IS - 10
JF - APL Materials
SN - 2166-532X
TI - Out-of-plane transport in ZrSiS and ZrSiSe microstructures
VL - 7
ER -
TY - JOUR
AB - In the Ca1−x La x FeAs2 (1 1 2) family of pnictide superconductors, we have investigated a highly overdoped composition (x = 0.56), prepared by a high-pressure, high-temperature synthesis. Magnetic measurements show an antiferromagnetic transition at T N = 120 K, well above the one at lower doping (0.15 < x < 0.27).
Below the onset of long-range magnetic order at T N, the electrical resistivity is strongly reduced and is dominated by electron–electron interactions, as evident from its temperature dependence. The Seebeck coefficient shows a clear metallic behavior as in narrow band conductors. The temperature dependence of the Hall coefficient and the violation of Kohler's rule agree with the multiband character of the material. No superconductivity was observed down to 1.8 K. The success of the high-pressure synthesis encourages further investigations of the so far only partially explored phase diagram in this family of Iron-based high temperature superconductors.
AU - Martino, Edoardo
AU - Bachmann, Maja D
AU - Rossi, Lidia
AU - Modic, Kimberly A
AU - Zivkovic, Ivica
AU - Rønnow, Henrik M
AU - Moll, Philip J W
AU - Akrap, Ana
AU - Forró, László
AU - Katrych, Sergiy
ID - 7056
IS - 48
JF - Journal of Physics: Condensed Matter
SN - 0953-8984
TI - Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2
VL - 31
ER -
TY - JOUR
AB - We present a high magnetic field study of NbP—a member of the monopnictide Weyl semimetal (WSM) family. While the monoarsenides (NbAs and TaAs) have topologically distinct left and right-handed Weyl fermi surfaces, NbP is argued to be “topologically trivial” due to the fact that all pairs of Weyl nodes are encompassed by a single Fermi surface. We use torque magnetometry to measure the magnetic response of NbP up to 60 tesla and uncover a Berry paramagnetic response, characteristic of the topological Weyl nodes, across the entire field range. At the quantum limit B* (≈32 T), τ/B experiences a change in slope when the chemical potential enters the last Landau level. Our calculations confirm that this magnetic response arises from band topology of the Weyl pocket, even though the Fermi surface encompasses both Weyl nodes at zero magnetic field. We also find that the magnetic field pulls the chemical potential to the chiral n = 0 Landau level in the quantum limit, providing a disorder-free way of accessing chiral Weyl fermions in systems that are “not quite” WSMs in zero magnetic field.
AU - Modic, Kimberly A
AU - Meng, Tobias
AU - Ronning, Filip
AU - Bauer, Eric D.
AU - Moll, Philip J. W.
AU - Ramshaw, B. J.
ID - 7057
IS - 1
JF - Scientific Reports
SN - 2045-2322
TI - Thermodynamic signatures of Weyl fermions in NbP
VL - 9
ER -
TY - JOUR
AB - Although crystals of strongly correlated metals exhibit a diverse set of electronic ground states, few approaches exist for spatially modulating their properties. In this study, we demonstrate disorder-free control, on the micrometer scale, over the superconducting state in samples of the heavy-fermion superconductor CeIrIn5. We pattern crystals by focused ion beam milling to tailor the boundary conditions for the elastic deformation upon thermal contraction during cooling. The resulting nonuniform strain fields induce complex patterns of superconductivity, owing to the strong dependence of the transition temperature on the strength and direction of strain. These results showcase a generic approach to manipulating electronic order on micrometer length scales in strongly correlated matter without compromising the cleanliness, stoichiometry, or mean free path.
AU - Bachmann, Maja D.
AU - Ferguson, G. M.
AU - Theuss, Florian
AU - Meng, Tobias
AU - Putzke, Carsten
AU - Helm, Toni
AU - Shirer, K. R.
AU - Li, You-Sheng
AU - Modic, Kimberly A
AU - Nicklas, Michael
AU - König, Markus
AU - Low, D.
AU - Ghosh, Sayak
AU - Mackenzie, Andrew P.
AU - Arnold, Frank
AU - Hassinger, Elena
AU - McDonald, Ross D.
AU - Winter, Laurel E.
AU - Bauer, Eric D.
AU - Ronning, Filip
AU - Ramshaw, B. J.
AU - Nowack, Katja C.
AU - Moll, Philip J. W.
ID - 7082
IS - 6462
JF - Science
SN - 0036-8075
TI - Spatial control of heavy-fermion superconductivity in CeIrIn5
VL - 366
ER -
TY - JOUR
AB - In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how "simple" or "thin" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth.
In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs).
We derive these results from work of Agol, of Scharlemann and Thompson, and of Scharlemann, Schultens and Saito by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 18(k+1) (resp. 4(3k+1)).
AU - Huszár, Kristóf
AU - Spreer, Jonathan
AU - Wagner, Uli
ID - 7093
IS - 2
JF - Journal of Computational Geometry
SN - 1920-180X
TI - On the treewidth of triangulated 3-manifolds
VL - 10
ER -
TY - JOUR
AB - BAX, a member of the BCL2 gene family, controls the committed step of the intrinsic apoptotic program. Mitochondrial fragmentation is a commonly observed feature of apoptosis, which occurs through the process of mitochondrial fission. BAX has consistently been associated with mitochondrial fission, yet how BAX participates in the process of mitochondrial fragmentation during apoptosis remains to be tested. Time-lapse imaging of BAX recruitment and mitochondrial fragmentation demonstrates that rapid mitochondrial fragmentation during apoptosis occurs after the complete recruitment of BAX to the mitochondrial outer membrane (MOM). The requirement of a fully functioning BAX protein for the fission process was demonstrated further in BAX/BAK-deficient HCT116 cells expressing a P168A mutant of BAX. The mutant performed fusion to restore the mitochondrial network. but was not demonstrably recruited to the MOM after apoptosis induction. Under these conditions, mitochondrial fragmentation was blocked. Additionally, we show that loss of the fission protein, dynamin-like protein 1 (DRP1), does not temporally affect the initiation time or rate of BAX recruitment, but does reduce the final level of BAX recruited to the MOM during the late phase of BAX recruitment. These correlative observations suggest a model where late-stage BAX oligomers play a functional part of the mitochondrial fragmentation machinery in apoptotic cells.
AU - Maes, Margaret E
AU - Grosser, J. A.
AU - Fehrman, R. L.
AU - Schlamp, C. L.
AU - Nickells, R. W.
ID - 7095
JF - Scientific Reports
TI - Completion of BAX recruitment correlates with mitochondrial fission during apoptosis
VL - 9
ER -
TY - JOUR
AB - Early endosomes, also called sorting endosomes, are known to mature into late endosomesvia the Rab5-mediated endolysosomal trafficking pathway. Thus, early endosome existence isthought to be maintained by the continual fusion of transport vesicles from the plasmamembrane and thetrans-Golgi network (TGN). Here we show instead that endocytosis isdispensable and post-Golgi vesicle transport is crucial for the formation of endosomes andthe subsequent endolysosomal traffic regulated by yeast Rab5 Vps21p. Fittingly, all threeproteins required for endosomal nucleotide exchange on Vps21p arefirst recruited to theTGN before transport to the endosome, namely the GEF Vps9p and the epsin-relatedadaptors Ent3/5p. The TGN recruitment of these components is distinctly controlled, withVps9p appearing to require the Arf1p GTPase, and the Rab11s, Ypt31p/32p. These resultsprovide a different view of endosome formation and identify the TGN as a critical location forregulating progress through the endolysosomal trafficking pathway.
AU - Nagano, Makoto
AU - Toshima, Junko Y.
AU - Siekhaus, Daria E
AU - Toshima, Jiro
ID - 7097
IS - 1
JF - Communications Biology
SN - 2399-3642
TI - Rab5-mediated endosome formation is regulated at the trans-Golgi network
VL - 2
ER -
TY - JOUR
AU - Kasugai, Yu
AU - Vogel, Elisabeth
AU - Hörtnagl, Heide
AU - Schönherr, Sabine
AU - Paradiso, Enrica
AU - Hauschild, Markus
AU - Göbel, Georg
AU - Milenkovic, Ivan
AU - Peterschmitt, Yvan
AU - Tasan, Ramon
AU - Sperk, Günther
AU - Shigemoto, Ryuichi
AU - Sieghart, Werner
AU - Singewald, Nicolas
AU - Lüthi, Andreas
AU - Ferraguti, Francesco
ID - 7099
IS - 4
JF - Neuron
SN - 0896-6273
TI - Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning
VL - 104
ER -
TY - JOUR
AB - We present microscopic derivations of the defocusing two-dimensional cubic nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman interacting N-particle system of bosons. We consider the interaction potential to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx), for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R). In both cases we prove the convergence of the reduced density corresponding to the exact time evolution to the projector onto the solution of the corresponding nonlinear Schrödinger equation in trace norm. For the latter potential VN we show that it is crucial to take the microscopic structure of the condensate into account in order to obtain the correct dynamics.
AU - Jeblick, Maximilian
AU - Leopold, Nikolai K
AU - Pickl, Peter
ID - 7100
IS - 1
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - Derivation of the time dependent Gross–Pitaevskii equation in two dimensions
VL - 372
ER -
TY - JOUR
AB - Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics.
AU - Wang, Jilin W. J. L.
AU - Lombardi, Fabrizio
AU - Zhang, Xiyun
AU - Anaclet, Christelle
AU - Ivanov, Plamen Ch.
ID - 7103
IS - 11
JF - PLOS Computational Biology
SN - 1553-7358
TI - Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture
VL - 15
ER -
TY - JOUR
AB - Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence.
AU - Yolland, Lawrence
AU - Burki, Mubarik
AU - Marcotti, Stefania
AU - Luchici, Andrei
AU - Kenny, Fiona N.
AU - Davis, John Robert
AU - Serna-Morales, Eduardo
AU - Müller, Jan
AU - Sixt, Michael K
AU - Davidson, Andrew
AU - Wood, Will
AU - Schumacher, Linus J.
AU - Endres, Robert G.
AU - Miodownik, Mark
AU - Stramer, Brian M.
ID - 7105
IS - 11
JF - Nature Cell Biology
SN - 1465-7392
TI - Persistent and polarized global actin flow is essential for directionality during cell migration
VL - 21
ER -
TY - JOUR
AB - PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes.
AU - Skokan, Roman
AU - Medvecká, Eva
AU - Viaene, Tom
AU - Vosolsobě, Stanislav
AU - Zwiewka, Marta
AU - Müller, Karel
AU - Skůpa, Petr
AU - Karady, Michal
AU - Zhang, Yuzhou
AU - Janacek, Dorina P.
AU - Hammes, Ulrich Z.
AU - Ljung, Karin
AU - Nodzyński, Tomasz
AU - Petrášek, Jan
AU - Friml, Jiří
ID - 7106
IS - 11
JF - Nature Plants
SN - 2055-0278
TI - PIN-driven auxin transport emerged early in streptophyte evolution
VL - 5
ER -
TY - JOUR
AB - We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable.
AU - Goaoc, Xavier
AU - Patak, Pavel
AU - Patakova, Zuzana
AU - Tancer, Martin
AU - Wagner, Uli
ID - 7108
IS - 3
JF - Journal of the ACM
SN - 0004-5411
TI - Shellability is NP-complete
VL - 66
ER -
TY - JOUR
AB - We show how to construct temporal testers for the logic MITL, a prominent linear-time logic for real-time systems. A temporal tester is a transducer that inputs a signal holding the Boolean value of atomic propositions and outputs the truth value of a formula along time. Here we consider testers over continuous-time Boolean signals that use clock variables to enforce duration constraints, as in timed automata. We first rewrite the MITL formula into a “simple” formula using a limited set of temporal modalities. We then build testers for these specific modalities and show how to compose testers for simple formulae into complex ones. Temporal testers can be turned into acceptors, yielding a compositional translation from MITL to timed automata. This construction is much simpler than previously known and remains asymptotically optimal. It supports both past and future operators and can easily be extended.
AU - Ferrere, Thomas
AU - Maler, Oded
AU - Ničković, Dejan
AU - Pnueli, Amir
ID - 7109
IS - 3
JF - Journal of the ACM
SN - 0004-5411
TI - From real-time logic to timed automata
VL - 66
ER -
TY - JOUR
AB - We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models.
AU - Hafner, Christian
AU - Schumacher, Christian
AU - Knoop, Espen
AU - Auzinger, Thomas
AU - Bickel, Bernd
AU - Bächer, Moritz
ID - 7117
IS - 6
JF - ACM Transactions on Graphics
SN - 0730-0301
TI - X-CAD: Optimizing CAD Models with Extended Finite Elements
VL - 38
ER -
TY - CONF
AB - Data-rich applications in machine-learning and control have motivated an intense research on large-scale optimization. Novel algorithms have been proposed and shown to have optimal convergence rates in terms of iteration counts. However, their practical performance is severely degraded by the cost of exchanging high-dimensional gradient vectors between computing nodes. Several gradient compression heuristics have recently been proposed to reduce communications, but few theoretical results exist that quantify how they impact algorithm convergence. This paper establishes and strengthens the convergence guarantees for gradient descent under a family of gradient compression techniques. For convex optimization problems, we derive admissible step sizes and quantify both the number of iterations and the number of bits that need to be exchanged to reach a target accuracy. Finally, we validate the performance of different gradient compression techniques in simulations. The numerical results highlight the properties of different gradient compression algorithms and confirm that fast convergence with limited information exchange is possible.
AU - Khirirat, Sarit
AU - Johansson, Mikael
AU - Alistarh, Dan-Adrian
ID - 7122
SN - 0743-1546
T2 - 2018 IEEE Conference on Decision and Control
TI - Gradient compression for communication-limited convex optimization
ER -
TY - JOUR
AB - Loss of functional cardiomyocytes is a major determinant of heart failure after myocardial infarction. Previous high throughput screening studies have identified a few microRNAs (miRNAs) that can induce cardiomyocyte proliferation and stimulate cardiac regeneration in mice. Here, we show that all of the most effective of these miRNAs activate nuclear localization of the master transcriptional cofactor Yes-associated protein (YAP) and induce expression of YAP-responsive genes. In particular, miR-199a-3p directly targets two mRNAs coding for proteins impinging on the Hippo pathway, the upstream YAP inhibitory kinase TAOK1, and the E3 ubiquitin ligase β-TrCP, which leads to YAP degradation. Several of the pro-proliferative miRNAs (including miR-199a-3p) also inhibit filamentous actin depolymerization by targeting Cofilin2, a process that by itself activates YAP nuclear translocation. Thus, activation of YAP and modulation of the actin cytoskeleton are major components of the pro-proliferative action of miR-199a-3p and other miRNAs that induce cardiomyocyte proliferation.
AU - Torrini, Consuelo
AU - Cubero, Ryan J
AU - Dirkx, Ellen
AU - Braga, Luca
AU - Ali, Hashim
AU - Prosdocimo, Giulia
AU - Gutierrez, Maria Ines
AU - Collesi, Chiara
AU - Licastro, Danilo
AU - Zentilin, Lorena
AU - Mano, Miguel
AU - Zacchigna, Serena
AU - Vendruscolo, Michele
AU - Marsili, Matteo
AU - Samal, Areejit
AU - Giacca, Mauro
ID - 7128
IS - 9
JF - Cell Reports
KW - cardiomyocyte
KW - cell cycle
KW - Cofilin2
KW - cytoskeleton
KW - Hippo
KW - microRNA
KW - regeneration
KW - YAP
SN - 2211-1247
TI - Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation
VL - 27
ER -
TY - JOUR
AB - We show that statistical criticality, i.e. the occurrence of power law frequency distributions, arises in samples that are maximally informative about the underlying generating process. In order to reach this conclusion, we first identify the frequency with which different outcomes occur in a sample, as the variable carrying useful information on the generative process. The entropy of the frequency, that we call relevance, provides an upper bound to the number of informative bits. This differs from the entropy of the data, that we take as a measure of resolution. Samples that maximise relevance at a given resolution—that we call maximally informative samples—exhibit statistical criticality. In particular, Zipf's law arises at the optimal trade-off between resolution (i.e. compression) and relevance. As a byproduct, we derive a bound of the maximal number of parameters that can be estimated from a dataset, in the absence of prior knowledge on the generative model.
Furthermore, we relate criticality to the statistical properties of the representation of the data generating process. We show that, as a consequence of the concentration property of the asymptotic equipartition property, representations that are maximally informative about the data generating process are characterised by an exponential distribution of energy levels. This arises from a principle of minimal entropy, that is conjugate of the maximum entropy principle in statistical mechanics. This explains why statistical criticality requires no parameter fine tuning in maximally informative samples.
AU - Cubero, Ryan J
AU - Jo, Junghyo
AU - Marsili, Matteo
AU - Roudi, Yasser
AU - Song, Juyong
ID - 7130
IS - 6
JF - Journal of Statistical Mechanics: Theory and Experiment
KW - optimization under uncertainty
KW - source coding
KW - large deviation
SN - 1742-5468
TI - Statistical criticality arises in most informative representations
VL - 2019
ER -
TY - CONF
AB - It is well established that the notion of min-entropy fails to satisfy the \emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy. Such a property would help to analyze how min-entropy is split among smaller blocks. Problems of this kind arise for example when constructing extractors and dispersers.
We show that any sequence of variables exhibits a very strong strong block-source structure (conditional distributions of blocks are nearly flat) when we \emph{spoil few correlated bits}. This implies, conditioned on the spoiled bits, that \emph{splitting-recombination properties} hold. In particular, we have many nice properties that min-entropy doesn't obey in general, for example strong chain rules, "information can't hurt" inequalities, equivalences of average and worst-case conditional entropy definitions and others. Quantitatively, for any sequence X1,…,Xt of random variables over an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt) bits of auxiliary information, all conditional distributions of the form Xi|X*= m >= 3, we prove that g_0(K_{m,n})/g(K_{m,n})=1-O(1/n). Similar results are proved also for the Euler Z_2-genus. We express the Z_2-genus of a graph using the minimum rank of partial symmetric matrices over Z_2; a problem that might be of independent interest.
AU - Fulek, Radoslav
AU - Kyncl, Jan
ID - 7401
SN - 1868-8969
T2 - 35th International Symposium on Computational Geometry (SoCG 2019)
TI - Z_2-Genus of graphs and minimum rank of partial symmetric matrices
VL - 129
ER -
TY - JOUR
AB - The formation of neuronal dendrite branches is fundamental for the wiring and function of the nervous system. Indeed, dendrite branching enhances the coverage of the neuron's receptive field and modulates the initial processing of incoming stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process of de novo branch formation, branch extension and retraction. The first step towards branch formation is the generation of a dynamic filopodium-like branchlet. The mechanisms underlying the initiation of dendrite branchlets are therefore crucial to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular localization of actin during the process of branching of Drosophila larva sensory neurons, combined with genetic analysis and electron tomography, we have identified the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved in the initiation of dendrite branchlet formation, under the control of the activator WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component marks the site of branchlet initiation in vivo. These data position the activation of Arp2/3 as an early hub for the initiation of branchlet formation.
AU - Stürner, Tomke
AU - Tatarnikova, Anastasia
AU - Müller, Jan
AU - Schaffran, Barbara
AU - Cuntz, Hermann
AU - Zhang, Yun
AU - Nemethova, Maria
AU - Bogdan, Sven
AU - Small, Vic
AU - Tavosanis, Gaia
ID - 7404
IS - 7
JF - Development
SN - 0950-1991
TI - Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo
VL - 146
ER -
TY - JOUR
AB - Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, for example connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis – connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena.
AU - Dura-Bernal, Salvador
AU - Suter, Benjamin
AU - Gleeson, Padraig
AU - Cantarelli, Matteo
AU - Quintana, Adrian
AU - Rodriguez, Facundo
AU - Kedziora, David J
AU - Chadderdon, George L
AU - Kerr, Cliff C
AU - Neymotin, Samuel A
AU - McDougal, Robert A
AU - Hines, Michael
AU - Shepherd, Gordon MG
AU - Lytton, William W
ID - 7405
JF - eLife
SN - 2050-084X
TI - NetPyNE, a tool for data-driven multiscale modeling of brain circuits
VL - 8
ER -
TY - JOUR
AB - Background
Synaptic vesicles (SVs) are an integral part of the neurotransmission machinery, and isolation of SVs from their host neuron is necessary to reveal their most fundamental biochemical and functional properties in in vitro assays. Isolated SVs from neurons that have been genetically engineered, e.g. to introduce genetically encoded indicators, are not readily available but would permit new insights into SV structure and function. Furthermore, it is unclear if cultured neurons can provide sufficient starting material for SV isolation procedures.
New method
Here, we demonstrate an efficient ex vivo procedure to obtain functional SVs from cultured rat cortical neurons after genetic engineering with a lentivirus.
Results
We show that ∼108 plated cortical neurons allow isolation of suitable SV amounts for functional analysis and imaging. We found that SVs isolated from cultured neurons have neurotransmitter uptake comparable to that of SVs isolated from intact cortex. Using total internal reflection fluorescence (TIRF) microscopy, we visualized an exogenous SV-targeted marker protein and demonstrated the high efficiency of SV modification.
Comparison with existing methods
Obtaining SVs from genetically engineered neurons currently generally requires the availability of transgenic animals, which is constrained by technical (e.g. cost and time) and biological (e.g. developmental defects and lethality) limitations.
Conclusions
These results demonstrate the modification and isolation of functional SVs using cultured neurons and viral transduction. The ability to readily obtain SVs from genetically engineered neurons will permit linking in situ studies to in vitro experiments in a variety of genetic contexts.
AU - Mckenzie, Catherine
AU - Spanova, Miroslava
AU - Johnson, Alexander J
AU - Kainrath, Stephanie
AU - Zheden, Vanessa
AU - Sitte, Harald H.
AU - Janovjak, Harald L
ID - 7406
JF - Journal of Neuroscience Methods
SN - 0165-0270
TI - Isolation of synaptic vesicles from genetically engineered cultured neurons
VL - 312
ER -
TY - CHAP
AB - Epiboly is a conserved gastrulation movement describing the thinning and spreading of a sheet or multi-layer of cells. The zebrafish embryo has emerged as a vital model system to address the cellular and molecular mechanisms that drive epiboly. In the zebrafish embryo, the blastoderm, consisting of a simple squamous epithelium (the enveloping layer) and an underlying mass of deep cells, as well as a yolk nuclear syncytium (the yolk syncytial layer) undergo epiboly to internalize the yolk cell during gastrulation. The major events during zebrafish epiboly are: expansion of the enveloping layer and the internal yolk syncytial layer, reduction and removal of the yolk membrane ahead of the advancing blastoderm margin and deep cell rearrangements between the enveloping layer and yolk syncytial layer to thin the blastoderm. Here, work addressing the cellular and molecular mechanisms as well as the sources of the mechanical forces that underlie these events is reviewed. The contribution of recent findings to the current model of epiboly as well as open questions and future prospects are also discussed.
AU - Bruce, Ashley E.E.
AU - Heisenberg, Carl-Philipp J
ED - Solnica-Krezel, Lilianna
ID - 7410
SN - 0070-2153
T2 - Gastrulation: From Embryonic Pattern to Form
TI - Mechanisms of zebrafish epiboly: A current view
VL - 136
ER -
TY - CONF
AB - Proofs of sequential work (PoSW) are proof systems where a prover, upon receiving a statement χ and a time parameter T computes a proof ϕ(χ,T) which is efficiently and publicly verifiable. The proof can be computed in T sequential steps, but not much less, even by a malicious party having large parallelism. A PoSW thus serves as a proof that T units of time have passed since χ
was received.
PoSW were introduced by Mahmoody, Moran and Vadhan [MMV11], a simple and practical construction was only recently proposed by Cohen and Pietrzak [CP18].
In this work we construct a new simple PoSW in the random permutation model which is almost as simple and efficient as [CP18] but conceptually very different. Whereas the structure underlying [CP18] is a hash tree, our construction is based on skip lists and has the interesting property that computing the PoSW is a reversible computation.
The fact that the construction is reversible can potentially be used for new applications like constructing proofs of replication. We also show how to “embed” the sloth function of Lenstra and Weselowski [LW17] into our PoSW to get a PoSW where one additionally can verify correctness of the output much more efficiently than recomputing it (though recent constructions of “verifiable delay functions” subsume most of the applications this construction was aiming at).
AU - Abusalah, Hamza M
AU - Kamath Hosdurg, Chethan
AU - Klein, Karen
AU - Pietrzak, Krzysztof Z
AU - Walter, Michael
ID - 7411
SN - 0302-9743
T2 - Advances in Cryptology – EUROCRYPT 2019
TI - Reversible proofs of sequential work
VL - 11477
ER -
TY - JOUR
AB - We develop a framework for the rigorous analysis of focused stochastic local search algorithms. These algorithms search a state space by repeatedly selecting some constraint that is violated in the current state and moving to a random nearby state that addresses the violation, while (we hope) not introducing many new violations. An important class of focused local search algorithms with provable performance guarantees has recently arisen from algorithmizations of the Lovász local lemma (LLL), a nonconstructive tool for proving the existence of satisfying states by introducing a background measure on the state space. While powerful, the state transitions of algorithms in this class must be, in a precise sense, perfectly compatible with the background measure. In many applications this is a very restrictive requirement, and one needs to step outside the class. Here we introduce the notion of measure distortion and develop a framework for analyzing arbitrary focused stochastic local search algorithms, recovering LLL algorithmizations as the special case of no distortion. Our framework takes as input an arbitrary algorithm of such type and an arbitrary probability measure and shows how to use the measure as a yardstick of algorithmic progress, even for algorithms designed independently of the measure.
AU - Achlioptas, Dimitris
AU - Iliopoulos, Fotis
AU - Kolmogorov, Vladimir
ID - 7412
IS - 5
JF - SIAM Journal on Computing
SN - 0097-5397
TI - A local lemma for focused stochastical algorithms
VL - 48
ER -
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