@article{439,
abstract = {We count points over a finite field on wild character varieties,of Riemann surfaces for singularities with regular semisimple leading term. The new feature in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras. Our result leads to the conjecture that the mixed Hodge polynomials of these character varieties agree with previously conjectured perverse Hodge polynomials of certain twisted parabolic Higgs moduli spaces, indicating the
possibility of a P = W conjecture for a suitable wild Hitchin system.},
author = {Hausel, Tamas and Mereb, Martin and Wong, Michael},
journal = {Journal of the European Mathematical Society},
publisher = {European Mathematical Society},
title = {{Arithmetic and representation theory of wild character varieties}},
year = {2019},
}
@inproceedings{5947,
abstract = {Graph algorithms applied in many applications, including social networks, communication networks, VLSI design, graphics, and several others, require dynamic modifications - addition and removal of vertices and/or edges - in the graph. This paper presents a novel concurrent non-blocking algorithm to implement a dynamic unbounded directed graph in a shared-memory machine. The addition and removal operations of vertices and edges are lock-free. For a finite sized graph, the lookup operations are wait-free. Most significant component of the presented algorithm is the reachability query in a concurrent graph. The reachability queries in our algorithm are obstruction-free and thus impose minimal additional synchronization cost over other operations. We prove that each of the data structure operations are linearizable. We extensively evaluate a sample C/C++ implementation of the algorithm through a number of micro-benchmarks. The experimental results show that the proposed algorithm scales well with the number of threads and on an average provides 5 to 7x performance improvement over a concurrent graph implementation using coarse-grained locking.},
author = {Chatterjee, Bapi and Peri, Sathya and Sa, Muktikanta and Singhal, Nandini},
booktitle = {ACM International Conference Proceeding Series},
isbn = {978-1-4503-6094-4 },
location = {Bangalore, India},
pages = {168--177},
publisher = {ACM},
title = {{A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries}},
doi = {10.1145/3288599.3288617},
year = {2019},
}
@article{6022,
abstract = {The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation.},
author = {Merrill, Richard M. and Rastas, Pasi and Martin, Simon H. and Melo Hurtado, Maria C and Barker, Sarah and Davey, John and Mcmillan, W. Owen and Jiggins, Chris D.},
journal = {PLoS Biology},
number = {2},
publisher = {Public Library of Science},
title = {{Genetic dissection of assortative mating behavior}},
doi = {10.1371/journal.pbio.2005902},
volume = {17},
year = {2019},
}
@article{6046,
abstract = {Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate‐limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses.},
author = {Mitosch, Karin and Rieckh, Georg and Bollenbach, Mark Tobias},
journal = {Molecular systems biology},
number = {2},
publisher = {Embo Press},
title = {{Temporal order and precision of complex stress responses in individual bacteria}},
doi = {10.15252/msb.20188470},
volume = {15},
year = {2019},
}
@article{6053,
abstract = {Recent technical developments in the fields of quantum electromechanics and optomechanics have spawned nanoscale mechanical transducers with the sensitivity to measure mechanical displacements at the femtometre scale and the ability to convert electromagnetic signals at the single photon level. A key challenge in this field is obtaining strong coupling between motion and electromagnetic fields without adding additional decoherence. Here we present an electromechanical transducer that integrates a high-frequency (0.42 GHz) hypersonic phononic crystal with a superconducting microwave circuit. The use of a phononic bandgap crystal enables quantum-level transduction of hypersonic mechanical motion and concurrently eliminates decoherence caused by acoustic radiation. Devices with hypersonic mechanical frequencies provide a natural pathway for integration with Josephson junction quantum circuits, a leading quantum computing technology, and nanophotonic systems capable of optical networking and distributing quantum information.},
author = {Kalaee, Mahmoud and Mirhosseini, Mohammad and Dieterle, Paul B. and Peruzzo, Matilda and Fink, Johannes M and Painter, Oskar},
journal = {Nature Nanotechnology},
publisher = {Springer Nature},
title = {{Quantum electromechanics of a hypersonic crystal}},
doi = {10.1038/s41565-019-0377-2},
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},
}
@article{6091,
abstract = {Cortical networks are characterized by sparse connectivity, with synapses found at only a subset of axo-dendritic contacts. Yet within these networks, neurons can exhibit high connection probabilities, suggesting that cell-intrinsic factors, not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a factor that determines synapse density by mediating a cell-cell competition that requires ephrin-B-EphB signaling. In a microisland culture system designed to isolate cell-cell competition, we find that eB3 determines winning and losing neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM) genetic mouse model system in vivo the relative levels of eB3 control spine density in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls synapse density independently of action potential-driven activity. Our findings illustrate a new class of competitive mechanism mediated by trans-synaptic organizing proteins which control the number of synapses neurons receive relative to neighboring neurons.},
author = {Henderson, Nathan T. and Le Marchand, Sylvain J. and Hruska, Martin and Hippenmeyer, Simon and Luo, Liqun and Dalva, Matthew B.},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs}},
doi = {10.7554/eLife.41563},
volume = {8},
year = {2019},
}
@unpublished{6313,
abstract = {We prove three principal results. First we exhibit a drawing of $K_{10}$ in the plane for which there do not exist extensions of the edges to simple closed curves with any two curves intersecting at most twice. Second, we exhibit a drawing of $K_9$ that has an extension of its edges to simple closed curves such that any two curves intersect in at most two points, but no extension to simple closed curves has every two curves intersecting in exactly two points. Third, we show that every h-convex drawing (introduced by Arroyo et al, submitted) has extensions of its edges to simple closed curves such that any two curves intersect in exactly two points. Using this result, we show that} a set of three axioms of simple closed curve extensions characterizes h-convexity.},
author = {Arroyo Guevara, Alan M and Richter, Bruce and Sunohara, Matthew},
pages = {35},
title = {{Extending drawings of complete graphs into arrangements of pseudocircles}},
year = {2019},
}
@article{6351,
abstract = {A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals.
Patterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing.},
author = {Marhavá, Petra and Hörmayer, Lukas and Yoshida, Saiko and Marhavy, Peter and Benková, Eva and Friml, Jiří},
issn = {10974172},
journal = {Cell},
number = {4},
pages = {957--969.e13},
publisher = {Elsevier},
title = {{Re-activation of stem cell pathways for pattern restoration in plant wound healing}},
doi = {10.1016/j.cell.2019.04.015},
volume = {177},
year = {2019},
}
@article{6262,
abstract = {Gravitropism is an adaptive response that orients plant growth parallel to the gravity vector. Asymmetric
distribution of the phytohormone auxin is a necessary prerequisite to the tropic bending both in roots and
shoots. During hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing
cells to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization to the bottom cell mem-
branes leads to the auxin accumulation at the lower side of the organ, initiating bending and, later, auxin
feedback-mediated repolarization restores symmetric auxin distribution to terminate bending. Here, we per-
formed a forward genetic screen to identify regulators of both PIN3 polarization events during gravitropic
response. We searched for mutants with defective PIN3 polarizations based on easy-to-score morphological
outputs of decreased or increased gravity-induced hypocotyl bending. We identified the number of
hypocotyl reduced bending (hrb) and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-
lated typically with defective gravity-induced PIN3 relocation whereas all analyzed hhb mutants showed
defects in the second, auxin-mediated PIN3 relocation. Next-generation sequencing-aided mutation map-
ping identified several candidate genes, including SCARECROW and ACTIN2, revealing roles of endodermis
specification and actin cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.
The hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms underlying cell
polarity and plant adaptive development.},
author = {Rakusová, Hana and Han, Huibin and Valošek, Petr and Friml, Jiří},
issn = {0960-7412},
journal = {The Plant Journal},
publisher = {Wiley},
title = {{Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls}},
doi = {10.1111/tpj.14301},
year = {2019},
}
@article{6515,
abstract = {We give non-degeneracy criteria for Riemannian simplices based on simplices in spaces of constant sectional curvature. It extends previous work on Riemannian simplices, where we developed Riemannian simplices with respect to Euclidean reference simplices. The criteria we give in this article are in terms of quality measures for spaces of constant curvature that we develop here. We see that simplices in spaces that have nearly constant curvature, are already non-degenerate under very weak quality demands. This is of importance because it allows for sampling of Riemannian manifolds based on anisotropy of the manifold and not (absolute) curvature.},
author = {Dyer, Ramsay and Vegter, Gert and Wintraecken, Mathijs},
issn = {1920-180X},
journal = {Journal of Computational Geometry },
number = {1},
pages = {223–256},
title = {{Simplices modelled on spaces of constant curvature}},
doi = {10.20382/jocg.v10i1a9},
volume = {10},
year = {2019},
}
@article{6488,
abstract = {We prove a central limit theorem for the difference of linear eigenvalue statistics of a sample covariance matrix W˜ and its minor W. We find that the fluctuation of this difference is much smaller than those of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of W˜ and W. Our result identifies the fluctuation of the spatial derivative of the approximate Gaussian field in the recent paper by Dumitru and Paquette. Unlike in a similar result for Wigner matrices, for sample covariance matrices, the fluctuation may entirely vanish.},
author = {Cipolloni, Giorgio and Erdös, László},
issn = {20103271},
journal = {Random Matrices: Theory and Application},
publisher = {World Scientific Publishing},
title = {{Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices}},
doi = {10.1142/S2010326320500069},
year = {2019},
}
@article{6419,
abstract = {Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible.},
author = {Pokusaeva, Victoria and Usmanova, Dinara R. and Putintseva, Ekaterina V. and Espinar, Lorena and Sarkisyan, Karen and Mishin, Alexander S. and Bogatyreva, Natalya S. and Ivankov, Dmitry and Akopyan, Arseniy and Avvakumov, Sergey and Povolotskaya, Inna S. and Filion, Guillaume J. and Carey, Lucas B. and Kondrashov, Fyodor},
issn = {15537404},
journal = {PLoS Genetics},
number = {4},
publisher = {Public Library of Science},
title = {{An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape}},
doi = {10.1371/journal.pgen.1008079},
volume = {15},
year = {2019},
}
@article{6596,
abstract = {It is well known that many problems in image recovery, signal processing, and machine learning can be modeled as finding zeros of the sum of maximal monotone and Lipschitz continuous monotone operators. Many papers have studied forward-backward splitting methods for finding zeros of the sum of two monotone operators in Hilbert spaces. Most of the proposed splitting methods in the literature have been proposed for the sum of maximal monotone and inverse-strongly monotone operators in Hilbert spaces. In this paper, we consider splitting methods for finding zeros of the sum of maximal monotone operators and Lipschitz continuous monotone operators in Banach spaces. We obtain weak and strong convergence results for the zeros of the sum of maximal monotone and Lipschitz continuous monotone operators in Banach spaces. Many already studied problems in the literature can be considered as special cases of this paper.},
author = {Shehu, Yekini},
issn = {1420-9012},
journal = {Results in Mathematics},
number = {4},
publisher = {Springer},
title = {{Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces}},
doi = {10.1007/s00025-019-1061-4},
volume = {74},
year = {2019},
}
@article{6609,
abstract = {Mechanical systems facilitate the development of a hybrid quantum technology comprising electrical, optical, atomic and acoustic degrees of freedom1, and entanglement is essential to realize quantum-enabled devices. Continuous-variable entangled fields—known as Einstein–Podolsky–Rosen (EPR) states—are spatially separated two-mode squeezed states that can be used for quantum teleportation and quantum communication2. In the optical domain, EPR states are typically generated using nondegenerate optical amplifiers3, and at microwave frequencies Josephson circuits can serve as a nonlinear medium4,5,6. An outstanding goal is to deterministically generate and distribute entangled states with a mechanical oscillator, which requires a carefully arranged balance between excitation, cooling and dissipation in an ultralow noise environment. Here we observe stationary emission of path-entangled microwave radiation from a parametrically driven 30-micrometre-long silicon nanostring oscillator, squeezing the joint field operators of two thermal modes by 3.40 decibels below the vacuum level. The motion of this micromechanical system correlates up to 50 photons per second per hertz, giving rise to a quantum discord that is robust with respect to microwave noise7. Such generalized quantum correlations of separable states are important for quantum-enhanced detection8 and provide direct evidence of the non-classical nature of the mechanical oscillator without directly measuring its state9. This noninvasive measurement scheme allows to infer information about otherwise inaccessible objects, with potential implications for sensing, open-system dynamics and fundamental tests of quantum gravity. In the future, similar on-chip devices could be used to entangle subsystems on very different energy scales, such as microwave and optical photons.},
author = {Barzanjeh, Shabir and Redchenko, Elena and Peruzzo, Matilda and Wulf, Matthias and Lewis, Dylan and Arnold, Georg M and Fink, Johannes M},
journal = {Nature},
pages = {480--483},
publisher = {Nature Publishing Group},
title = {{Stationary entangled radiation from micromechanical motion}},
doi = {10.1038/s41586-019-1320-2},
volume = {570},
year = {2019},
}
@article{6717,
abstract = {With the recent publication by Silpe and Bassler (2019), considering phage detection of a bacterial quorum-sensing (QS) autoinducer, we now have as many as five examples of phage-associated intercellular communication (Table 1). Each potentially involves ecological inferences by phages as to concentrations of surrounding phage-infected or uninfected bacteria. While the utility of phage detection of bacterial QS molecules may at first glance appear to be straightforward, we suggest in this commentary that the underlying ecological explanation is unlikely to be simple.},
author = {Igler, Claudia and Abedon, Stephen T.},
journal = {Frontiers in Microbiology},
publisher = {Frontiers},
title = {{Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision}},
doi = {10.3389/fmicb.2019.01171},
volume = {10},
year = {2019},
}
@article{6611,
abstract = {Cell polarity is crucial for the coordinated development of all multicellular organisms. In plants, this is exemplified by the PIN-FORMED (PIN) efflux carriers of the phytohormone auxin: The polar subcellular localization of the PINs is instructive to the directional intercellular auxin transport, and thus to a plethora of auxin-regulated growth and developmental processes. Despite its importance, the regulation of PIN polar subcellular localization remains poorly understood. Here, we have employed advanced live-cell imaging techniques to study the roles of microtubules and actin microfilaments in the establishment of apical polar localization of PIN2 in the epidermis of the Arabidopsis root meristem. We report that apical PIN2 polarity requires neither intact actin microfilaments nor microtubules, suggesting that the primary spatial cue for polar PIN distribution is likely independent of cytoskeleton-guided endomembrane trafficking.},
author = {Glanc, Matous and Fendrych, Matyas and Friml, Jiří},
journal = {Biomolecules},
number = {6},
publisher = {MDPI},
title = {{PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton}},
doi = {10.3390/biom9060222},
volume = {9},
year = {2019},
}
@inproceedings{6628,
abstract = {Fejes Tóth [5] and Schneider [9] studied approximations of smooth convex hypersurfaces in Euclidean space by piecewise flat triangular meshes with a given number of vertices on the hypersurface that are optimal with respect to Hausdorff distance. They proved that this Hausdorff distance decreases inversely proportional with m 2/(d−1), where m is the number of vertices and d is the dimension of Euclidean space. Moreover the pro-portionality constant can be expressed in terms of the Gaussian curvature, an intrinsic quantity. In this short note, we prove the extrinsic nature of this constant for manifolds of sufficiently high codimension. We do so by constructing an family of isometric embeddings of the flat torus in Euclidean space.},
author = {Vegter, Gert and Wintraecken, Mathijs},
booktitle = {The 31st Canadian Conference in Computational Geometry},
location = {Edmonton, Canada},
title = {{The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds}},
year = {2019},
}
@inproceedings{6642,
abstract = {We present a thermodynamically based approach to the design of models for viscoelastic fluids with stress diffusion effect. In particular, we show how to add a stress diffusion term to some standard viscoelastic rate-type models (Giesekus, FENE-P, Johnson–Segalman, Phan-Thien–Tanner and Bautista–Manero–Puig) so that the resulting models with the added stress diffusion term are thermodynamically consistent in the sense that they obey the first and the second law of thermodynamics. We point out the potential applications of the provided thermodynamical background in the study of flows of fluids described by the proposed models.},
author = {Dostalík, Mark and Průša, Vít and Skrivan, Tomas},
booktitle = {AIP Conference Proceedings},
location = {Zlin, Czech Republic},
publisher = {AIP},
title = {{On diffusive variants of some classical viscoelastic rate-type models}},
doi = {10.1063/1.5109493},
volume = {2107},
year = {2019},
}
@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},
}