@article{7253,
abstract = {The cyclin-dependent kinase inhibitor p57KIP2 is encoded by the imprinted Cdkn1c locus, exhibits maternal expression, and is essential for cerebral cortex development. How Cdkn1c regulates corticogenesis is however not clear. To this end we employ Mosaic Analysis with Double Markers (MADM) technology to genetically dissect Cdkn1c gene function in corticogenesis at single cell resolution. We find that the previously described growth-inhibitory Cdkn1c function is a non-cell-autonomous one, acting on the whole organism. In contrast we reveal a growth-promoting cell-autonomous Cdkn1c function which at the mechanistic level mediates radial glial progenitor cell and nascent projection neuron survival. Strikingly, the growth-promoting function of Cdkn1c is highly dosage sensitive but not subject to genomic imprinting. Collectively, our results suggest that the Cdkn1c locus regulates cortical development through distinct cell-autonomous and non-cell-autonomous mechanisms. More generally, our study highlights the importance to probe the relative contributions of cell intrinsic gene function and tissue-wide mechanisms to the overall phenotype.},
author = {Laukoter, Susanne and Beattie, Robert J and Pauler, Florian and Amberg, Nicole and Nakayama, Keiichi I. and Hippenmeyer, Simon},
issn = {2041-1723},
journal = {Nature Communications},
publisher = {Springer Nature},
title = {{Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development}},
doi = {10.1038/s41467-019-14077-2},
volume = {11},
year = {2020},
}
@article{6997,
author = {Zhang, Yuzhou and Friml, Jiří},
issn = {1469-8137},
journal = {New Phytologist},
number = {3},
pages = {1049--1052},
publisher = {Wiley},
title = {{Auxin guides roots to avoid obstacles during gravitropic growth}},
doi = {10.1111/nph.16203},
volume = {225},
year = {2020},
}
@article{319,
abstract = {We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition.},
author = {Gerencser, Mate and Hairer, Martin},
issn = {14322064},
journal = {Probability Theory and Related Fields},
number = {3-4},
pages = {697–758},
publisher = {Springer},
title = {{Singular SPDEs in domains with boundaries}},
doi = {10.1007/s00440-018-0841-1},
volume = {173},
year = {2019},
}
@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},
issn = {1435-9855},
journal = {Journal of the European Mathematical Society},
number = {10},
pages = {2995--3052},
publisher = {European Mathematical Society},
title = {{Arithmetic and representation theory of wild character varieties}},
doi = {10.4171/JEMS/896},
volume = {21},
year = {2019},
}
@article{441,
author = {Kalinin, Nikita and Shkolnikov, Mikhail},
issn = {2199-6768},
journal = {European Journal of Mathematics},
number = {3},
pages = {909–928},
publisher = {Springer Nature},
title = {{Tropical formulae for summation over a part of SL(2,Z)}},
doi = {10.1007/s40879-018-0218-0},
volume = {5},
year = {2019},
}
@article{5790,
abstract = {The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest.},
author = {Chaplick, Steven and Fulek, Radoslav and Klavík, Pavel},
issn = {03649024},
journal = {Journal of Graph Theory},
number = {4},
pages = {365--394},
publisher = {Wiley},
title = {{Extending partial representations of circle graphs}},
doi = {10.1002/jgt.22436},
volume = {91},
year = {2019},
}
@article{5911,
abstract = {Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved.},
author = {Faria, Rui and Johannesson, Kerstin and Butlin, Roger K. and Westram, Anja M},
issn = {01695347},
journal = {Trends in Ecology and Evolution},
number = {3},
pages = {239--248},
publisher = {Elsevier},
title = {{Evolving inversions}},
doi = {10.1016/j.tree.2018.12.005},
volume = {34},
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},
issn = {1748-3395},
journal = {Nature Nanotechnology},
number = {4},
pages = {334–339},
publisher = {Springer Nature},
title = {{Quantum electromechanics of a hypersonic crystal}},
doi = {10.1038/s41565-019-0377-2},
volume = {14},
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},
}
@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},
}
@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{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 = {1365-313x},
journal = {The Plant Journal},
number = {6},
pages = {1048--1059},
publisher = {Wiley},
title = {{Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls}},
doi = {10.1111/tpj.14301},
volume = {98},
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{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},
publisher = {Carleton University},
title = {{Simplices modelled on spaces of constant curvature}},
doi = {10.20382/jocg.v10i1a9},
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},
pages = {275--279},
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 Pruša, 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},
}
@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{6779,
abstract = {Recent studies suggest that unstable recurrent solutions of the Navier-Stokes equation provide new insights
into dynamics of turbulent flows. In this study, we compute an extensive network of dynamical connections
between such solutions in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion symmetric subspace. In particular, we find numerous isolated heteroclinic connections between different
types of solutions—equilibria, periodic, and quasiperiodic orbits—as well as continua of connections forming
higher-dimensional connecting manifolds. We also compute a homoclinic connection of a periodic orbit and
provide strong evidence that the associated homoclinic tangle forms the chaotic repeller that underpins transient
turbulence in the symmetric subspace.},
author = {Suri, Balachandra and Pallantla, Ravi Kumar and Schatz, Michael F. and Grigoriev, Roman O.},
issn = {2470-0053},
journal = {Physical Review E},
number = {1},
publisher = {APS},
title = {{Heteroclinic and homoclinic connections in a Kolmogorov-like flow}},
doi = {10.1103/physreve.100.013112},
volume = {100},
year = {2019},
}
@article{6786,
abstract = {Dipolar coupling plays a fundamental role in the interaction between electrically or magnetically polarized species such as magnetic atoms and dipolar molecules in a gas or dipolar excitons in the solid state. Unlike Coulomb or contactlike interactions found in many atomic, molecular, and condensed-matter systems, this interaction is long-ranged and highly anisotropic, as it changes from repulsive to attractive depending on the relative positions and orientation of the dipoles. Because of this unique property, many exotic, symmetry-breaking collective states have been recently predicted for cold dipolar gases, but only a few have been experimentally detected and only in dilute atomic dipolar Bose-Einstein condensates. Here, we report on the first observation of attractive dipolar coupling between excitonic dipoles using a new design of stacked semiconductor bilayers. We show that the presence of a dipolar exciton fluid in one bilayer modifies the spatial distribution and increases the binding energy of excitonic dipoles in a vertically remote layer. The binding energy changes are explained using a many-body polaron model describing the deformation of the exciton cloud due to its interaction with a remote dipolar exciton. The surprising nonmonotonic dependence on the cloud density indicates the important role of dipolar correlations, which is unique to dense, strongly interacting dipolar solid-state systems. Our concept provides a route for the realization of dipolar lattices with strong anisotropic interactions in semiconductor systems, which open the way for the observation of theoretically predicted new and exotic collective phases, as well as for engineering and sensing their collective excitations.},
author = {Hubert, Colin and Baruchi, Yifat and Mazuz-Harpaz, Yotam and Cohen, Kobi and Biermann, Klaus and Lemeshko, Mikhail and West, Ken and Pfeiffer, Loren and Rapaport, Ronen and Santos, Paulo},
issn = {2160-3308},
journal = {Physical Review X},
number = {2},
publisher = {APS},
title = {{Attractive dipolar coupling between stacked exciton fluids}},
doi = {10.1103/PhysRevX.9.021026},
volume = {9},
year = {2019},
}
@article{6793,
abstract = {The Regge symmetry is a set of remarkable relations between two tetrahedra whose edge lengths are related in a simple fashion. It was first discovered as a consequence of an asymptotic formula in mathematical physics. Here, we give a simple geometric proof of Regge symmetries in Euclidean, spherical, and hyperbolic geometry.},
author = {Akopyan, Arseniy and Izmestiev, Ivan},
issn = {14692120},
journal = {Bulletin of the London Mathematical Society},
number = {5},
pages = {765--775},
publisher = {London Mathematical Society},
title = {{The Regge symmetry, confocal conics, and the Schläfli formula}},
doi = {10.1112/blms.12276},
volume = {51},
year = {2019},
}
@unpublished{6748,
abstract = {Fitting a function by using linear combinations of a large number N of `simple' components is one of the most fruitful ideas in statistical learning. This idea lies at the core of a variety of methods, from two-layer neural networks to kernel regression, to boosting. In general, the resulting risk minimization problem is non-convex and is solved by gradient descent or its variants. Unfortunately, little is known about global convergence properties of these approaches.
Here we consider the problem of learning a concave function f on a compact convex domain Ω⊆ℝd, using linear combinations of `bump-like' components (neurons). The parameters to be fitted are the centers of N bumps, and the resulting empirical risk minimization problem is highly non-convex. We prove that, in the limit in which the number of neurons diverges, the evolution of gradient descent converges to a Wasserstein gradient flow in the space of probability distributions over Ω. Further, when the bump width δ tends to 0, this gradient flow has a limit which is a viscous porous medium equation. Remarkably, the cost function optimized by this gradient flow exhibits a special property known as displacement convexity, which implies exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory appears to capture well the behavior for moderate values of δ,N. Explaining this phenomenon, and understanding the dependence on δ,N in a quantitative manner remains an outstanding challenge.},
author = {Javanmard, Adel and Mondelli, Marco and Montanari, Andrea},
booktitle = {arXiv:1901.01375},
title = {{Analysis of a two-layer neural network via displacement convexity}},
year = {2019},
}
@article{6750,
abstract = {Polar codes have gained extensive attention during the past few years and recently they have been selected for the next generation of wireless communications standards (5G). Successive-cancellation-based (SC-based) decoders, such as SC list (SCL) and SC flip (SCF), provide a reasonable error performance for polar codes at the cost of low decoding speed. Fast SC-based decoders, such as Fast-SSC, Fast-SSCL, and Fast-SSCF, identify the special constituent codes in a polar code graph off-line, produce a list of operations, store the list in memory, and feed the list to the decoder to decode the constituent codes in order efficiently, thus increasing the decoding speed. However, the list of operations is dependent on the code rate and as the rate changes, a new list is produced, making fast SC-based decoders not rate-flexible. In this paper, we propose a completely rate-flexible fast SC-based decoder by creating the list of operations directly in hardware, with low implementation complexity. We further propose a hardware architecture implementing the proposed method and show that the area occupation of the rate-flexible fast SC-based decoder in this paper is only 38% of the total area of the memory-based base-line decoder when 5G code rates are supported. },
author = {Hashemi, Seyyed Ali and Condo, Carlo and Mondelli, Marco and Gross, Warren J},
issn = {1053587X},
journal = {IEEE Transactions on Signal Processing},
number = {22},
publisher = {IEEE},
title = {{Rate-flexible fast polar decoders}},
doi = {10.1109/TSP.2019.2944738},
volume = {67},
year = {2019},
}
@article{6762,
abstract = {We present and study novel optimal control problems motivated by the search for photovoltaic materials with high power-conversion efficiency. The material must perform the first step: convert light (photons) into electronic excitations. We formulate various desirable properties of the excitations as mathematical control goals at the Kohn-Sham-DFT level
of theory, with the control being given by the nuclear charge distribution. We prove that nuclear distributions exist which give rise to optimal HOMO-LUMO excitations, and present illustrative numerical simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features such as large electron-hole separation, and a hierarchy of length scales: internal HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the doping profiles < system size.},
author = {Friesecke, Gero and Kniely, Michael},
issn = {15403467},
journal = {Multiscale Modeling and Simulation},
number = {3},
pages = {926--947},
publisher = {SIAM},
title = {{New optimal control problems in density functional theory motivated by photovoltaics}},
doi = {10.1137/18M1207272},
volume = {17},
year = {2019},
}
@article{6755,
abstract = {Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.},
author = {Picard, Marion A L and Vicoso, Beatriz and Roquis, David and Bulla, Ingo and Augusto, Ronaldo C. and Arancibia, Nathalie and Grunau, Christoph and Boissier, Jérôme and Cosseau, Céline},
issn = {17596653},
journal = {Genome biology and evolution},
number = {7},
pages = {1909--1922},
publisher = {Oxford Academic Press},
title = {{Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome}},
doi = {10.1093/gbe/evz133},
volume = {11},
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{6680,
abstract = {This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed.},
author = {Sachdeva, Himani},
issn = {1558-5646},
journal = {Evolution},
number = {9},
pages = {1729--1745},
publisher = {Wiley},
title = {{Effect of partial selfing and polygenic selection on establishment in a new habitat}},
doi = {10.1111/evo.13812},
volume = {73},
year = {2019},
}
@article{6856,
abstract = {Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation.},
author = {Pickup, Melinda and Barton, Nicholas H and Brandvain, Yaniv and Fraisse, Christelle and Yakimowski, Sarah and Dixit, Tanmay and Lexer, Christian and Cereghetti, Eva and Field, David},
journal = {New Phytologist},
number = {3},
pages = {1035--1047},
title = {{Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow}},
doi = {10.1111/nph.16180},
volume = {224},
year = {2019},
}
@article{6868,
abstract = {Hyperpolarization-activated cyclic-nucleotide-gated (HCN) channels control electrical rhythmicity and excitability in the heart and brain, but the function of HCN channels at the subcellular level in axons remains poorly understood. Here, we show that the action potential conduction velocity in both myelinated and unmyelinated central axons can be bidirectionally modulated by a HCN channel blocker, cyclic adenosine monophosphate (cAMP), and neuromodulators. Recordings from mouse cerebellar mossy fiber boutons show that HCN channels ensure reliable high-frequency firing and are strongly modulated by cAMP (EC50 40 mM; estimated endogenous cAMP concentration 13 mM). In addition, immunogold-electron microscopy revealed HCN2 as the dominating subunit in cerebellar mossy fibers. Computational modeling indicated that HCN2 channels control conduction velocity primarily by altering the resting membrane potential
and are associated with significant metabolic costs. These results suggest that the cAMP-HCN pathway provides neuromodulators with an opportunity to finely tune energy consumption and temporal delays across axons in the brain.},
author = {Byczkowicz, Niklas and Eshra, Abdelmoneim and Montanaro-Punzengruber, Jacqueline-Claire and Trevisiol, Andrea and Hirrlinger, Johannes and Kole, Maarten Hp and Shigemoto, Ryuichi and Hallermann, Stefan},
issn = {2050084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons}},
doi = {10.7554/eLife.42766},
volume = {8},
year = {2019},
}
@article{6919,
author = {Qi, Chao and Minin, Giulio Di and Vercellino, Irene and Wutz, Anton and Korkhov, Volodymyr M.},
issn = {23752548},
journal = {Science Advances},
number = {9},
publisher = {American Association for the Advancement of Science},
title = {{Structural basis of sterol recognition by human hedgehog receptor PTCH1}},
doi = {10.1126/sciadv.aaw6490},
volume = {5},
year = {2019},
}
@inproceedings{6933,
abstract = {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 problem 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 problem from O(√n) sources in O(log² n / 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 Õ(n^{1/6}) rounds.},
author = {Censor-Hillel, Keren and Dory, Michal and Korhonen, Janne and Leitersdorf, Dean},
booktitle = {Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin},
isbn = {9781450362177},
location = {Toronto, ON, Canada},
pages = {74--83},
publisher = {ACM},
title = {{Fast approximate shortest paths in the congested clique}},
doi = {10.1145/3293611.3331633},
year = {2019},
}
@article{6940,
abstract = {We study the effect of a linear tunneling coupling between two-dimensional systems, each separately
exhibiting the topological Berezinskii-Kosterlitz-Thouless (BKT) transition. In the uncoupled limit, there
are two phases: one where the one-body correlation functions are algebraically decaying and the other with
exponential decay. When the linear coupling is turned on, a third BKT-paired phase emerges, in which one-body correlations are exponentially decaying, while two-body correlation functions exhibit power-law
decay. We perform numerical simulations in the paradigmatic case of two coupled XY models at finite
temperature, finding evidences that for any finite value of the interlayer coupling, the BKT-paired phase is
present. We provide a picture of the phase diagram using a renormalization group approach.},
author = {Bighin, Giacomo and Defenu, Nicolò and Nándori, István and Salasnich, Luca and Trombettoni, Andrea},
issn = {1079-7114},
journal = {Physical Review Letters},
number = {10},
publisher = {American Physical Society (APS)},
title = {{Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models}},
doi = {10.1103/physrevlett.123.100601},
volume = {123},
year = {2019},
}
@article{6952,
abstract = {We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, most existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to existing approaches, while also supporting weaker supervision. Importantly, it can be trained purely from 2D images, without pose annotations, and with only a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to reason over lighting parameters and exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach in various settings, showing that: (i) it learns to disentangle shape from pose and lighting; (ii) using shading in the loss improves performance compared to just silhouettes; (iii) when using a standard single white light, our model outperforms state-of-the-art 2D-supervised methods, both with and without pose supervision, thanks to exploiting shading cues; (iv) performance improves further when using multiple coloured lights, even approaching that of state-of-the-art 3D-supervised methods; (v) shapes produced by our model capture smooth surfaces and fine details better than voxel-based approaches; and (vi) our approach supports concave classes such as bathtubs and sofas, which methods based on silhouettes cannot learn.},
author = {Henderson, Paul M and Ferrari, Vittorio},
issn = {1573-1405},
journal = {International Journal of Computer Vision},
publisher = {Springer Nature},
title = {{Learning single-image 3D reconstruction by generative modelling of shape, pose and shading}},
doi = {10.1007/s11263-019-01219-8},
year = {2019},
}
@phdthesis{6957,
abstract = {In many shear flows like pipe flow, plane Couette flow, plane Poiseuille flow, etc. turbulence emerges subcritically. Here, when subjected to strong enough perturbations, the flow becomes turbulent in spite of the laminar base flow being linearly stable. The nature of this instability has puzzled the scientific community for decades. At onset, turbulence appears in localized patches and flows are spatio-temporally intermittent. In pipe flow the localized turbulent structures are referred to as puffs and in planar flows like plane Couette and channel flow, patches arise in the form of localized oblique bands. In this thesis, we study the onset of turbulence in channel flow in direct numerical simulations from a dynamical system theory perspective, as well as by performing experiments in a large aspect ratio channel.
The aim of the experimental work is to determine the critical Reynolds number where turbulence first becomes sustained. Recently, the onset of turbulence has been described in analogy to absorbing state phase transition (i.e. directed percolation). In particular, it has been shown that the critical point can be estimated from the competition between spreading and decay processes. Here, by performing experiments, we identify the mechanisms underlying turbulence proliferation in channel flow and find the critical Reynolds number, above which turbulence becomes sustained. Above the critical point, the continuous growth at the tip of the stripes outweighs the stochastic shedding of turbulent patches at the tail and the stripes expand. For growing stripes, the probability to decay decreases while the probability of stripe splitting increases. Consequently, and unlike for the puffs in pipe flow, neither of these two processes is time-independent i.e. memoryless. Coupling between stripe expansion and creation of new stripes via splitting leads to a significantly lower critical point ($Re_c=670+/-10$) than most earlier studies suggest.
While the above approach sheds light on how turbulence first becomes sustained, it provides no insight into the origin of the stripes themselves. In the numerical part of the thesis we investigate how turbulent stripes form from invariant solutions of the Navier-Stokes equations. The origin of these turbulent stripes can be identified by applying concepts from the dynamical system theory. In doing so, we identify the exact coherent structures underlying stripes and their bifurcations and how they give rise to the turbulent attractor in phase space. We first report a family of localized nonlinear traveling wave solutions of the Navier-Stokes equations in channel flow. These solutions show structural similarities with turbulent stripes in experiments like obliqueness, quasi-streamwise streaks and vortices, etc. A parametric study of these traveling wave solution is performed, with parameters like Reynolds number, stripe tilt angle and domain size, including the stability of the solutions. These solutions emerge through saddle-node bifurcations and form a phase space skeleton for the turbulent stripes observed in the experiments. The lower branches of these TW solutions at different tilt angles undergo Hopf bifurcation and new solutions branches of relative periodic orbits emerge. These RPO solutions do not belong to the same family and therefore the routes to chaos for different angles are different.
In shear flows, turbulence at onset is transient in nature. Consequently,turbulence can not be tracked to lower Reynolds numbers, where the dynamics may simplify. Before this happens, turbulence becomes short-lived and laminarizes. In the last part of the thesis, we show that using numerical simulations we can continue turbulent stripes in channel flow past the 'relaminarization barrier' all the way to their origin. Here, turbulent stripe dynamics simplifies and the fluctuations are no longer stochastic and the stripe settles down to a relative periodic orbit. This relative periodic orbit originates from the aforementioned traveling wave solutions. Starting from the relative periodic orbit, a small increase in speed i.e. Reynolds number gives rise to chaos and the attractor dimension sharply increases in contrast to the classical transition scenario where the instabilities affect the flow globally and give rise to much more gradual route to turbulence.},
author = {Paranjape, Chaitanya S},
issn = {2663-337X},
keyword = {Instabilities, Turbulence, Nonlinear dynamics},
pages = {138},
publisher = {IST Austria},
title = {{Onset of turbulence in plane Poiseuille flow}},
doi = {10.15479/AT:ISTA:6957},
year = {2019},
}
@article{6844,
abstract = {Studying the progression of the proliferative and differentiative patterns of neural stem cells at the individual cell level is crucial to the understanding of cortex development and how the disruption of such patterns can lead to malformations and neurodevelopmental diseases. However, our understanding of the precise lineage progression programme at single-cell resolution is still incomplete due to the technical variations in lineage- tracing approaches. One of the key challenges involves developing a robust theoretical framework in which we can integrate experimental observations and introduce correction factors to obtain a reliable and representative description of the temporal modulation of proliferation and differentiation. In order to obtain more conclusive insights, we carry out virtual clonal analysis using mathematical modelling and compare our results against experimental data. Using a dataset obtained with Mosaic Analysis with Double Markers, we illustrate how the theoretical description can be exploited to interpret and reconcile the disparity between virtual and experimental results.},
author = {Picco, Noemi and Hippenmeyer, Simon and Rodarte, Julio and Streicher, Carmen and Molnár, Zoltán and Maini, Philip K. and Woolley, Thomas E.},
issn = {1469-7580},
journal = {Journal of Anatomy},
number = {3},
pages = {686--696},
publisher = {Wiley},
title = {{A mathematical insight into cell labelling experiments for clonal analysis}},
doi = {10.1111/joa.13001},
volume = {235},
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{6899,
abstract = {Intra-organ communication guides morphogenetic processes that are essential for an organ to carry out complex physiological functions. In the heart, the growth of the myocardium is tightly coupled to that of the endocardium, a specialized endothelial tissue that lines its interior. Several molecular pathways have been implicated in the communication between these tissues including secreted factors, components of the extracellular matrix, or proteins involved in cell-cell communication. Yet, it is unknown how the growth of the endocardium is coordinated with that of the myocardium. Here, we show that an increased expansion of the myocardial atrial chamber volume generates higher junctional forces within endocardial cells. This leads to biomechanical signaling involving VE-cadherin, triggering nuclear localization of the Hippo pathway transcriptional regulator Yap1 and endocardial proliferation. Our work suggests that the growth of the endocardium results from myocardial chamber volume expansion and ends when the tension on the tissue is relaxed.},
author = {Bornhorst, Dorothee and Xia, Peng and Nakajima, Hiroyuki and Dingare, Chaitanya and Herzog, Wiebke and Lecaudey, Virginie and Mochizuki, Naoki and Heisenberg, Carl-Philipp J and Yelon, Deborah and Abdelilah-Seyfried, Salim},
issn = {20411723},
journal = {Nature communications},
number = {1},
pages = {4113},
publisher = {Nature Publishing Group},
title = {{Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions}},
doi = {10.1038/s41467-019-12068-x},
volume = {10},
year = {2019},
}
@inproceedings{6887,
abstract = {The fundamental model-checking problem, given as input a model and a specification, asks for the algorithmic verification of whether the model satisfies the specification. Two classical models for reactive systems are graphs and Markov decision processes (MDPs). A basic specification formalism in the verification of reactive systems is the strong fairness (aka Streett) objective, where given different types of requests and corresponding grants, the requirement is that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All omega-regular objectives can be expressed as Streett objectives and hence they are canonical in verification. Consider graphs/MDPs with n vertices, m edges, and a Streett objectives with k pairs, and let b denote the size of the description of the Streett objective for the sets of requests and grants. The current best-known algorithm for the problem requires time O(min(n^2, m sqrt{m log n}) + b log n). In this work we present randomized near-linear time algorithms, with expected running time O~(m + b), where the O~ notation hides poly-log factors. Our randomized algorithms are near-linear in the size of the input, and hence optimal up to poly-log factors. },
author = {Chatterjee, Krishnendu and Dvorák, Wolfgang and Henzinger, Monika and Svozil, Alexander},
booktitle = {Leibniz International Proceedings in Informatics},
location = {Amsterdam, Netherlands},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Near-linear time algorithms for Streett objectives in graphs and MDPs}},
doi = {10.4230/LIPICS.CONCUR.2019.7},
volume = {140},
year = {2019},
}
@article{7056,
abstract = {In the Ca1−x La x FeAs2 (1 1 2) family of pnictide superconductors, we have investigated a highly overdoped composition (x = 0.56), prepared by a high-pressure, high-temperature synthesis. Magnetic measurements show an antiferromagnetic transition at T N = 120 K, well above the one at lower doping (0.15 < x < 0.27).
Below the onset of long-range magnetic order at T N, the electrical resistivity is strongly reduced and is dominated by electron–electron interactions, as evident from its temperature dependence. The Seebeck coefficient shows a clear metallic behavior as in narrow band conductors. The temperature dependence of the Hall coefficient and the violation of Kohler's rule agree with the multiband character of the material. No superconductivity was observed down to 1.8 K. The success of the high-pressure synthesis encourages further investigations of the so far only partially explored phase diagram in this family of Iron-based high temperature superconductors.
},
author = {Martino, Edoardo and Bachmann, Maja D and Rossi, Lidia and Modic, Kimberly A and Zivkovic, Ivica and Rønnow, Henrik M and Moll, Philip J W and Akrap, Ana and Forró, László and Katrych, Sergiy},
issn = {1361-648X},
journal = {Journal of Physics: Condensed Matter},
number = {48},
publisher = {IOP Publishing},
title = {{Persistent antiferromagnetic order in heavily overdoped Ca1−x La x FeAs2}},
doi = {10.1088/1361-648x/ab3b43},
volume = {31},
year = {2019},
}
@article{7013,
abstract = {Chains of superconducting circuit devices provide a natural platform for studies of synthetic bosonic quantum matter. Motivated by the recent experimental progress in realizing disordered and interacting chains of superconducting transmon devices, we study the bosonic many-body localization phase transition using the methods of exact diagonalization as well as matrix product state dynamics. We estimate the location of transition separating the ergodic and the many-body localized phases as a function of the disorder strength and the many-body on-site interaction strength. The main difference between the bosonic model realized by superconducting circuits and similar fermionic model is that the effect of the on-site interaction is stronger due to the possibility of multiple excitations occupying the same site. The phase transition is found to be robust upon including longer-range hopping and interaction terms present in the experiments. Furthermore, we calculate experimentally relevant local observables and show that their temporal fluctuations can be used to distinguish between the dynamics of Anderson insulator, many-body localization, and delocalized phases. While we consider unitary dynamics, neglecting the effects of dissipation, decoherence, and measurement back action, the timescales on which the dynamics is unitary are sufficient for observation of characteristic dynamics in the many-body localized phase. Moreover, the experimentally available disorder strength and interactions allow for tuning the many-body localization phase transition, thus making the arrays of superconducting circuit devices a promising platform for exploring localization physics and phase transition.},
author = {Orell, Tuure and Michailidis, Alexios and Serbyn, Maksym and Silveri, Matti},
issn = {2469-9950},
journal = {Physical Review B},
number = {13},
publisher = {APS},
title = {{Probing the many-body localization phase transition with superconducting circuits}},
doi = {10.1103/physrevb.100.134504},
volume = {100},
year = {2019},
}
@article{6983,
abstract = {Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver.},
author = {Kelemen, Réka K and Rajakaruna, H and Cockburn, IA and Ganusov, VV},
issn = {1664-3224},
journal = {Frontiers in Immunology},
publisher = {Frontiers},
title = {{Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells}},
doi = {10.3389/fimmu.2019.02153},
volume = {10},
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{7145,
abstract = {End-to-end correlated bound states are investigated in superconductor-semiconductor hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently identified from each wire end, and a cross-correlation function is computed that counts end-to-end coincidences, averaging over thousands of subgap features. Strong correlations in a short, 300-nm device are reduced by a factor of 4 in a long, 900-nm device. In addition, subgap conductance distributions are investigated, and correlations between the left and right distributions are identified based on their mutual information.},
author = {Anselmetti, G. L. R. and Martinez, E. A. and Ménard, G. C. and Puglia, D. and Malinowski, F. K. and Lee, J. S. and Choi, S. and Pendharkar, M. and Palmstrøm, C. J. and Marcus, C. M. and Casparis, L. and Higginbotham, Andrew P},
issn = {2469-9969},
journal = {Physical Review B},
number = {20},
publisher = {APS},
title = {{End-to-end correlated subgap states in hybrid nanowires}},
doi = {10.1103/physrevb.100.205412},
volume = {100},
year = {2019},
}