TY - JOUR
AB - This short note aims to study quantum Hellinger distances investigated recently by Bhatia et al. (Lett Math Phys 109:1777–1804, 2019) with a particular emphasis on barycenters. We introduce the family of generalized quantum Hellinger divergences that are of the form ϕ(A,B)=Tr((1−c)A+cB−AσB), where σ is an arbitrary Kubo–Ando mean, and c∈(0,1) is the weight of σ. We note that these divergences belong to the family of maximal quantum f-divergences, and hence are jointly convex, and satisfy the data processing inequality. We derive a characterization of the barycenter of finitely many positive definite operators for these generalized quantum Hellinger divergences. We note that the characterization of the barycenter as the weighted multivariate 1/2-power mean, that was claimed in Bhatia et al. (2019), is true in the case of commuting operators, but it is not correct in the general case.
AU - Pitrik, Jozsef
AU - Virosztek, Daniel
ID - 7618
IS - 8
JF - Letters in Mathematical Physics
SN - 0377-9017
TI - Quantum Hellinger distances revisited
VL - 110
ER -
TY - JOUR
AB - Cell polarity is a fundamental feature of all multicellular organisms. In plants, prominent cell polarity markers are PIN auxin transporters crucial for plant development. To identify novel components involved in cell polarity establishment and maintenance, we carried out a forward genetic screening with PIN2:PIN1-HA;pin2 Arabidopsis plants, which ectopically express predominantly basally localized PIN1 in the root epidermal cells leading to agravitropic root growth. From the screen, we identified the regulator of PIN polarity 12 (repp12) mutation, which restored gravitropic root growth and caused PIN1-HA polarity switch from basal to apical side of root epidermal cells. Complementation experiments established the repp12 causative mutation as an amino acid substitution in Aminophospholipid ATPase3 (ALA3), a phospholipid flippase with predicted function in vesicle formation. ala3 T-DNA mutants show defects in many auxin-regulated processes, in asymmetric auxin distribution and in PIN trafficking. Analysis of quintuple and sextuple mutants confirmed a crucial role of ALA proteins in regulating plant development and in PIN trafficking and polarity. Genetic and physical interaction studies revealed that ALA3 functions together with GNOM and BIG3 ARF GEFs. Taken together, our results identified ALA3 flippase as an important interactor and regulator of ARF GEF functioning in PIN polarity, trafficking and auxin-mediated development.
AU - Zhang, Xixi
AU - Adamowski, Maciek
AU - Marhavá, Petra
AU - Tan, Shutang
AU - Zhang, Yuzhou
AU - Rodriguez Solovey, Lesia
AU - Zwiewka, Marta
AU - Pukyšová, Vendula
AU - Sánchez, Adrià Sans
AU - Raxwal, Vivek Kumar
AU - Hardtke, Christian S.
AU - Nodzynski, Tomasz
AU - Friml, Jiří
ID - 7619
IS - 5
JF - The Plant Cell
SN - 1040-4651
TI - Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters
VL - 32
ER -
TY - JOUR
AB - The International Young Physicists' Tournament (IYPT) continued in 2018 in Beijing, China and 2019 in Warsaw, Poland with its 31st and 32nd editions. The IYPT is a modern scientific competition for teams of high school students, also known as the Physics World Cup. It involves long-term theoretical and experimental work focused on solving 17 publicly announced open-ended problems in teams of five. On top of that, teams have to present their solutions in front of other teams and a scientific jury, and get opposed and reviewed by their peers. Here we present a brief information about the competition with a specific focus on one of the IYPT 2018 tasks, the 'Ring Oiler'. This seemingly simple mechanical problem appeared to be of such a complexity that even the dozens of participating teams and jurying scientists were not able to solve all of its subtleties.
AU - Plesch, Martin
AU - Plesník, Samuel
AU - Ruzickova, Natalia
ID - 7622
IS - 3
JF - European Journal of Physics
SN - 01430807
TI - The IYPT and the 'Ring Oiler' problem
VL - 41
ER -
TY - THES
AB - This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck
equation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.
The second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.
In the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of
corresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals.
AU - Forkert, Dominik L
ID - 7629
SN - 2663-337X
TI - Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains
ER -
TY - JOUR
AB - The posterior parietal cortex (PPC) and frontal motor areas comprise a cortical network supporting goal-directed behaviour, with functions including sensorimotor transformations and decision making. In primates, this network links performed and observed actions via mirror neurons, which fire both when individuals perform an action and when they observe the same action performed by a conspecific. Mirror neurons are believed to be important for social learning, but it is not known whether mirror-like neurons occur in similar networks in other social species, such as rodents, or if they can be measured in such models using paradigms where observers passively view a demonstrator. Therefore, we imaged Ca2+ responses in PPC and secondary motor cortex (M2) while mice performed and observed pellet-reaching and wheel-running tasks, and found that cell populations in both areas robustly encoded several naturalistic behaviours. However, neural responses to the same set of observed actions were absent, although we verified that observer mice were attentive to performers and that PPC neurons responded reliably to visual cues. Statistical modelling also indicated that executed actions outperformed observed actions in predicting neural responses. These results raise the possibility that sensorimotor action recognition in rodents could take place outside of the parieto-frontal circuit, and underscore that detecting socially-driven neural coding depends critically on the species and behavioural paradigm used.
AU - Tombaz, Tuce
AU - Dunn, Benjamin A.
AU - Hovde, Karoline
AU - Cubero, Ryan J
AU - Mimica, Bartul
AU - Mamidanna, Pranav
AU - Roudi, Yasser
AU - Whitlock, Jonathan R.
ID - 7632
IS - 1
JF - Scientific reports
TI - Action representation in the mouse parieto-frontal network
VL - 10
ER -
TY - JOUR
AB - The evolution of finitely many particles obeying Langevin dynamics is described by Dean–Kawasaki equations, a class of stochastic equations featuring a non-Lipschitz multiplicative noise in divergence form. We derive a regularised Dean–Kawasaki model based on second order Langevin dynamics by analysing a system of particles interacting via a pairwise potential. Key tools of our analysis are the propagation of chaos and Simon's compactness criterion. The model we obtain is a small-noise stochastic perturbation of the undamped McKean–Vlasov equation. We also provide a high-probability result for existence and uniqueness for our model.
AU - Cornalba, Federico
AU - Shardlow, Tony
AU - Zimmer, Johannes
ID - 7637
IS - 2
JF - Nonlinearity
SN - 09517715
TI - From weakly interacting particles to a regularised Dean-Kawasaki model
VL - 33
ER -
TY - JOUR
AB - Following on from our recent work, we investigate a stochastic approach to non-equilibrium quantum spin systems. We show how the method can be applied to a variety of physical observables and for different initial conditions. We provide exact formulae of broad applicability for the time-dependence of expectation values and correlation functions following a quantum quench in terms of averages over classical stochastic processes. We further explore the behavior of the classical stochastic variables in the presence of dynamical quantum phase transitions, including results for their distributions and correlation functions. We provide details on the numerical solution of the associated stochastic differential equations, and examine the growth of fluctuations in the classical description. We discuss the strengths and limitations of the current implementation of the stochastic approach and the potential for further development.
AU - De Nicola, Stefano
AU - Doyon, B.
AU - Bhaseen, M. J.
ID - 7638
IS - 1
JF - Journal of Statistical Mechanics: Theory and Experiment
TI - Non-equilibrium quantum spin dynamics from classical stochastic processes
VL - 2020
ER -
TY - JOUR
AB - 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.
AU - Larsson, J.
AU - Westram, Anja M
AU - Bengmark, S.
AU - Lundh, T.
AU - Butlin, R. K.
ID - 7651
IS - 163
JF - Journal of The Royal Society Interface
SN - 1742-5689
TI - A developmentally descriptive method for quantifying shape in gastropod shells
VL - 17
ER -
TY - JOUR
AB - We propose that correlations among neurons are generically strong enough to organize neural activity patterns into a discrete set of clusters, which can each be viewed as a population codeword. Our reasoning starts with the analysis of retinal ganglion cell data using maximum entropy models, showing that the population is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads to an argument that neural populations in many other brain areas might share this structure. Next, we use latent variable models to show that this glassy state possesses well-defined clusters of neural activity. Clusters have three appealing properties: (i) clusters exhibit error correction, i.e., they are reproducibly elicited by the same stimulus despite variability at the level of constituent neurons; (ii) clusters encode qualitatively different visual features than their constituent neurons; and (iii) clusters can be learned by downstream neural circuits in an unsupervised fashion. We hypothesize that these properties give rise to a “learnable” neural code which the cortical hierarchy uses to extract increasingly complex features without supervision or reinforcement.
AU - Berry, Michael J.
AU - Tkačik, Gašper
ID - 7656
JF - Frontiers in Computational Neuroscience
TI - Clustering of neural activity: A design principle for population codes
VL - 14
ER -
TY - JOUR
AB - Wood, as the most abundant carbon dioxide storing bioresource, is currently driven beyond its traditional use through creative innovations and nanotechnology. For many properties the micro- and nanostructure plays a crucial role and one key challenge is control and detection of chemical and physical processes in the confined microstructure and nanopores of the wooden cell wall. In this study, correlative Raman and atomic force microscopy show high potential for tracking in situ molecular rearrangement of wood polymers during compression. More water molecules (interpreted as wider cellulose microfibril distances) and disentangling of hemicellulose chains are detected in the opened cell wall regions, whereas an increase of lignin is revealed in the compressed areas. These results support a new more “loose” cell wall model based on flexible lignin nanodomains and advance our knowledge of the molecular reorganization during deformation of wood for optimized processing and utilization.
AU - Felhofer, Martin
AU - Bock, Peter
AU - Singh, Adya
AU - Prats Mateu, Batirtze
AU - Zirbs, Ronald
AU - Gierlinger, Notburga
ID - 7663
IS - 4
JF - Nano letters
TI - Wood deformation leads to rearrangement of molecules at the nanoscale
VL - 20
ER -
TY - JOUR
AB - Metabotropic γ-aminobutyric acid (GABAB) receptors contribute to the control of network activity and information processing in hippocampal circuits by regulating neuronal excitability and synaptic transmission. The dysfunction in the dentate gyrus (DG) has been implicated in Alzheimer´s disease (AD). Given the involvement of GABAB receptors in AD, to determine their subcellular localisation and possible alteration in granule cells of the DG in a mouse model of AD at 12 months of age, we used high-resolution immunoelectron microscopic analysis. Immunohistochemistry at the light microscopic level showed that the regional and cellular expression pattern of GABAB1 was similar in an AD model mouse expressing mutated human amyloid precursor protein and presenilin1 (APP/PS1) and in age-matched wild type mice. High-resolution immunoelectron microscopy revealed a distance-dependent gradient of immunolabelling for GABAB receptors, increasing from proximal to distal dendrites in both wild type and APP/PS1 mice. However, the overall density of GABAB receptors at the neuronal surface of these postsynaptic compartments of granule cells was significantly reduced in APP/PS1 mice. Parallel to this reduction in surface receptors, we found a significant increase in GABAB1 at cytoplasmic sites. GABAB receptors were also detected at presynaptic sites in the molecular layer of the DG. We also found a decrease in plasma membrane GABAB receptors in axon terminals contacting dendritic spines of granule cells, which was more pronounced in the outer than in the inner molecular layer. Altogether, our data showing post- and presynaptic reduction in surface GABAB receptors in the DG suggest the alteration of the GABAB-mediated modulation of excitability and synaptic transmission in granule cells, which may contribute to the cognitive dysfunctions in the APP/PS1 model of AD
AU - Martín-Belmonte, Alejandro
AU - Aguado, Carolina
AU - Alfaro-Ruíz, Rocío
AU - Moreno-Martínez, Ana Esther
AU - De La Ossa, Luis
AU - Martínez-Hernández, José
AU - Buisson, Alain
AU - Shigemoto, Ryuichi
AU - Fukazawa, Yugo
AU - Luján, Rafael
ID - 7664
IS - 7
JF - International journal of molecular sciences
TI - Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer's disease
VL - 21
ER -
TY - JOUR
AB - Acute brain slice preparation is a powerful experimental model for investigating the characteristics of synaptic function in the brain. Although brain tissue is usually cut at ice-cold temperature (CT) to facilitate slicing and avoid neuronal damage, exposure to CT causes molecular and architectural changes of synapses. To address these issues, we investigated ultrastructural and electrophysiological features of synapses in mouse acute cerebellar slices prepared at ice-cold and physiological temperature (PT). In the slices prepared at CT, we found significant spine loss and reconstruction, synaptic vesicle rearrangement and decrease in synaptic proteins, all of which were not detected in slices prepared at PT. Consistent with these structural findings, slices prepared at PT showed higher release probability. Furthermore, preparation at PT allows electrophysiological recording immediately after slicing resulting in higher detectability of long-term depression (LTD) after motor learning compared with that at CT. These results indicate substantial advantages of the slice preparation at PT for investigating synaptic functions in different physiological conditions.
AU - Eguchi, Kohgaku
AU - Velicky, Philipp
AU - Hollergschwandtner, Elena
AU - Itakura, Makoto
AU - Fukazawa, Yugo
AU - Danzl, Johann G
AU - Shigemoto, Ryuichi
ID - 7665
JF - Frontiers in Cellular Neuroscience
SN - 16625102
TI - Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions
VL - 14
ER -
TY - JOUR
AB - For any free oriented Borel–Moore homology theory A, we construct an associative product on the A-theory of the stack of Higgs torsion sheaves over a projective curve C. We show that the resulting algebra AHa0C admits a natural shuffle presentation, and prove it is faithful when A is replaced with usual Borel–Moore homology groups. We also introduce moduli spaces of stable triples, heavily inspired by Nakajima quiver varieties, whose A-theory admits an AHa0C-action. These triples can be interpreted as certain sheaves on PC(ωC⊕OC). In particular, we obtain an action of AHa0C on the cohomology of Hilbert schemes of points on T∗C.
AU - Minets, Sasha
ID - 7683
IS - 2
JF - Selecta Mathematica, New Series
SN - 10221824
TI - Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces
VL - 26
ER -
TY - JOUR
AB - We consider a gas of interacting bosons trapped in a box of side length one in the Gross–Pitaevskii limit. We review the proof of the validity of Bogoliubov’s prediction for the ground state energy and the low-energy excitation spectrum. This note is based on joint work with C. Brennecke, S. Cenatiempo and B. Schlein.
AU - Boccato, Chiara
ID - 7685
JF - Reviews in Mathematical Physics
SN - 0129055X
TI - The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime
ER -
TY - DATA
AB - These are the supplementary research data to the publication "Zero field splitting of heavy-hole states in quantum dots". All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file.
AU - Katsaros, Georgios
ID - 7689
TI - Supplementary data for "Zero field splitting of heavy-hole states in quantum dots"
ER -
TY - JOUR
AB - The growing sample size of genome-wide association studies has facilitated the discovery of gene-environment interactions (GxE). Here we propose a maximum likelihood method to estimate the contribution of GxE to continuous traits taking into account all interacting environmental variables, without the need to measure any. Extensive simulations demonstrate that our method provides unbiased interaction estimates and excellent coverage. We also offer strategies to distinguish specific GxE from general scale effects. Applying our method to 32 traits in the UK Biobank reveals that while the genetic risk score (GRS) of 376 variants explains 5.2% of body mass index (BMI) variance, GRSxE explains an additional 1.9%. Nevertheless, this interaction holds for any variable with identical correlation to BMI as the GRS, hence may not be GRS-specific. Still, we observe that the global contribution of specific GRSxE to complex traits is substantial for nine obesity-related measures (including leg impedance and trunk fat-free mass).
AU - Sulc, Jonathan
AU - Mounier, Ninon
AU - Günther, Felix
AU - Winkler, Thomas
AU - Wood, Andrew R.
AU - Frayling, Timothy M.
AU - Heid, Iris M.
AU - Robinson, Matthew Richard
AU - Kutalik, Zoltán
ID - 7707
JF - Nature Communications
SN - 2041-1723
TI - Quantification of the overall contribution of gene-environment interaction for obesity-related traits
VL - 11
ER -
TY - JOUR
AB - We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor.
AU - Nabais, Marta F.
AU - Lin, Tian
AU - Benyamin, Beben
AU - Williams, Kelly L.
AU - Garton, Fleur C.
AU - Vinkhuyzen, Anna A. E.
AU - Zhang, Futao
AU - Vallerga, Costanza L.
AU - Restuadi, Restuadi
AU - Freydenzon, Anna
AU - Zwamborn, Ramona A. J.
AU - Hop, Paul J.
AU - Robinson, Matthew Richard
AU - Gratten, Jacob
AU - Visscher, Peter M.
AU - Hannon, Eilis
AU - Mill, Jonathan
AU - Brown, Matthew A.
AU - Laing, Nigel G.
AU - Mather, Karen A.
AU - Sachdev, Perminder S.
AU - Ngo, Shyuan T.
AU - Steyn, Frederik J.
AU - Wallace, Leanne
AU - Henders, Anjali K.
AU - Needham, Merrilee
AU - Veldink, Jan H.
AU - Mathers, Susan
AU - Nicholson, Garth
AU - Rowe, Dominic B.
AU - Henderson, Robert D.
AU - McCombe, Pamela A.
AU - Pamphlett, Roger
AU - Yang, Jian
AU - Blair, Ian P.
AU - McRae, Allan F.
AU - Wray, Naomi R.
ID - 7708
JF - npj Genomic Medicine
SN - 2056-7944
TI - Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis
VL - 5
ER -
TY - GEN
AB - Recent advances in synthetic post-translational protein circuits are significantly impacting the landscape of biomimicry engineering. However, designing sustained dynamic phenomena in these circuits remains an outstanding challenge. Inspired by the KaiABC system regulating the circadian clock in cyanobacteria, we develop two experimentally realizable post-translational oscillators. The oscillators rely on a small number of components interacting only through reversible binding and phosphorylation/dephosphorylation reactions.
AU - Kimchi, Ofer
AU - Goodrich, Carl Peter
AU - Courbet, Alexis
AU - Curatolo, Agnese I.
AU - Woodall, Nicholas B.
AU - Baker, David
AU - Brenner, Michael P.
ID - 7778
T2 - bioRxiv
TI - Self-assembly based post-translational protein oscillators
ER -
TY - JOUR
AB - During embryonic and postnatal development, organs and tissues grow steadily to achieve their final size at the end of puberty. However, little is known about the cellular dynamics that mediate postnatal growth. By combining in vivo clonal lineage tracing, proliferation kinetics, single-cell transcriptomics, andin vitro micro-pattern experiments, we resolved the cellular dynamics taking place during postnatal skin epidermis expansion. Our data revealed that harmonious growth is engineered by a single population of developmental progenitors presenting a fixed fate imbalance of self-renewing divisions with an ever-decreasing proliferation rate. Single-cell RNA sequencing revealed that epidermal developmental progenitors form a more uniform population compared with adult stem and progenitor cells. Finally, we found that the spatial pattern of cell division orientation is dictated locally by the underlying collagen fiber orientation. Our results uncover a simple design principle of organ growth where progenitors and differentiated cells expand in harmony with their surrounding tissues.
AU - Dekoninck, Sophie
AU - Hannezo, Edouard B
AU - Sifrim, Alejandro
AU - Miroshnikova, Yekaterina A.
AU - Aragona, Mariaceleste
AU - Malfait, Milan
AU - Gargouri, Souhir
AU - De Neunheuser, Charlotte
AU - Dubois, Christine
AU - Voet, Thierry
AU - Wickström, Sara A.
AU - Simons, Benjamin D.
AU - Blanpain, Cédric
ID - 7789
IS - 3
JF - Cell
SN - 00928674
TI - Defining the design principles of skin epidermis postnatal growth
VL - 181
ER -
TY - JOUR
AB - We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density 𝜌 and inverse temperature 𝛽 differs from the one of the noninteracting system by the correction term 𝜋𝜌𝜌𝛽𝛽 . Here, is the scattering length of the interaction potential, and 𝛽 is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. The result is valid in the dilute limit 𝜌 and if 𝛽𝜌 .
AU - Deuchert, Andreas
AU - Mayer, Simon
AU - Seiringer, Robert
ID - 7790
JF - Forum of Mathematics, Sigma
TI - The free energy of the two-dimensional dilute Bose gas. I. Lower bound
VL - 8
ER -
TY - JOUR
AB - Hormonal signalling in animals often involves direct transcription factor-hormone interactions that modulate gene expression. In contrast, plant hormone signalling is most commonly based on de-repression via the degradation of transcriptional repressors. Recently, we uncovered a non-canonical signalling mechanism for the plant hormone auxin whereby auxin directly affects the activity of the atypical auxin response factor (ARF), ETTIN towards target genes without the requirement for protein degradation. Here we show that ETTIN directly binds auxin, leading to dissociation from co-repressor proteins of the TOPLESS/TOPLESS-RELATED family followed by histone acetylation and induction of gene expression. This mechanism is reminiscent of animal hormone signalling as it affects the activity towards regulation of target genes and provides the first example of a DNA-bound hormone receptor in plants. Whilst auxin affects canonical ARFs indirectly by facilitating degradation of Aux/IAA repressors, direct ETTIN-auxin interactions allow switching between repressive and de-repressive chromatin states in an instantly-reversible manner.
AU - Kuhn, André
AU - Ramans Harborough, Sigurd
AU - McLaughlin, Heather M
AU - Natarajan, Bhavani
AU - Verstraeten, Inge
AU - Friml, Jiří
AU - Kepinski, Stefan
AU - Østergaard, Lars
ID - 7793
JF - eLife
SN - 2050-084X
TI - Direct ETTIN-auxin interaction controls chromatin states in gynoecium development
VL - 9
ER -
TY - CONF
AB - The Massively Parallel Computation (MPC) model is an emerging model which distills core aspects of distributed and parallel computation. It has been developed as a tool to solve (typically graph) problems in systems where the input is distributed over many machines with limited space.
Recent work has focused on the regime in which machines have sublinear (in $n$, the number of nodes in the input graph) space, with randomized algorithms presented for fundamental graph problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms.
A major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all the edges incident to a single node. This poses a considerable obstacle compared to the classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph with additional desired properties. The degree of the nodes in this subgraph is small in the sense that the edges of each node can be now stored on a single machine. This low-degree subgraph also has the property that solving the problem on this subgraph provides \emph{significant} global progress, i.e., progress towards solving the problem for the original input graph.
Using this framework to derandomize the well-known randomized algorithm of Luby [SICOMP'86], we obtain $O(\log \Delta+\log\log n)$-round deterministic MPC algorithms for solving the fundamental problems of Maximal Matching and Maximal Independent Set with $O(n^{\epsilon})$ space on each machine for any constant $\epsilon > 0$. Based on the recent work of Ghaffari et al. [FOCS'18], this additive $O(\log\log n)$ factor is conditionally essential. These algorithms can also be shown to run in $O(\log \Delta)$ rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of $O(\log^2 \Delta)$ rounds by Censor-Hillel et al. [DISC'17].
AU - Czumaj, Artur
AU - Davies, Peter
AU - Parter, Merav
ID - 7802
IS - 7
T2 - Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020)
TI - Graph sparsification for derandomizing massively parallel computation with low space
ER -
TY - JOUR
AB - Besides pro-inflammatory roles, the ancient cytokine interleukin-17 (IL-17) modulates neural circuit function. We investigate IL-17 signaling in neurons, and the extent it can alter organismal phenotypes. We combine immunoprecipitation and mass spectrometry to biochemically characterize endogenous signaling complexes that function downstream of IL-17 receptors in C. elegans neurons. We identify the paracaspase MALT-1 as a critical output of the pathway. MALT1 mediates signaling from many immune receptors in mammals, but was not previously implicated in IL-17 signaling or nervous system function. C. elegans MALT-1 forms a complex with homologs of Act1 and IRAK and appears to function both as a scaffold and a protease. MALT-1 is expressed broadly in the C. elegans nervous system, and neuronal IL-17–MALT-1 signaling regulates multiple phenotypes, including escape behavior, associative learning, immunity and longevity. Our data suggest MALT1 has an ancient role modulating neural circuit function downstream of IL-17 to remodel physiology and behavior.
AU - Flynn, Sean M.
AU - Chen, Changchun
AU - Artan, Murat
AU - Barratt, Stephen
AU - Crisp, Alastair
AU - Nelson, Geoffrey M.
AU - Peak-Chew, Sew Yeu
AU - Begum, Farida
AU - Skehel, Mark
AU - De Bono, Mario
ID - 7804
JF - Nature Communications
TI - MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity
VL - 11
ER -
TY - CONF
AB - 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.
AU - Filakovský, Marek
AU - Wagner, Uli
AU - Zhechev, Stephan Y
ID - 7806
SN - 9781611975994
T2 - Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
TI - Embeddability of simplicial complexes is undecidable
VL - 2020-January
ER -
TY - CONF
AB - 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.
AU - Wagner, Uli
AU - Welzl, Emo
ID - 7807
SN - 9781611975994
T2 - Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms
TI - Connectivity of triangulation flip graphs in the plane (Part I: Edge flips)
VL - 2020-January
ER -
TY - CONF
AB - 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.
AU - Giacobbe, Mirco
AU - Henzinger, Thomas A
AU - Lechner, Mathias
ID - 7808
SN - 03029743
T2 - International Conference on Tools and Algorithms for the Construction and Analysis of Systems
TI - How many bits does it take to quantize your neural network?
VL - 12079
ER -
TY - CONF
AB - Interprocedural data-flow analyses form an expressive and useful paradigm of numerous static analysis applications, such as live variables analysis, alias analysis and null pointers analysis. The most widely-used framework for interprocedural data-flow analysis is IFDS, which encompasses distributive data-flow functions over a finite domain. On-demand data-flow analyses restrict the focus of the analysis on specific program locations and data facts. This setting provides a natural split between (i) an offline (or preprocessing) phase, where the program is partially analyzed and analysis summaries are created, and (ii) an online (or query) phase, where analysis queries arrive on demand and the summaries are used to speed up answering queries.
In this work, we consider on-demand IFDS analyses where the queries concern program locations of the same procedure (aka same-context queries). We exploit the fact that flow graphs of programs have low treewidth to develop faster algorithms that are space and time optimal for many common data-flow analyses, in both the preprocessing and the query phase. We also use treewidth to develop query solutions that are embarrassingly parallelizable, i.e. the total work for answering each query is split to a number of threads such that each thread performs only a constant amount of work. Finally, we implement a static analyzer based on our algorithms, and perform a series of on-demand analysis experiments on standard benchmarks. Our experimental results show a drastic speed-up of the queries after only a lightweight preprocessing phase, which significantly outperforms existing techniques.
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
AU - Ibsen-Jensen, Rasmus
AU - Pavlogiannis, Andreas
ID - 7810
SN - 03029743
T2 - European Symposium on Programming
TI - Optimal and perfectly parallel algorithms for on-demand data-flow analysis
VL - 12075
ER -
TY - JOUR
AB - 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.
AU - Beattie, Robert J
AU - Hippenmeyer, Simon
AU - Pauler, Florian
ID - 7814
JF - Frontiers in Education
SN - 2504-284X
TI - SCOPES: Sparking curiosity through Open-Source platforms in education and science
VL - 5
ER -
TY - JOUR
AB - Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present.
AU - Beattie, Robert J
AU - Streicher, Carmen
AU - Amberg, Nicole
AU - Cheung, Giselle T
AU - Contreras, Ximena
AU - Hansen, Andi H
AU - Hippenmeyer, Simon
ID - 7815
IS - 159
JF - Journal of Visual Experiments (JoVE)
SN - 1940-087X
TI - Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)
ER -
TY - JOUR
AB - 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.
AU - Fellner, Klemens
AU - Kniely, Michael
ID - 7866
JF - Journal of Elliptic and Parabolic Equations
SN - 22969020
TI - Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model
ER -
TY - JOUR
AB - The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations inNIPBLaccount for most cases ofthe rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report aMAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus.Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable fornormal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fataloutcome of an out-of-frame single nucleotide duplication inNIPBL, engineered in two different cell lines,alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interactwith MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protectiveagainst out-of-frame mutations that is potentially relevant for other genetic conditions.
AU - Parenti, Ilaria
AU - Diab, Farah
AU - Gil, Sara Ruiz
AU - Mulugeta, Eskeatnaf
AU - Casa, Valentina
AU - Berutti, Riccardo
AU - Brouwer, Rutger W.W.
AU - Dupé, Valerie
AU - Eckhold, Juliane
AU - Graf, Elisabeth
AU - Puisac, Beatriz
AU - Ramos, Feliciano
AU - Schwarzmayr, Thomas
AU - Gines, Macarena Moronta
AU - Van Staveren, Thomas
AU - Van Ijcken, Wilfred F.J.
AU - Strom, Tim M.
AU - Pié, Juan
AU - Watrin, Erwan
AU - Kaiser, Frank J.
AU - Wendt, Kerstin S.
ID - 7877
IS - 7
JF - Cell Reports
TI - MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome
VL - 31
ER -
TY - JOUR
AB - Type 1 metabotropic glutamate receptors (mGluR1s) are key elements in neuronal signaling. While their function is well documented in slices, requirements for their activation in vivo are poorly understood. We examine this question in adult mice in vivo using 2-photon imaging of cerebellar molecular layer interneurons (MLIs) expressing GCaMP. In anesthetized mice, parallel fiber activation evokes beam-like Cai rises in postsynaptic MLIs which depend on co-activation of mGluR1s and ionotropic glutamate receptors (iGluRs). In awake mice, blocking mGluR1 decreases Cai rises associated with locomotion. In vitro studies and freeze-fracture electron microscopy show that the iGluR-mGluR1 interaction is synergistic and favored by close association of the two classes of receptors. Altogether our results suggest that mGluR1s, acting in synergy with iGluRs, potently contribute to processing cerebellar neuronal signaling under physiological conditions.
AU - Bao, Jin
AU - Graupner, Michael
AU - Astorga, Guadalupe
AU - Collin, Thibault
AU - Jalil, Abdelali
AU - Indriati, Dwi Wahyu
AU - Bradley, Jonathan
AU - Shigemoto, Ryuichi
AU - Llano, Isabel
ID - 7878
JF - eLife
TI - Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo
VL - 9
ER -
TY - JOUR
AU - Han, Huibin
AU - Rakusová, Hana
AU - Verstraeten, Inge
AU - Zhang, Yuzhou
AU - Friml, Jiří
ID - 7879
IS - 5
JF - Plant physiology
TI - SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism
VL - 183
ER -
TY - JOUR
AB - Following its evoked release, dopamine (DA) signaling is rapidly terminated by presynaptic reuptake, mediated by the cocaine-sensitive DA transporter (DAT). DAT surface availability is dynamically regulated by endocytic trafficking, and direct protein kinase C (PKC) activation acutely diminishes DAT surface expression by accelerating DAT internalization. Previous cell line studies demonstrated that PKC-stimulated DAT endocytosis requires both Ack1 inactivation, which releases a DAT-specific endocytic brake, and the neuronal GTPase, Rit2, which binds DAT. However, it is unknown whether Rit2 is required for PKC-stimulated DAT endocytosis in DAergic terminals or whether there are region- and/or sex-dependent differences in PKC-stimulated DAT trafficking. Moreover, the mechanisms by which Rit2 controls PKC-stimulated DAT endocytosis are unknown. Here, we directly examined these important questions. Ex vivo studies revealed that PKC activation acutely decreased DAT surface expression selectively in ventral, but not dorsal, striatum. AAV-mediated, conditional Rit2 knockdown in DAergic neurons impacted baseline DAT surface:intracellular distribution in DAergic terminals from female ventral, but not dorsal, striatum. Further, Rit2 was required for PKC-stimulated DAT internalization in both male and female ventral striatum. FRET and surface pulldown studies in cell lines revealed that PKC activation drives DAT-Rit2 surface dissociation and that the DAT N terminus is required for both PKC-mediated DAT-Rit2 dissociation and DAT internalization. Finally, we found that Rit2 and Ack1 independently converge on DAT to facilitate PKC-stimulated DAT endocytosis. Together, our data provide greater insight into mechanisms that mediate PKC-regulated DAT internalization and reveal unexpected region-specific differences in PKC-stimulated DAT trafficking in bona fide DAergic terminals.
AU - Fagan, Rita R.
AU - Kearney, Patrick J.
AU - Sweeney, Carolyn G.
AU - Luethi, Dino
AU - Schoot Uiterkamp, Florianne E
AU - Schicker, Klaus
AU - Alejandro, Brian S.
AU - O'Connor, Lauren C.
AU - Sitte, Harald H.
AU - Melikian, Haley E.
ID - 7880
IS - 16
JF - Journal of Biological Chemistry
SN - 00219258
TI - Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact
VL - 295
ER -
TY - JOUR
AB - A few-body cluster is a building block of a many-body system in a gas phase provided the temperature at most is of the order of the binding energy of this cluster. Here we illustrate this statement by considering a system of tubes filled with dipolar distinguishable particles. We calculate the partition function, which determines the probability to find a few-body cluster at a given temperature. The input for our calculations—the energies of few-body clusters—is estimated using the harmonic approximation. We first describe and demonstrate the validity of our numerical procedure. Then we discuss the results featuring melting of the zero-temperature many-body state into a gas of free particles and few-body clusters. For temperature higher than its binding energy threshold, the dimers overwhelmingly dominate the ensemble, where the remaining probability is in free particles. At very high temperatures free (harmonic oscillator trap-bound) particle dominance is eventually reached. This structure evolution appears both for one and two particles in each layer providing crucial information about the behavior of ultracold dipolar gases. The investigation addresses the transition region between few- and many-body physics as a function of temperature using a system of ten dipoles in five tubes.
AU - Armstrong, Jeremy R.
AU - Jensen, Aksel S.
AU - Volosniev, Artem
AU - Zinner, Nikolaj T.
ID - 7882
IS - 4
JF - Mathematics
TI - Clusters in separated tubes of tilted dipoles
VL - 8
ER -
TY - JOUR
AB - Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order.
AU - Schauer, Alexandra
AU - Nunes Pinheiro, Diana C
AU - Hauschild, Robert
AU - Heisenberg, Carl-Philipp J
ID - 7888
JF - eLife
SN - 2050-084X
TI - Zebrafish embryonic explants undergo genetically encoded self-assembly
VL - 9
ER -
TY - JOUR
AB - Hartree–Fock theory has been justified as a mean-field approximation for fermionic systems. However, it suffers from some defects in predicting physical properties, making necessary a theory of quantum correlations. Recently, bosonization of many-body correlations has been rigorously justified as an upper bound on the correlation energy at high density with weak interactions. We review the bosonic approximation, deriving an effective Hamiltonian. We then show that for systems with Coulomb interaction this effective theory predicts collective excitations (plasmons) in accordance with the random phase approximation of Bohm and Pines, and with experimental observation.
AU - Benedikter, Niels P
ID - 7900
JF - Reviews in Mathematical Physics
SN - 0129-055X
TI - Bosonic collective excitations in Fermi gases
ER -
TY - JOUR
AB - Volatile anesthetics are widely used for surgery, but neuronal mechanisms of anesthesia remain unidentified. At the calyx of Held in brainstem slices from rats of either sex, isoflurane at clinical doses attenuated EPSCs by decreasing the release probability and the number of readily releasable vesicles. In presynaptic recordings of Ca2+ currents and exocytic capacitance changes, isoflurane attenuated exocytosis by inhibiting Ca2+ currents evoked by a short presynaptic depolarization, whereas it inhibited exocytosis evoked by a prolonged depolarization via directly blocking exocytic machinery downstream of Ca2+ influx. Since the length of presynaptic depolarization can simulate the frequency of synaptic inputs, isoflurane anesthesia is likely mediated by distinct dual mechanisms, depending on input frequencies. In simultaneous presynaptic and postsynaptic action potential recordings, isoflurane impaired the fidelity of repetitive spike transmission, more strongly at higher frequencies. Furthermore, in the cerebrum of adult mice, isoflurane inhibited monosynaptic corticocortical spike transmission, preferentially at a higher frequency. We conclude that dual presynaptic mechanisms operate for the anesthetic action of isoflurane, of which direct inhibition of exocytic machinery plays a low-pass filtering role in spike transmission at central excitatory synapses.
AU - Wang, Han Ying
AU - Eguchi, Kohgaku
AU - Yamashita, Takayuki
AU - Takahashi, Tomoyuki
ID - 7908
IS - 21
JF - Journal of Neuroscience
TI - Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms
VL - 40
ER -
TY - JOUR
AB - Cell migration entails networks and bundles of actin filaments termed lamellipodia and microspikes or filopodia, respectively, as well as focal adhesions, all of which recruit Ena/VASP family members hitherto thought to antagonize efficient cell motility. However, we find these proteins to act as positive regulators of migration in different murine cell lines. CRISPR/Cas9-mediated loss of Ena/VASP proteins reduced lamellipodial actin assembly and perturbed lamellipodial architecture, as evidenced by changed network geometry as well as reduction of filament length and number that was accompanied by abnormal Arp2/3 complex and heterodimeric capping protein accumulation. Loss of Ena/VASP function also abolished the formation of microspikes normally embedded in lamellipodia, but not of filopodia capable of emanating without lamellipodia. Ena/VASP-deficiency also impaired integrin-mediated adhesion accompanied by reduced traction forces exerted through these structures. Our data thus uncover novel Ena/VASP functions of these actin polymerases that are fully consistent with their promotion of cell migration.
AU - Damiano-Guercio, Julia
AU - Kurzawa, Laëtitia
AU - Müller, Jan
AU - Dimchev, Georgi A
AU - Schaks, Matthias
AU - Nemethova, Maria
AU - Pokrant, Thomas
AU - Brühmann, Stefan
AU - Linkner, Joern
AU - Blanchoin, Laurent
AU - Sixt, Michael K
AU - Rottner, Klemens
AU - Faix, Jan
ID - 7909
JF - eLife
TI - Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion
VL - 9
ER -
TY - JOUR
AB - Quantum illumination uses entangled signal-idler photon pairs to boost the detection efficiency of low-reflectivity objects in environments with bright thermal noise. Its advantage is particularly evident at low signal powers, a promising feature for applications such as noninvasive biomedical scanning or low-power short-range radar. Here, we experimentally investigate the concept of quantum illumination at microwave frequencies. We generate entangled fields to illuminate a room-temperature object at a distance of 1 m in a free-space detection setup. We implement a digital phase-conjugate receiver based on linear quadrature measurements that outperforms a symmetric classical noise radar in the same conditions, despite the entanglement-breaking signal path. Starting from experimental data, we also simulate the case of perfect idler photon number detection, which results in a quantum advantage compared with the relative classical benchmark. Our results highlight the opportunities and challenges in the way toward a first room-temperature application of microwave quantum circuits.
AU - Barzanjeh, Shabir
AU - Pirandola, S.
AU - Vitali, D
AU - Fink, Johannes M
ID - 7910
IS - 19
JF - Science Advances
TI - Microwave quantum illumination using a digital receiver
VL - 6
ER -
TY - JOUR
AB - 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.
AU - Mistakidis, S. I.
AU - Volosniev, Artem
AU - Schmelcher, P.
ID - 7919
JF - Physical Review Research
SN - 2643-1564
TI - Induced correlations between impurities in a one-dimensional quenched Bose gas
VL - 2
ER -
TY - JOUR
AB - In this paper, we introduce a relaxed CQ method with alternated inertial step for solving split feasibility problems. We give convergence of the sequence generated by our method under some suitable assumptions. Some numerical implementations from sparse signal and image deblurring are reported to show the efficiency of our method.
AU - Shehu, Yekini
AU - Gibali, Aviv
ID - 7925
JF - Optimization Letters
SN - 1862-4472
TI - New inertial relaxed method for solving split feasibilities
ER -
TY - JOUR
AB - In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data.
AU - Uroshlev, Leonid A.
AU - Abdullaev, Eldar T.
AU - Umarova, Iren R.
AU - Il’Icheva, Irina A.
AU - Panchenko, Larisa A.
AU - Polozov, Robert V.
AU - Kondrashov, Fyodor
AU - Nechipurenko, Yury D.
AU - Grokhovsky, Sergei L.
ID - 7931
JF - Scientific Reports
TI - A method for identification of the methylation level of CpG islands from NGS data
VL - 10
ER -
TY - JOUR
AB - Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer.
AU - Xu, Duo
AU - Varshney, Atul
AU - Ma, Xingyu
AU - Song, Baofang
AU - Riedl, Michael
AU - Avila, Marc
AU - Hof, Björn
ID - 7932
IS - 21
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 00278424
TI - Nonlinear hydrodynamic instability and turbulence in pulsatile flow
VL - 117
ER -
TY - JOUR
AB - We study a mobile quantum impurity, possessing internal rotational degrees of freedom, confined to a ring in the presence of a many-particle bosonic bath. By considering the recently introduced rotating polaron problem, we define the Hamiltonian and examine the energy spectrum. The weak-coupling regime is studied by means of a variational ansatz in the truncated Fock space. The corresponding spectrum indicates that there emerges a coupling between the internal and orbital angular momenta of the impurity as a consequence of the phonon exchange. We interpret the coupling as a phonon-mediated spin-orbit coupling and quantify it by using a correlation function between the internal and the orbital angular momentum operators. The strong-coupling regime is investigated within the Pekar approach, and it is shown that the correlation function of the ground state shows a kink at a critical coupling, that is explained by a sharp transition from the noninteracting state to the states that exhibit strong interaction with the surroundings. The results might find applications in such fields as spintronics or topological insulators where spin-orbit coupling is of crucial importance.
AU - Maslov, Mikhail
AU - Lemeshko, Mikhail
AU - Yakaboylu, Enderalp
ID - 7933
IS - 18
JF - Physical Review B
SN - 24699950
TI - Synthetic spin-orbit coupling mediated by a bosonic environment
VL - 101
ER -
TY - JOUR
AB - We design fast deterministic algorithms for distance computation in the Congested Clique model. Our key contributions include:
A (2+ϵ)-approximation for all-pairs shortest paths in O(log2n/ϵ) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.
A (1+ϵ)-approximation for multi-source shortest paths from O(n−−√) sources in O(log2n/ϵ) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.
Our main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in O~(n1/6) rounds.
AU - Censor-Hillel, Keren
AU - Dory, Michal
AU - Korhonen, Janne
AU - Leitersdorf, Dean
ID - 7939
JF - Distributed Computing
SN - 01782770
TI - Fast approximate shortest paths in the congested clique
ER -
TY - JOUR
AB - We prove that the Yangian associated to an untwisted symmetric affine Kac–Moody Lie algebra is isomorphic to the Drinfeld double of a shuffle algebra. The latter is constructed in [YZ14] as an algebraic formalism of cohomological Hall algebras. As a consequence, we obtain the Poincare–Birkhoff–Witt (PBW) theorem for this class of affine Yangians. Another independent proof of the PBW theorem is given recently by Guay, Regelskis, and Wendlandt [GRW18].
AU - Yang, Yaping
AU - Zhao, Gufang
ID - 7940
JF - Transformation Groups
SN - 10834362
TI - The PBW theorem for affine Yangians
ER -
TY - JOUR
AB - An understanding of the missing antinodal electronic excitations in the pseudogap state is essential for uncovering the physics of the underdoped cuprate high-temperature superconductors1,2,3,4,5,6. The majority of high-temperature experiments performed thus far, however, have been unable to discern whether the antinodal states are rendered unobservable due to their damping or whether they vanish due to their gapping7,8,9,10,11,12,13,14,15,16,17,18. Here, we distinguish between these two scenarios by using quantum oscillations to examine whether the small Fermi surface pocket, found to occupy only 2% of the Brillouin zone in the underdoped cuprates19,20,21,22,23,24, exists in isolation against a majority of completely gapped density of states spanning the antinodes, or whether it is thermodynamically coupled to a background of ungapped antinodal states. We find that quantum oscillations associated with the small Fermi surface pocket exhibit a signature sawtooth waveform characteristic of an isolated two-dimensional Fermi surface pocket25,26,27,28,29,30,31,32. This finding reveals that the antinodal states are destroyed by a hard gap that extends over the majority of the Brillouin zone, placing strong constraints on a drastic underlying origin of quasiparticle disappearance over almost the entire Brillouin zone in the pseudogap regime7,8,9,10,11,12,13,14,15,16,17,18.
AU - Hartstein, Máté
AU - Hsu, Yu Te
AU - Modic, Kimberly A
AU - Porras, Juan
AU - Loew, Toshinao
AU - Tacon, Matthieu Le
AU - Zuo, Huakun
AU - Wang, Jinhua
AU - Zhu, Zengwei
AU - Chan, Mun K.
AU - Mcdonald, Ross D.
AU - Lonzarich, Gilbert G.
AU - Keimer, Bernhard
AU - Sebastian, Suchitra E.
AU - Harrison, Neil
ID - 7942
JF - Nature Physics
SN - 17452473
TI - Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors
ER -
TY - THES
AB - This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.
For triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.
In the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars.
AU - Masárová, Zuzana
ID - 7944
KW - reconfiguration
KW - reconfiguration graph
KW - triangulations
KW - flip
KW - constrained triangulations
KW - shellability
KW - piecewise-linear balls
KW - token swapping
KW - trees
KW - coloured weighted token swapping
SN - 978-3-99078-005-3
TI - Reconfiguration problems
ER -
TY - JOUR
AB - In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule for plant growth, development and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). In addition, our present study shows that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene expression in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing cell wall remodeling required for overlying tissues separation during LRP emergence. Both NRT1.1-mediated repression of TAR2 and LAX3 are suppressed at high nitrate availability, resulting in the nitrate induction of TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously anticipated in regulating the nitrate response of root system architecture.
AU - Maghiaoui, A
AU - Bouguyon, E
AU - Cuesta, Candela
AU - Perrine-Walker, F
AU - Alcon, C
AU - Krouk, G
AU - Benková, Eva
AU - Nacry, P
AU - Gojon, A
AU - Bach, L
ID - 7948
JF - Journal of Experimental Botany
SN - 0022-0957
TI - The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate
ER -
TY - JOUR
AB - Peptides derived from non-functional precursors play important roles in various developmental processes, but also in (a)biotic stress signaling. Our (phospho)proteome-wide analyses of C-terminally encoded peptide 5 (CEP5)-mediated changes revealed an impact on abiotic stress-related processes. Drought has a dramatic impact on plant growth, development and reproduction, and the plant hormone auxin plays a role in drought responses. Our genetic, physiological, biochemical and pharmacological results demonstrated that CEP5-mediated signaling is relevant for osmotic and drought stress tolerance in Arabidopsis, and that CEP5 specifically counteracts auxin effects. Specifically, we found that CEP5 signaling stabilizes AUX/IAA transcriptional repressors, suggesting the existence of a novel peptide-dependent control mechanism that tunes auxin signaling. These observations align with the recently described role of AUX/IAAs in stress tolerance and provide a novel role for CEP5 in osmotic and drought stress tolerance.
AU - Smith, S
AU - Zhu, S
AU - Joos, L
AU - Roberts, I
AU - Nikonorova, N
AU - Vu, LD
AU - Stes, E
AU - Cho, H
AU - Larrieu, A
AU - Xuan, W
AU - Goodall, B
AU - van de Cotte, B
AU - Waite, JM
AU - Rigal, A
AU - R Harborough, SR
AU - Persiau, G
AU - Vanneste, S
AU - Kirschner, GK
AU - Vandermarliere, E
AU - Martens, L
AU - Stahl, Y
AU - Audenaert, D
AU - Friml, Jiří
AU - Felix, G
AU - Simon, R
AU - Bennett, M
AU - Bishopp, A
AU - De Jaeger, G
AU - Ljung, K
AU - Kepinski, S
AU - Robert, S
AU - Nemhauser, J
AU - Hwang, I
AU - Gevaert, K
AU - Beeckman, T
AU - De Smet, I
ID - 7949
IS - 8
JF - Molecular & Cellular Proteomics
SN - 1535-9476
TI - The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis
VL - 19
ER -
TY - CONF
AB - Simple stochastic games are turn-based 2½-player games with a reachability objective. The basic question asks whether one player can ensure reaching a given target with at least a given probability. A natural extension is games with a conjunction of such conditions as objective. Despite a plethora of recent results on the analysis of systems with multiple objectives, the decidability of this basic problem remains open. In this paper, we present an algorithm approximating the Pareto frontier of the achievable values to a given precision. Moreover, it is an anytime algorithm, meaning it can be stopped at any time returning the current approximation and its error bound.
AU - Ashok, Pranav
AU - Chatterjee, Krishnendu
AU - Kretinsky, Jan
AU - Weininger, Maximilian
AU - Winkler, Tobias
ID - 7955
SN - 9781450371049
T2 - Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science
TI - Approximating values of generalized-reachability stochastic games
ER -
TY - JOUR
AB - We prove edge universality for a general class of correlated real symmetric or complex Hermitian Wigner matrices with arbitrary expectation. Our theorem also applies to internal edges of the self-consistent density of states. In particular, we establish a strong form of band rigidity which excludes mismatches between location and label of eigenvalues close to internal edges in these general models.
AU - Alt, Johannes
AU - Erdös, László
AU - Krüger, Torben H
AU - Schröder, Dominik J
ID - 6184
IS - 2
JF - Annals of Probability
TI - Correlated random matrices: Band rigidity and edge universality
VL - 48
ER -
TY - JOUR
AB - 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.
AU - Filakovský, Marek
AU - Vokřínek, Lukas
ID - 6563
JF - Foundations of Computational Mathematics
SN - 16153375
TI - Are two given maps homotopic? An algorithmic viewpoint
VL - 20
ER -
TY - JOUR
AB - 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.
AU - Shehu, Yekini
AU - Li, Xiao-Huan
AU - Dong, Qiao-Li
ID - 6593
JF - Numerical Algorithms
SN - 1017-1398
TI - An efficient projection-type method for monotone variational inequalities in Hilbert spaces
VL - 84
ER -
TY - JOUR
AB - 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.
AU - Benedikter, Niels P
AU - Nam, Phan Thành
AU - Porta, Marcello
AU - Schlein, Benjamin
AU - Seiringer, Robert
ID - 6649
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime
VL - 374
ER -
TY - JOUR
AB - 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.
AU - Stella, Federico
AU - Urdapilleta, Eugenio
AU - Luo, Yifan
AU - Treves, Alessandro
ID - 6796
IS - 4
JF - Hippocampus
SN - 10509631
TI - Partial coherence and frustration in self-organizing spherical grids
VL - 30
ER -
TY - JOUR
AB - 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.
AU - Jahr, Wiebke
AU - Velicky, Philipp
AU - Danzl, Johann G
ID - 6808
IS - 3
JF - Methods
SN - 1046-2023
TI - Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens
VL - 174
ER -
TY - JOUR
AB - When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles.
AU - Pȩkalski, J.
AU - Rzadkowski, Wojciech
AU - Panagiotopoulos, A. Z.
ID - 7956
IS - 20
JF - The Journal of chemical physics
TI - Shear-induced ordering in systems with competing interactions: A machine learning study
VL - 152
ER -
TY - JOUR
AU - Parenti, Ilaria
AU - Garcia Rabaneda, Luis E
AU - Schön, Hanna
AU - Novarino, Gaia
ID - 7957
JF - Trends in Neurosciences
SN - 01662236
TI - Neurodevelopmental disorders: From genetics to functional pathways
ER -
TY - JOUR
AB - Let A={A1,…,An} be a family of sets in the plane. For 0≤i2b be integers. We prove that if each k-wise or (k+1)-wise intersection of sets from A has at most b path-connected components, which all are open, then fk+1=0 implies fk≤cfk−1 for some positive constant c depending only on b and k. These results also extend to two-dimensional compact surfaces.
AU - Kalai, Gil
AU - Patakova, Zuzana
ID - 7960
JF - Discrete and Computational Geometry
SN - 01795376
TI - Intersection patterns of planar sets
ER -
TY - JOUR
AB - A string graph is the intersection graph of a family of continuous arcs in the plane. The intersection graph of a family of plane convex sets is a string graph, but not all string graphs can be obtained in this way. We prove the following structure theorem conjectured by Janson and Uzzell: The vertex set of almost all string graphs on n vertices can be partitioned into five cliques such that some pair of them is not connected by any edge (n→∞). We also show that every graph with the above property is an intersection graph of plane convex sets. As a corollary, we obtain that almost all string graphs on n vertices are intersection graphs of plane convex sets.
AU - Pach, János
AU - Reed, Bruce
AU - Yuditsky, Yelena
ID - 7962
IS - 4
JF - Discrete and Computational Geometry
SN - 01795376
TI - Almost all string graphs are intersection graphs of plane convex sets
VL - 63
ER -
TY - CONF
AB - For 1≤m≤n, we consider a natural m-out-of-n multi-instance scenario for a public-key encryption (PKE) scheme. An adversary, given n independent instances of PKE, wins if he breaks at least m out of the n instances. In this work, we are interested in the scaling factor of PKE schemes, SF, which measures how well the difficulty of breaking m out of the n instances scales in m. That is, a scaling factor SF=ℓ indicates that breaking m out of n instances is at least ℓ times more difficult than breaking one single instance. A PKE scheme with small scaling factor hence provides an ideal target for mass surveillance. In fact, the Logjam attack (CCS 2015) implicitly exploited, among other things, an almost constant scaling factor of ElGamal over finite fields (with shared group parameters).
For Hashed ElGamal over elliptic curves, we use the generic group model to argue that the scaling factor depends on the scheme's granularity. In low granularity, meaning each public key contains its independent group parameter, the scheme has optimal scaling factor SF=m; In medium and high granularity, meaning all public keys share the same group parameter, the scheme still has a reasonable scaling factor SF=√m. Our findings underline that instantiating ElGamal over elliptic curves should be preferred to finite fields in a multi-instance scenario.
As our main technical contribution, we derive new generic-group lower bounds of Ω(√(mp)) on the difficulty of solving both the m-out-of-n Gap Discrete Logarithm and the m-out-of-n Gap Computational Diffie-Hellman problem over groups of prime order p, extending a recent result by Yun (EUROCRYPT 2015). We establish the lower bound by studying the hardness of a related computational problem which we call the search-by-hypersurface problem.
AU - Auerbach, Benedikt
AU - Giacon, Federico
AU - Kiltz, Eike
ID - 7966
SN - 0302-9743
T2 - Advances in Cryptology – EUROCRYPT 2020
TI - Everybody’s a target: Scalability in public-key encryption
VL - 12107
ER -
TY - JOUR
AB - Multilayer graphene lattices allow for an additional tunability of the band structure by the strong perpendicular electric field. In particular, the emergence of the new multiple Dirac points in ABA stacked trilayer graphene subject to strong transverse electric fields was proposed theoretically and confirmed experimentally. These new Dirac points dubbed “gullies” emerge from the interplay between strong electric field and trigonal warping. In this work, we first characterize the properties of new emergent Dirac points and show that the electric field can be used to tune the distance between gullies in the momentum space. We demonstrate that the band structure has multiple Lifshitz transitions and higher-order singularity of “monkey saddle” type. Following the characterization of the band structure, we consider the spectrum of Landau levels and structure of their wave functions. In the limit of strong electric fields when gullies are well separated in momentum space, they give rise to triply degenerate Landau levels. In the second part of this work, we investigate how degeneracy between three gully Landau levels is lifted in the presence of interactions. Within the Hartree-Fock approximation we show that the symmetry breaking state interpolates between the fully gully polarized state that breaks C3 symmetry at high displacement field and the gully symmetric state when the electric field is decreased. The discontinuous transition between these two states is driven by enhanced intergully tunneling and exchange. We conclude by outlining specific experimental predictions for the existence of such a symmetry-breaking state.
AU - Rao, Peng
AU - Serbyn, Maksym
ID - 7971
IS - 24
JF - Physical Review B
SN - 2469-9950
TI - Gully quantum Hall ferromagnetism in biased trilayer graphene
VL - 101
ER -
TY - JOUR
AB - The goal of limiting global warming to 1.5 °C requires a drastic reduction in CO2 emissions across many sectors of the world economy. Batteries are vital to this endeavor, whether used in electric vehicles, to store renewable electricity, or in aviation. Present lithium-ion technologies are preparing the public for this inevitable change, but their maximum theoretical specific capacity presents a limitation. Their high cost is another concern for commercial viability. Metal–air batteries have the highest theoretical energy density of all possible secondary battery technologies and could yield step changes in energy storage, if their practical difficulties could be overcome. The scope of this review is to provide an objective, comprehensive, and authoritative assessment of the intensive work invested in nonaqueous rechargeable metal–air batteries over the past few years, which identified the key problems and guides directions to solve them. We focus primarily on the challenges and outlook for Li–O2 cells but include Na–O2, K–O2, and Mg–O2 cells for comparison. Our review highlights the interdisciplinary nature of this field that involves a combination of materials chemistry, electrochemistry, computation, microscopy, spectroscopy, and surface science. The mechanisms of O2 reduction and evolution are considered in the light of recent findings, along with developments in positive and negative electrodes, electrolytes, electrocatalysis on surfaces and in solution, and the degradative effect of singlet oxygen, which is typically formed in Li–O2 cells.
AU - Kwak, WJ
AU - Sharon, D
AU - Xia, C
AU - Kim, H
AU - Johnson, LR
AU - Bruce, PG
AU - Nazar, LF
AU - Sun, YK
AU - Frimer, AA
AU - Noked, M
AU - Freunberger, Stefan Alexander
AU - Aurbach, D
ID - 7985
JF - Chemical Reviews
SN - 0009-2665
TI - Lithium-oxygen batteries and related systems: Potential, status, and future
ER -
TY - CONF
AB - 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).
AU - Wagner, Uli
AU - Welzl, Emo
ID - 7990
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips)
VL - 164
ER -
TY - CONF
AB - 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.
AU - Patakova, Zuzana
AU - Tancer, Martin
AU - Wagner, Uli
ID - 7992
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Barycentric cuts through a convex body
VL - 164
ER -
TY - JOUR
AB - When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.
AU - Perini, Samuel
AU - Rafajlović, Marina
AU - Westram, Anja M
AU - Johannesson, Kerstin
AU - Butlin, Roger K.
ID - 7995
JF - Evolution
SN - 00143820
TI - Assortative mating, sexual selection, and their consequences for gene flow in Littorina
ER -
TY - JOUR
AU - Vandael, David H
AU - Borges Merjane, Carolina
AU - Zhang, Xiaomin
AU - Jonas, Peter M
ID - 8001
JF - Neuron
SN - 0896-6273
TI - Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation
ER -
TY - JOUR
AB - Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity.
AU - Hörmayer, Lukas
AU - Montesinos López, Juan C
AU - Marhavá, Petra
AU - Benková, Eva
AU - Yoshida, Saiko
AU - Friml, Jiří
ID - 8002
IS - 26
JF - Proceedings of the National Academy of Sciences
SN - 0027-8424
TI - Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots
VL - 117
ER -
TY - JOUR
AB - 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.
AU - Michailidis, Alexios
AU - Turner, C. J.
AU - Papić, Z.
AU - Abanin, D. A.
AU - Serbyn, Maksym
ID - 8011
IS - 2
JF - Physical Review Research
SN - 2643-1564
TI - Stabilizing two-dimensional quantum scars by deformation and synchronization
VL - 2
ER -
TY - CONF
AB - Asynchronous programs are notoriously difficult to reason about because they spawn computation tasks which take effect asynchronously in a nondeterministic way. Devising inductive invariants for such programs requires understanding and stating complex relationships between an unbounded number of computation tasks in arbitrarily long executions. In this paper, we introduce inductive sequentialization, a new proof rule that sidesteps this complexity via a sequential reduction, a sequential program that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed. We have implemented and integrated our proof rule in the CIVL verifier, allowing us to provably derive fine-grained implementations of asynchronous programs. We have successfully applied our proof rule to a diverse set of message-passing protocols, including leader election protocols, two-phase commit, and Paxos.
AU - Kragl, Bernhard
AU - Enea, Constantin
AU - Henzinger, Thomas A
AU - Mutluergil, Suha Orhun
AU - Qadeer, Shaz
ID - 8012
SN - 9781450376136
T2 - Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation
TI - Inductive sequentialization of asynchronous programs
ER -
TY - JOUR
AB - When tiny soft ferromagnetic particles are placed along a liquid interface and exposed to a vertical magnetic field, the balance between capillary attraction and magnetic repulsion leads to self-organization into well-defined patterns. Here, we demonstrate experimentally that precessing magnetic fields induce metachronal waves on the periphery of these assemblies, similar to the ones observed in ciliates and some arthropods. The outermost layer of particles behaves like an array of cilia or legs whose sequential movement causes a net and controllable locomotion. This bioinspired many-particle swimming strategy is effective even at low Reynolds number, using only spatially uniform fields to generate the waves.
AU - Collard, Ylona
AU - Grosjean, Galien M
AU - Vandewalle, Nicolas
ID - 8036
JF - Communications Physics
TI - Magnetically powered metachronal waves induce locomotion in self-assemblies
VL - 3
ER -
TY - JOUR
AB - Genetic perturbations that affect bacterial resistance to antibiotics have been characterized genome-wide, but how do such perturbations interact with subsequent evolutionary adaptation to the drug? Here, we show that strong epistasis between resistance mutations and systematically identified genes can be exploited to control spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12 mutant populations in parallel, using a robotic platform that tightly controls population size and selection pressure. We find a global diminishing-returns epistasis pattern: strains that are initially more sensitive generally undergo larger resistance gains. However, some gene deletion strains deviate from this general trend and curtail the evolvability of resistance, including deletions of genes for membrane transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force evolution on inferior mutational paths, not explored in the wild type, and some of these essentially block resistance evolution. This effect is due to strong negative epistasis with resistance mutations. The identified genes and cellular functions provide potential targets for development of adjuvants that may block spontaneous resistance evolution when combined with antibiotics.
AU - Lukacisinova, Marta
AU - Fernando, Booshini
AU - Bollenbach, Mark Tobias
ID - 8037
JF - Nature Communications
TI - Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance
VL - 11
ER -
TY - JOUR
AB - We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N.
AU - Boccato, Chiara
AU - Brennecke, Christian
AU - Cenatiempo, Serena
AU - Schlein, Benjamin
ID - 8042
IS - 7
JF - Journal of the European Mathematical Society
SN - 14359855
TI - The excitation spectrum of Bose gases interacting through singular potentials
VL - 22
ER -
TY - JOUR
AB - With decreasing Reynolds number, Re, turbulence in channel flow becomes spatio-temporally intermittent and self-organises into solitary stripes oblique to the mean flow direction. We report here the existence of localised nonlinear travelling wave solutions of the Navier–Stokes equations possessing this obliqueness property. Such solutions are identified numerically using edge tracking coupled with arclength continuation. All solutions emerge in saddle-node bifurcations at values of Re lower than the non-localised solutions. Relative periodic orbit solutions bifurcating from branches of travelling waves have also been computed. A complete parametric study is performed, including their stability, the investigation of their large-scale flow, and the robustness to changes of the numerical domain.
AU - Paranjape, Chaitanya S
AU - Duguet, Yohann
AU - Hof, Björn
ID - 8043
JF - Journal of Fluid Mechanics
SN - 00221120
TI - Oblique stripe solutions of channel flow
VL - 897
ER -
TY - GEN
AB - With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the
mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7.
AU - Varzi, Alberto
AU - Thanner, Katharina
AU - Scipioni, Roberto
AU - Di Lecce, Daniele
AU - Hassoun, Jusef
AU - Dörfler, Susanne
AU - Altheus, Holger
AU - Kaskel, Stefan
AU - Prehal, Christian
AU - Freunberger, Stefan Alexander
ID - 8067
KW - Battery
KW - Lithium metal
KW - Lithium-sulphur
KW - Lithium-air
KW - All-solid-state
SN - 2664-1690
TI - Current status and future perspectives of Lithium metal batteries
ER -
TY - JOUR
AB - The projection methods with vanilla inertial extrapolation step for variational inequalities have been of interest to many authors recently due to the improved convergence speed contributed by the presence of inertial extrapolation step. However, it is discovered that these projection methods with inertial steps lose the Fejér monotonicity of the iterates with respect to the solution, which is being enjoyed by their corresponding non-inertial projection methods for variational inequalities. This lack of Fejér monotonicity makes projection methods with vanilla inertial extrapolation step for variational inequalities not to converge faster than their corresponding non-inertial projection methods at times. Also, it has recently been proved that the projection methods with vanilla inertial extrapolation step may provide convergence rates that are worse than the classical projected gradient methods for strongly convex functions. In this paper, we introduce projection methods with alternated inertial extrapolation step for solving variational inequalities. We show that the sequence of iterates generated by our methods converges weakly to a solution of the variational inequality under some appropriate conditions. The Fejér monotonicity of even subsequence is recovered in these methods and linear rate of convergence is obtained. The numerical implementations of our methods compared with some other inertial projection methods show that our method is more efficient and outperforms some of these inertial projection methods.
AU - Shehu, Yekini
AU - Iyiola, Olaniyi S.
ID - 8077
JF - Applied Numerical Mathematics
SN - 0168-9274
TI - Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence
VL - 157
ER -
TY - GEN
AB - 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.
AU - Hobisch, Mathias A.
AU - Mourad, Eléonore
AU - Fischer, Wolfgang J.
AU - Prehal, Christian
AU - Eyley, Samuel
AU - Childress, Anthony
AU - Zankel, Armin
AU - Mautner, Andreas
AU - Breitenbach, Stefan
AU - Rao, Apparao M.
AU - Thielemans, Wim
AU - Freunberger, Stefan Alexander
AU - Eckhart, Rene
AU - Bauer, Wolfgang
AU - Spirk, Stefan
ID - 8081
TI - High specific capacitance supercapacitors from hierarchically organized all-cellulose composites
ER -
TY - JOUR
AB - Origin and functions of intermittent transitions among sleep stages, including brief 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 sleep on scales of seconds and minutes results from intrinsic non-equilibrium critical dynamics. We investigate θ- and δ-wave dynamics in control rats and in rats where the sleep-promoting ventrolateral preoptic nucleus (VLPO) is lesioned (male Sprague-Dawley rats). We demonstrate that bursts in θ and δ cortical rhythms exhibit complex temporal organization, with long-range correlations and robust duality of power-law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, features typical of non-equilibrium systems self-organizing at criticality. We show that such non-equilibrium behavior relates to anti-correlated coupling between θ- and δ-bursts, persists across a range of time scales, and is independent of the dominant physiologic state; indications of a basic principle in sleep regulation. Further, we find that VLPO lesions lead to a modulation of cortical dynamics resulting in altered dynamical parameters of θ- and δ-bursts and significant reduction in θ–δ coupling. Our empirical findings and model simulations demonstrate that θ–δ coupling is essential for the emerging non-equilibrium critical dynamics observed across the sleep–wake cycle, and indicate that VLPO neurons may have dual role for both sleep and arousal/brief wake activation. The uncovered critical behavior in sleep- and wake-related cortical rhythms indicates a mechanism essential for the micro-architecture of spontaneous sleep-stage and arousal transitions within a novel, non-homeostatic paradigm of sleep regulation.
AU - Lombardi, Fabrizio
AU - Gómez-Extremera, Manuel
AU - Bernaola-Galván, Pedro
AU - Vetrivelan, Ramalingam
AU - Saper, Clifford B.
AU - Scammell, Thomas E.
AU - Ivanov, Plamen Ch.
ID - 8084
IS - 1
JF - Journal of Neuroscience
SN - 0270-6474
TI - Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake
VL - 40
ER -
TY - CONF
AB - We consider the classical problem of invariant generation for programs with polynomial assignments and focus on synthesizing invariants that are a conjunction of strict polynomial inequalities. We present a sound and semi-complete method based on positivstellensaetze, i.e. theorems in semi-algebraic geometry that characterize positive polynomials over a semi-algebraic set.
On the theoretical side, the worst-case complexity of our approach is subexponential, whereas the worst-case complexity of the previous complete method (Kapur, ACA 2004) is doubly-exponential. Even when restricted to linear invariants, the best previous complexity for complete invariant generation is exponential (Colon et al, CAV 2003). On the practical side, we reduce the invariant generation problem to quadratic programming (QCLP), which is a classical optimization problem with many industrial solvers. We demonstrate the applicability of our approach by providing experimental results on several academic benchmarks. To the best of our knowledge, the only previous invariant generation method that provides completeness guarantees for invariants consisting of polynomial inequalities is (Kapur, ACA 2004), which relies on quantifier elimination and cannot even handle toy programs such as our running example.
AU - Chatterjee, Krishnendu
AU - Fu, Hongfei
AU - Goharshady, Amir Kafshdar
AU - Goharshady, Ehsan Kafshdar
ID - 8089
SN - 9781450376136
T2 - Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation
TI - Polynomial invariant generation for non-deterministic recursive programs
ER -
TY - JOUR
AB - In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level.
AU - Seiringer, Robert
AU - Yngvason, Jakob
ID - 8091
JF - Journal of Statistical Physics
SN - 00224715
TI - Emergence of Haldane pseudo-potentials in systems with short-range interactions
ER -
TY - DATA
AB - Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by "translation bottlenecks": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of "continuous epistasis" in bacterial physiology.
AU - Kavcic, Bor
ID - 8097
KW - Escherichia coli
KW - antibiotic combinations
KW - translation
KW - growth laws
KW - drug interactions
KW - bacterial physiology
KW - translation inhibitors
TI - Analysis scripts and research data for the paper "Mechanisms of drug interactions between translation-inhibiting antibiotics"
ER -
TY - JOUR
AB - Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses.
AU - Gammerdinger, William J
AU - Toups, Melissa A
AU - Vicoso, Beatriz
ID - 8099
JF - Molecular Ecology Resources
SN - 1755-098X
TI - Disagreement in FST estimators: A case study from sex chromosomes
ER -
TY - JOUR
AB - 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.
AU - Lombardi, Fabrizio
AU - Wang, Jilin W.J.L.
AU - Zhang, Xiyun
AU - Ivanov, Plamen Ch
ID - 8105
JF - EPJ Web of Conferences
SN - 2100-014X
TI - Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality
VL - 230
ER -
TY - GEN
AB - Context, such as behavioral state, is known to modulate memory formation and retrieval, but is usually ignored in associative memory models. Here, we propose several types of contextual modulation for associative memory networks that greatly increase their performance. In these networks, context inactivates specific neurons and connections, which modulates the effective connectivity of the network. Memories are stored only by the active components, thereby reducing interference from memories acquired in other contexts. Such networks exhibit several beneficial characteristics, including enhanced memory capacity, high robustness to noise, increased robustness to memory overloading, and better memory retention during continual learning. Furthermore, memories can be biased to have different relative strengths, or even gated on or off, according to contextual cues, providing a candidate model for cognitive control of memory and efficient memory search. An external context-encoding network can dynamically switch the memory network to a desired state, which we liken to experimentally observed contextual signals in prefrontal cortex and hippocampus. Overall, our work illustrates the benefits of organizing memory around context, and provides an important link between behavioral studies of memory and mechanistic details of neural circuits.SIGNIFICANCEMemory is context dependent — both encoding and recall vary in effectiveness and speed depending on factors like location and brain state during a task. We apply this idea to a simple computational model of associative memory through contextual gating of neurons and synaptic connections. Intriguingly, this results in several advantages, including vastly enhanced memory capacity, better robustness, and flexible memory gating. Our model helps to explain (i) how gating and inhibition contribute to memory processes, (ii) how memory access dynamically changes over time, and (iii) how context representations, such as those observed in hippocampus and prefrontal cortex, may interact with and control memory processes.
AU - Podlaski, William F.
AU - Agnes, Everton J.
AU - Vogels, Tim P
ID - 8125
T2 - bioRxiv
TI - Context-modular memory networks support high-capacity, flexible, and robust associative memories
ER -
TY - JOUR
AB - We study the dynamics of a system of N interacting bosons in a disc-shaped trap, which is realised by an external potential that confines the bosons in one spatial dimension to an interval of length of order ε. The interaction is non-negative and scaled in such a way that its scattering length is of order ε/N, while its range is proportional to (ε/N)β with scaling parameter β∈(0,1]. We consider the simultaneous limit (N,ε)→(∞,0) and assume that the system initially exhibits Bose–Einstein condensation. We prove that condensation is preserved by the N-body dynamics, where the time-evolved condensate wave function is the solution of a two-dimensional non-linear equation. The strength of the non-linearity depends on the scaling parameter β. For β∈(0,1), we obtain a cubic defocusing non-linear Schrödinger equation, while the choice β=1 yields a Gross–Pitaevskii equation featuring the scattering length of the interaction. In both cases, the coupling parameter depends on the confining potential.
AU - Bossmann, Lea
ID - 8130
JF - Archive for Rational Mechanics and Analysis
SN - 0003-9527
TI - Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons
ER -
TY - JOUR
AB - The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets.In this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS) on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel). We employ a Bayesian framework (BayesR+) which can account for issues pertaining to data structure and unknown confounding variables (with sensitivity analyses using ordinary least squares- (OLS) and mixed model-based approaches). We identified 13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged genetic variants accounted for up to 45% of variance in protein levels (for MCP2, 36% of variance alone attributable to 1 polymorphism). Methylation data accounted for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation in protein levels (for VEGFA) was explained using genetic and epigenetic data combined. We demonstrated putative causal relationships between CD6 and IL18R1 with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data may aid understanding of the molecular regulation of the circulating inflammatory proteome as well as causal relationships between inflammatory mediators and disease.
AU - Hillary, Robert F.
AU - Trejo-Banos, Daniel
AU - Kousathanas, Athanasios
AU - Mccartney, Daniel L.
AU - Harris, Sarah E.
AU - Stevenson, Anna J.
AU - Patxot, Marion
AU - Ojavee, Sven Erik
AU - Zhang, Qian
AU - Liewald, David C.
AU - Ritchie, Craig W.
AU - Evans, Kathryn L.
AU - Tucker-Drob, Elliot M.
AU - Wray, Naomi R.
AU - Mcrae, Allan F.
AU - Visscher, Peter M.
AU - Deary, Ian J.
AU - Robinson, Matthew Richard
AU - Marioni, Riccardo E.
ID - 8133
IS - 1
JF - Genome Medicine
TI - Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults
VL - 12
ER -
TY - JOUR
AB - We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion.
AU - Mayer, Simon
AU - Seiringer, Robert
ID - 8134
IS - 6
JF - Journal of Mathematical Physics
SN - 00222488
TI - The free energy of the two-dimensional dilute Bose gas. II. Upper bound
VL - 61
ER -
TY - JOUR
AB - Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration.
AU - Zhang, J
AU - Mazur, E
AU - Balla, J
AU - Gallei, Michelle C
AU - Kalousek, P
AU - Medveďová, Z
AU - Li, Y
AU - Wang, Y
AU - Prat, Tomas
AU - Vasileva, Mina K
AU - Reinöhl, V
AU - Procházka, S
AU - Halouzka, R
AU - Tarkowski, P
AU - Luschnig, C
AU - Brewer, PB
AU - Friml, Jiří
ID - 8138
IS - 1
JF - Nature Communications
SN - 2041-1723
TI - Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization
VL - 11
ER -
TY - JOUR
AB - Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.
AU - Montesinos López, Juan C
AU - Abuzeineh, A
AU - Kopf, Aglaja
AU - Juanes Garcia, Alba
AU - Ötvös, Krisztina
AU - Petrášek, J
AU - Sixt, Michael K
AU - Benková, Eva
ID - 8142
JF - The Embo Journal
SN - 0261-4189
TI - Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage
ER -
TY - THES
AB - We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry.
AU - Avvakumov, Sergey
ID - 8156
TI - Topological methods in geometry and discrete mathematics
ER -
TY - JOUR
AB - The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.
AU - Stankowski, Sean
AU - Westram, Anja M
AU - Zagrodzka, Zuzanna B.
AU - Eyres, Isobel
AU - Broquet, Thomas
AU - Johannesson, Kerstin
AU - Butlin, Roger K.
ID - 8167
IS - 1806
JF - Philosophical Transactions of the Royal Society. Series B: Biological Sciences
TI - The evolution of strong reproductive isolation between sympatric intertidal snails
VL - 375
ER -
TY - JOUR
AB - Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.
AU - Kulmuni, Jonna
AU - Butlin, Roger K.
AU - Lucek, Kay
AU - Savolainen, Vincent
AU - Westram, Anja M
ID - 8168
IS - 1806
JF - Philosophical Transactions of the Royal Society. Series B: Biological sciences
SN - 0962-8436
TI - Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers
VL - 375
ER -
TY - JOUR
AB - Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation.
AU - Shang, Huiying
AU - Hess, Jaqueline
AU - Pickup, Melinda
AU - Field, David
AU - Ingvarsson, Pär K.
AU - Liu, Jianquan
AU - Lexer, Christian
ID - 8169
IS - 1806
JF - Philosophical Transactions of the Royal Society. Series B: Biological Sciences
TI - Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group
VL - 375
ER -
TY - JOUR
AB - Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function
of time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct
peaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and
centrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For
CS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the
gas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in
detail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in
helium droplets introduced here should apply to a range of molecules and complexes.
AU - Chatterley, Adam S.
AU - Christiansen, Lars
AU - Schouder, Constant A.
AU - Jørgensen, Anders V.
AU - Shepperson, Benjamin
AU - Cherepanov, Igor
AU - Bighin, Giacomo
AU - Zillich, Robert E.
AU - Lemeshko, Mikhail
AU - Stapelfeldt, Henrik
ID - 8170
IS - 1
JF - Physical Review Letters
SN - 00319007
TI - Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains
VL - 125
ER -
TY - CONF
AB - Numerous methods have been proposed for probabilistic generative modelling of
3D objects. However, none of these is able to produce textured objects, which
renders them of limited use for practical tasks. In this work, we present the
first generative model of textured 3D meshes. Training such a model would
traditionally require a large dataset of textured meshes, but unfortunately,
existing datasets of meshes lack detailed textures. We instead propose a new
training methodology that allows learning from collections of 2D images without
any 3D information. To do so, we train our model to explain a distribution of
images by modelling each image as a 3D foreground object placed in front of a
2D background. Thus, it learns to generate meshes that when rendered, produce
images similar to those in its training set.
A well-known problem when generating meshes with deep networks is the
emergence of self-intersections, which are problematic for many use-cases. As a
second contribution we therefore introduce a new generation process for 3D
meshes that guarantees no self-intersections arise, based on the physical
intuition that faces should push one another out of the way as they move.
We conduct extensive experiments on our approach, reporting quantitative and
qualitative results on both synthetic data and natural images. These show our
method successfully learns to generate plausible and diverse textured 3D
samples for five challenging object classes.
AU - Henderson, Paul M
AU - Tsiminaki, Vagia
AU - Lampert, Christoph
ID - 8186
T2 - Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition
TI - Leveraging 2D data to learn textured 3D mesh generation
ER -
TY - JOUR
AU - Sixt, Michael K
AU - Huttenlocher, Anna
ID - 8190
IS - 8
JF - The Journal of cell biology
TI - Zena Werb (1945-2020): Cell biology in context
VL - 219
ER -
TY - CONF
AB - Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks.
AU - Baranowski, Marek
AU - He, Shaobo
AU - Lechner, Mathias
AU - Nguyen, Thanh Son
AU - Rakamarić, Zvonimir
ID - 8194
SN - 03029743
T2 - Automated Reasoning
TI - An SMT theory of fixed-point arithmetic
VL - 12166
ER -
TY - CONF
AB - This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier.
AU - Kragl, Bernhard
AU - Qadeer, Shaz
AU - Henzinger, Thomas A
ID - 8195
SN - 0302-9743
T2 - Computer Aided Verification
TI - Refinement for structured concurrent programs
VL - 12224
ER -