@inproceedings{6647,
abstract = {The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r, all share a common point. In this paper, we prove a strengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span floor[n/3] vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing triangles. Our result generalizes to a result about simplices in R^d,d >=2.},
author = {Fulek, Radoslav and Gärtner, Bernd and Kupavskii, Andrey and Valtr, Pavel and Wagner, Uli},
booktitle = {35th International Symposium on Computational Geometry},
isbn = {9783959771047},
issn = {1868-8969},
location = {Portland, OR, United States},
pages = {38:1--38:13},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{The crossing Tverberg theorem}},
doi = {10.4230/LIPICS.SOCG.2019.38},
volume = {129},
year = {2019},
}
@phdthesis{6894,
abstract = {Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.
Nevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.
While, previously, directions were given by the user, we introduce (1) the first method
for computing template directions from spurious counterexamples, so as to generalize and
eliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid
automata with (possibly non-linear) convex constraints on derivatives only, while for linear
ODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,
which, partitioning the state space into appropriate (possibly non-uniform) cones, divide
curvy trajectories into relatively straight sections, suitable for polyhedral abstractions.
Finally, we introduce (3) space-time interpolation, which, combining interval arithmetic
and template refinement, computes appropriate (possibly non-uniform) time partitioning
and template directions along spurious trajectories, so as to eliminate them.
We obtain sound and automatic methods for the reachability analysis over dense
and unbounded time of convex hybrid automata and hybrid automata with linear ODE.
We build prototype tools and compare—favorably—our methods against the respective
state-of-the-art tools, on several benchmarks.},
author = {Giacobbe, Mirco},
issn = {2663-337X},
pages = {132},
publisher = {IST Austria},
title = {{Automatic time-unbounded reachability analysis of hybrid systems}},
doi = {10.15479/AT:ISTA:6894},
year = {2019},
}
@article{7227,
abstract = {Gastrulation entails specification and formation of three embryonic germ layers—ectoderm, mesoderm and endoderm—thereby establishing the basis for the future body plan. In zebrafish embryos, germ layer specification occurs during blastula and early gastrula stages (Ho & Kimmel, 1993), a period when the main morphogenetic movements underlying gastrulation are initiated. Hence, the signals driving progenitor cell fate specification, such as Nodal ligands from the TGF-β family, also play key roles in regulating germ layer progenitor cell segregation (Carmany-Rampey & Schier, 2001; David & Rosa, 2001; Feldman et al., 2000; Gritsman et al., 1999; Keller et al., 2008). In this review, we summarize and discuss the main signaling pathways involved in germ layer progenitor cell fate specification and segregation, specifically focusing on recent advances in understanding the interplay between mesoderm and endoderm specification and the internalization movements at the onset of zebrafish gastrulation.},
author = {Nunes Pinheiro, Diana C and Heisenberg, Carl-Philipp J},
issn = {00702153},
journal = {Current Topics in Developmental Biology},
publisher = {Elsevier},
title = {{Zebrafish gastrulation: Putting fate in motion}},
doi = {10.1016/bs.ctdb.2019.10.009},
year = {2019},
}
@article{73,
abstract = {We consider the space of probability measures on a discrete set X, endowed with a dynamical optimal transport metric. Given two probability measures supported in a subset Y⊆X, it is natural to ask whether they can be connected by a constant speed geodesic with support in Y at all times. Our main result answers this question affirmatively, under a suitable geometric condition on Y introduced in this paper. The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi equations, which is of independent interest.},
author = {Erbar, Matthias and Maas, Jan and Wirth, Melchior},
issn = {09442669},
journal = {Calculus of Variations and Partial Differential Equations},
number = {1},
publisher = {Springer},
title = {{On the geometry of geodesics in discrete optimal transport}},
doi = {10.1007/s00526-018-1456-1},
volume = {58},
year = {2019},
}
@article{80,
abstract = {We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer.},
author = {Deuchert, Andreas and Seiringer, Robert and Yngvason, Jakob},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {723--776},
publisher = {Springer},
title = {{Bose–Einstein condensation in a dilute, trapped gas at positive temperature}},
doi = {10.1007/s00220-018-3239-0},
volume = {368},
year = {2019},
}
@inproceedings{7183,
abstract = {A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2).},
author = {Brázdil, Tomás and Chatterjee, Krishnendu and Kucera, Antonín and Novotný, Petr and Velan, Dominik},
booktitle = {International Symposium on Automated Technology for Verification and Analysis},
isbn = {9783030317836},
issn = {16113349},
location = {Taipei, Taiwan},
pages = {462--478},
publisher = {Springer Nature},
title = {{Deciding fast termination for probabilistic VASS with nondeterminism}},
doi = {10.1007/978-3-030-31784-3_27},
volume = {11781},
year = {2019},
}
@article{7001,
author = {Schwayer, Cornelia and Shamipour, Shayan and Pranjic-Ferscha, Kornelija and Schauer, Alexandra and Balda, M and Tada, M and Matter, K and Heisenberg, Carl-Philipp J},
issn = {1097-4172},
journal = {Cell},
number = {4},
pages = {937--952.e18},
publisher = {Cell Press},
title = {{Mechanosensation of tight junctions depends on ZO-1 phase separation and flow}},
doi = {10.1016/j.cell.2019.10.006},
volume = {179},
year = {2019},
}
@article{7210,
abstract = {The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants. But these amplifiers of natural selection typically increase fixation time. Here we study population structures that achieve a tradeoff between fixation probability and time. First, we show that no amplifiers can have an asymptotically lower absorption time than the well-mixed population. Then we design population structures that substantially augment the fixation probability with just a minor increase in fixation time. Finally, we show that those structures enable higher effective rate of evolution than the well-mixed population provided that the rate of generating advantageous mutants is relatively low. Our work sheds light on how population structure affects the rate of evolution. Moreover, our structures could be useful for lab-based, medical, or industrial applications of evolutionary optimization.},
author = {Tkadlec, Josef and Pavlogiannis, Andreas and Chatterjee, Krishnendu and Nowak, Martin A.},
issn = {2399-3642},
journal = {Communications Biology},
publisher = {Springer Nature},
title = {{Population structure determines the tradeoff between fixation probability and fixation time}},
doi = {10.1038/s42003-019-0373-y},
volume = {2},
year = {2019},
}
@article{6089,
abstract = {Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.},
author = {Fraisse, Christelle and Puixeu Sala, Gemma and Vicoso, Beatriz},
journal = {Molecular biology and evolution},
number = {3},
pages = {500--515},
publisher = {Oxford Academic},
title = {{Pleiotropy modulates the efficacy of selection in drosophila melanogaster}},
doi = {10.1093/molbev/msy246},
volume = {36},
year = {2019},
}
@misc{6060,
author = {Vicoso, Beatriz},
publisher = {IST Austria},
title = {{Supplementary data for "Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome" (Huylman, Toups et al., 2019). }},
doi = {10.15479/AT:ISTA:6060},
year = {2019},
}
@article{151,
abstract = {We construct planar bi-Sobolev mappings whose local volume distortion is bounded from below by a given function f∈Lp with p>1. More precisely, for any 1<q<(p+1)/2 we construct W1,q-bi-Sobolev maps with identity boundary conditions; for f∈L∞, we provide bi-Lipschitz maps. The basic building block of our construction are bi-Lipschitz maps which stretch a given compact subset of the unit square by a given factor while preserving the boundary. The construction of these stretching maps relies on a slight strengthening of the celebrated covering result of Alberti, Csörnyei, and Preiss for measurable planar sets in the case of compact sets. We apply our result to a model functional in nonlinear elasticity, the integrand of which features fast blowup as the Jacobian determinant of the deformation becomes small. For such functionals, the derivation of the equilibrium equations for minimizers requires an additional regularization of test functions, which our maps provide.},
author = {Fischer, Julian L and Kneuss, Olivier},
journal = {Journal of Differential Equations},
number = {1},
pages = {257 -- 311},
publisher = {Academic Press},
title = {{Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity}},
doi = {10.1016/j.jde.2018.07.045},
volume = {266},
year = {2019},
}
@article{175,
abstract = {An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points.},
author = {Browning, Timothy D and Loughran, Daniel},
issn = {10886850},
journal = {Transactions of the American Mathematical Society},
number = {8},
pages = {5757--5785},
publisher = {American Mathematical Society},
title = {{Sieving rational points on varieties}},
volume = {371},
year = {2019},
}
@article{5,
abstract = {In this paper, we introduce a quantum version of the wonderful compactification of a group as a certain noncommutative projective scheme. Our approach stems from the fact that the wonderful compactification encodes the asymptotics of matrix coefficients, and from its realization as a GIT quotient of the Vinberg semigroup. In order to define the wonderful compactification for a quantum group, we adopt a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key to our construction is a quantum version of the Vinberg semigroup, which we define as a q-deformation of a certain Rees algebra, compatible with a standard Poisson structure. Furthermore, we discuss quantum analogues of the stratification of the wonderful compactification by orbits for a certain group action, and provide explicit computations in the case of SL2.},
author = {Ganev, Iordan V},
journal = {Journal of the London Mathematical Society},
number = {3},
pages = {778--806},
publisher = {Wiley},
title = {{The wonderful compactification for quantum groups}},
doi = {10.1112/jlms.12193},
volume = {99},
year = {2019},
}
@article{5789,
abstract = {Tissue morphogenesis is driven by mechanical forces that elicit changes in cell size, shape and motion. The extent by which forces deform tissues critically depends on the rheological properties of the recipient tissue. Yet, whether and how dynamic changes in tissue rheology affect tissue morphogenesis and how they are regulated within the developing organism remain unclear. Here, we show that blastoderm spreading at the onset of zebrafish morphogenesis relies on a rapid, pronounced and spatially patterned tissue fluidization. Blastoderm fluidization is temporally controlled by mitotic cell rounding-dependent cell–cell contact disassembly during the last rounds of cell cleavages. Moreover, fluidization is spatially restricted to the central blastoderm by local activation of non-canonical Wnt signalling within the blastoderm margin, increasing cell cohesion and thereby counteracting the effect of mitotic rounding on contact disassembly. Overall, our results identify a fluidity transition mediated by loss of cell cohesion as a critical regulator of embryo morphogenesis.},
author = {Petridou, Nicoletta and Grigolon, Silvia and Salbreux, Guillaume and Hannezo, Edouard and Heisenberg, Carl-Philipp J},
issn = {14657392},
journal = {Nature Cell Biology},
pages = {169–178},
publisher = {Nature Publishing Group},
title = {{Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling}},
doi = {10.1038/s41556-018-0247-4},
volume = {21},
year = {2019},
}
@article{5878,
abstract = {We consider the motion of a droplet bouncing on a vibrating bath of the same fluid in the presence of a central potential. We formulate a rotation symmetry-reduced description of this system, which allows for the straightforward application of dynamical systems theory tools. As an illustration of the utility of the symmetry reduction, we apply it to a model of the pilot-wave system with a central harmonic force. We begin our analysis by identifying local bifurcations and the onset of chaos. We then describe the emergence of chaotic regions and their merging bifurcations, which lead to the formation of a global attractor. In this final regime, the droplet’s angular momentum spontaneously changes its sign as observed in the experiments of Perrard et al.},
author = {Budanur, Nazmi B and Fleury, Marc},
issn = {1089-7682},
journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science},
number = {1},
publisher = {AIP Publishing},
title = {{State space geometry of the chaotic pilot-wave hydrodynamics}},
doi = {10.1063/1.5058279},
volume = {29},
year = {2019},
}
@article{5943,
abstract = {The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow velocity ratio is investigated experimentally for a velocity ratio range of R ∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral analysis we characterize the Strouhal number and amplitude of the hairpin instability as a function of R and ReD. We demonstrate that the dynamics of the hairpins is well described by the Landau model, and, hence, that the instability occurs through Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind different bluff bodies. Using the Landau model, we determine the precise threshold values of hairpin shedding. We also study the spatial dependence of this hydrodynamical instability, which shows a global behaviour.},
author = {Klotz, Lukasz and Gumowski, Konrad and Wesfreid, José Eduardo},
journal = {Journal of Fluid Mechanics},
pages = {386--406},
publisher = {Cambridge University Press},
title = {{Experiments on a jet in a crossflow in the low-velocity-ratio regime}},
doi = {10.1017/jfm.2018.974},
volume = {863},
year = {2019},
}
@article{6023,
abstract = {Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain.},
author = {Yoshida, Saiko and Van Der Schuren, Alja and Van Dop, Maritza and Van Galen, Luc and Saiga, Shunsuke and Adibi, Milad and Möller, Barbara and Ten Hove, Colette A. and Marhavy, Peter and Smith, Richard and Friml, Jiří and Weijers, Dolf},
journal = {Nature Plants},
number = {2},
pages = {160--166},
publisher = {Springer Nature},
title = {{A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis}},
doi = {10.1038/s41477-019-0363-6},
volume = {5},
year = {2019},
}
@article{6028,
abstract = {We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small.},
author = {Gerencser, Mate and Hairer, Martin},
journal = {Communications on Pure and Applied Mathematics},
number = {9},
pages = {1983--2005},
publisher = {Wiley},
title = {{A solution theory for quasilinear singular SPDEs}},
doi = {10.1002/cpa.21816},
volume = {72},
year = {2019},
}
@article{6105,
abstract = { Hosts can alter their strategy towards pathogens during their lifetime; that is, they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e., resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fecundity consequences that result from a high pathogen burden. Finally, previous exposure may also lead to life‐history adjustments, such as terminal investment into reproduction.
Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested whether previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute‐phase infection (one day post‐challenge). We then asked whether previous pathogen exposure affects chronic‐phase pathogen persistence and longer‐term survival (28 days post‐challenge).
We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long‐term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses.
We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection.
To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi‐faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host–pathogen system and that infection persistence may be bacterium‐specific.
},
author = {Kutzer, Megan and Kurtz, Joachim and Armitage, Sophie A.O.},
issn = {13652656},
journal = {Journal of Animal Ecology},
number = {4},
pages = {566--578},
publisher = {Wiley},
title = {{A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance}},
doi = {10.1111/1365-2656.12953},
volume = {88},
year = {2019},
}
@article{6174,
abstract = {We propose a scaling theory for the many-body localization (MBL) phase transition in one dimension, building on the idea that it proceeds via a “quantum avalanche.” We argue that the critical properties can be captured at a coarse-grained level by a Kosterlitz-Thouless (KT) renormalization group (RG) flow. On phenomenological grounds, we identify the scaling variables as the density of thermal regions and the length scale that controls the decay of typical matrix elements. Within this KT picture, the MBL phase is a line of fixed points that terminates at the delocalization transition. We discuss two possible scenarios distinguished by the distribution of rare, fractal thermal inclusions within the MBL phase. In the first scenario, these regions have a stretched exponential distribution in the MBL phase. In the second scenario, the near-critical MBL phase hosts rare thermal regions that are power-law-distributed in size. This points to the existence of a second transition within the MBL phase, at which these power laws change to the stretched exponential form expected at strong disorder. We numerically simulate two different phenomenological RGs previously proposed to describe the MBL transition. Both RGs display a universal power-law length distribution of thermal regions at the transition with a critical exponent αc=2, and continuously varying exponents in the MBL phase consistent with the KT picture.},
author = {Dumitrescu, Philipp T. and Goremykina, Anna and Parameswaran, Siddharth A. and Serbyn, Maksym and Vasseur, Romain},
issn = {2469-9950},
journal = {Physical Review B},
number = {9},
publisher = {American Physical Society (APS)},
title = {{Kosterlitz-Thouless scaling at many-body localization phase transitions}},
doi = {10.1103/physrevb.99.094205},
volume = {99},
year = {2019},
}