@article{6511,
abstract = {Let U and V be two independent N by N random matrices that are distributed according to Haar measure on U(N). Let Σ be a nonnegative deterministic N by N matrix. The single ring theorem [Ann. of Math. (2) 174 (2011) 1189–1217] asserts that the empirical eigenvalue distribution of the matrix X:=UΣV∗ converges weakly, in the limit of large N, to a deterministic measure which is supported on a single ring centered at the origin in ℂ. Within the bulk regime, that is, in the interior of the single ring, we establish the convergence of the empirical eigenvalue distribution on the optimal local scale of order N−1/2+ε and establish the optimal convergence rate. The same results hold true when U and V are Haar distributed on O(N).},
author = {Bao, Zhigang and Erdös, László and Schnelli, Kevin},
issn = {00911798},
journal = {Annals of Probability},
number = {3},
pages = {1270--1334},
publisher = {Project Euclid},
title = {{Local single ring theorem on optimal scale}},
doi = {10.1214/18-AOP1284},
volume = {47},
year = {2019},
}
@inproceedings{6528,
abstract = {We construct a verifiable delay function (VDF) by showing how the Rivest-Shamir-Wagner time-lock puzzle can be made publicly verifiable. Concretely, we give a statistically sound public-coin protocol to prove that a tuple (N,x,T,y) satisfies y=x2T (mod N) where the prover doesn’t know the factorization of N and its running time is dominated by solving the puzzle, that is, compute x2T, which is conjectured to require T sequential squarings. To get a VDF we make this protocol non-interactive using the Fiat-Shamir heuristic.The motivation for this work comes from the Chia blockchain design, which uses a VDF as akey ingredient. For typical parameters (T≤2 40, N= 2048), our proofs are of size around 10K B, verification cost around three RSA exponentiations and computing the proof is 8000 times faster than solving the puzzle even without any parallelism.},
author = {Pietrzak, Krzysztof Z},
booktitle = {10th Innovations in Theoretical Computer Science Conference},
isbn = {978-3-95977-095-8},
issn = {1868-8969},
location = {San Diego, CA, United States},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Simple verifiable delay functions}},
doi = {10.4230/LIPICS.ITCS.2019.60},
volume = {124},
year = {2019},
}
@article{6617,
abstract = {The effective large-scale properties of materials with random heterogeneities on a small scale are typically determined by the method of representative volumes: a sample of the random material is chosen—the representative volume—and its effective properties are computed by the cell formula. Intuitively, for a fixed sample size it should be possible to increase the accuracy of the method by choosing a material sample which captures the statistical properties of the material particularly well; for example, for a composite material consisting of two constituents, one would select a representative volume in which the volume fraction of the constituents matches closely with their volume fraction in the overall material. Inspired by similar attempts in materials science, Le Bris, Legoll and Minvielle have designed a selection approach for representative volumes which performs remarkably well in numerical examples of linear materials with moderate contrast. In the present work, we provide a rigorous analysis of this selection approach for representative volumes in the context of stochastic homogenization of linear elliptic equations. In particular, we prove that the method essentially never performs worse than a random selection of the material sample and may perform much better if the selection criterion for the material samples is chosen suitably.},
author = {Fischer, Julian L},
journal = {Archive for Rational Mechanics and Analysis},
publisher = {Springer},
title = {{The choice of representative volumes in the approximation of effective properties of random materials}},
doi = {10.1007/s00205-019-01400-w},
year = {2019},
}
@inproceedings{6648,
abstract = {Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory
needed for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context.},
author = {Edelsbrunner, Herbert and Virk, Ziga and Wagner, Hubert},
booktitle = {35th International Symposium on Computational Geometry},
isbn = {9783959771047},
location = {Portland, OR, United States},
pages = {31:1--31:14},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Topological data analysis in information space}},
doi = {10.4230/LIPICS.SOCG.2019.31},
volume = {129},
year = {2019},
}
@article{6477,
abstract = {Thermalizing quantum systems are conventionallydescribed by statistical mechanics at equilib-rium. However, not all systems fall into this category, with many-body localization providinga generic mechanism for thermalization to fail in strongly disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators at nonzero temperature, which do notthermalize and therefore cannot be describedusing statistical mechanics. This Colloquiumreviews recent theoretical and experimental advances in studies of MBL systems, focusing onthe new perspective provided by entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically, MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal integrals of motion emerges, which provides an intuitive explanationof the breakdown of thermalization. A description based on quasilocal integrals of motion isused to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement, the behavior of local observables, and the response to external dissipativeprocesses. Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing of the quantum-to-classical transitionbetween many-body localized and ergodic phasesand anomalous transport in the vicinity of that transition. Experimentally, synthetic quantumsystems, which are well isolated from an external thermal reservoir, provide natural platforms forrealizing the MBL phase. Recent experiments with ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in which different signatures of many-body localization have beenobserved, are reviewed. This Colloquium concludes by listing outstanding challenges andpromising future research directions.},
author = {Abanin, Dmitry A. and Altman, Ehud and Bloch, Immanuel and Serbyn, Maksym},
issn = {0034-6861},
journal = {Reviews of Modern Physics},
number = {2},
publisher = {APS Physics},
title = {{Colloquium: Many-body localization, thermalization, and entanglement}},
doi = {10.1103/revmodphys.91.021001},
volume = {91},
year = {2019},
}
@article{6650,
abstract = {We propose a novel technique for the automatic design of molds to cast highly complex shapes. The technique generates composite, two-piece molds. Each mold piece is made up of a hard plastic shell and a flexible silicone part. Thanks to the thin, soft, and smartly shaped silicone part, which is kept in place by a hard plastic shell, we can cast objects of unprecedented complexity. An innovative algorithm based on a volumetric analysis defines the layout of the internal cuts in the silicone mold part. Our approach can robustly handle thin protruding features and intertwined topologies that have caused previous methods to fail. We compare our results with state of the art techniques, and we demonstrate the casting of shapes with extremely complex geometry.},
author = {Alderighi, Thomas and Malomo, Luigi and Giorgi, Daniela and Bickel, Bernd and Cignoni, Paolo and Pietroni, Nico},
issn = {0730-0301},
journal = {ACM Transactions on Graphics},
number = {4},
publisher = {ACM},
title = {{Volume-aware design of composite molds}},
doi = {10.1145/3306346.3322981},
volume = {38},
year = {2019},
}
@article{6756,
abstract = {We study the topology generated by the temperature fluctuations of the cosmic microwave background (CMB) radiation, as quantified by the number of components and holes, formally given by the Betti numbers, in the growing excursion sets. We compare CMB maps observed by the Planck satellite with a thousand simulated maps generated according to the ΛCDM paradigm with Gaussian distributed fluctuations. The comparison is multi-scale, being performed on a sequence of degraded maps with mean pixel separation ranging from 0.05 to 7.33°. The survey of the CMB over 𝕊2 is incomplete due to obfuscation effects by bright point sources and other extended foreground objects like our own galaxy. To deal with such situations, where analysis in the presence of “masks” is of importance, we introduce the concept of relative homology. The parametric χ2-test shows differences between observations and simulations, yielding p-values at percent to less than permil levels roughly between 2 and 7°, with the difference in the number of components and holes peaking at more than 3σ sporadically at these scales. The highest observed deviation between the observations and simulations for b0 and b1 is approximately between 3σ and 4σ at scales of 3–7°. There are reports of mildly unusual behaviour of the Euler characteristic at 3.66° in the literature, computed from independent measurements of the CMB temperature fluctuations by Planck’s predecessor, the Wilkinson Microwave Anisotropy Probe (WMAP) satellite. The mildly anomalous behaviour of the Euler characteristic is phenomenologically related to the strongly anomalous behaviour of components and holes, or the zeroth and first Betti numbers, respectively. Further, since these topological descriptors show consistent anomalous behaviour over independent measurements of Planck and WMAP, instrumental and systematic errors may be an unlikely source. These are also the scales at which the observed maps exhibit low variance compared to the simulations, and approximately the range of scales at which the power spectrum exhibits a dip with respect to the theoretical model. Non-parametric tests show even stronger differences at almost all scales. Crucially, Gaussian simulations based on power-spectrum matching the characteristics of the observed dipped power spectrum are not able to resolve the anomaly. Understanding the origin of the anomalies in the CMB, whether cosmological in nature or arising due to late-time effects, is an extremely challenging task. Regardless, beyond the trivial possibility that this may still be a manifestation of an extreme Gaussian case, these observations, along with the super-horizon scales involved, may motivate the study of primordial non-Gaussianity. Alternative scenarios worth exploring may be models with non-trivial topology, including topological defect models.},
author = {Pranav, Pratyush and Adler, Robert J. and Buchert, Thomas and Edelsbrunner, Herbert and Jones, Bernard J.T. and Schwartzman, Armin and Wagner, Hubert and Van De Weygaert, Rien},
issn = {14320746},
journal = {Astronomy and Astrophysics},
publisher = {EDP Sciences},
title = {{Unexpected topology of the temperature fluctuations in the cosmic microwave background}},
doi = {10.1051/0004-6361/201834916},
volume = {627},
year = {2019},
}
@article{6819,
abstract = {Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome.},
author = {Antoniou, Michael N. and Nicolas, Armel and Mesnage, Robin and Biserni, Martina and Rao, Francesco V. and Martin, Cristina Vazquez},
issn = {1756-0500},
journal = {BMC Research Notes},
publisher = {Springer Nature},
title = {{Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells}},
doi = {10.1186/s13104-019-4534-3},
volume = {12},
year = {2019},
}
@article{6840,
abstract = {We discuss thermodynamic properties of harmonically trapped
imperfect quantum gases. The spatial inhomogeneity of these systems imposes
a redefinition of the mean-field interparticle potential energy as compared
to the homogeneous case. In our approach, it takes the form a
2N2 ωd, where
N is the number of particles, ω—the harmonic trap frequency, d—system’s
dimensionality, and a is a parameter characterizing the interparticle interaction.
We provide arguments that this model corresponds to the limiting case of
a long-ranged interparticle potential of vanishingly small amplitude. This
conclusion is drawn from a computation similar to the well-known Kac scaling
procedure, which is presented here in a form adapted to the case of an isotropic
harmonic trap. We show that within the model, the imperfect gas of trapped
repulsive bosons undergoes the Bose–Einstein condensation provided d > 1.
The main result of our analysis is that in d = 1 the gas of attractive imperfect
fermions with a = −aF < 0 is thermodynamically equivalent to the gas of
repulsive bosons with a = aB > 0 provided the parameters aF and aB fulfill
the relation aB + aF = . This result supplements similar recent conclusion
about thermodynamic equivalence of two-dimensional (2D) uniform imperfect
repulsive Bose and attractive Fermi gases.},
author = {Mysliwy, Krzysztof and Napiórkowski, Marek},
issn = {1742-5468},
journal = {Journal of Statistical Mechanics: Theory and Experiment},
number = {6},
publisher = {IOP Publishing},
title = {{Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps}},
doi = {10.1088/1742-5468/ab190d},
volume = {2019},
year = {2019},
}
@phdthesis{6681,
abstract = {The first part of the thesis considers the computational aspects of the homotopy groups πd(X) of a topological space X. It is well known that there is no algorithm to decide whether the fundamental group π1(X) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute the higher homotopy group πd(X) for any given d ≥ 2.
However, these algorithms come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of πd(X). We present an algorithm that, given a simply connected space X, computes πd(X) and represents its elements as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed d, the algorithm runs in time exponential in size(X), the number of simplices of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,
we construct a family of simply connected spaces X such that for any simplicial map representing a generator of πd(X), the size of the triangulation of S d on which the map is defined, is exponential in size(X).
In the second part of the thesis, we prove that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋, k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable range: Given a finite simplicial complex K of dimension k, decide whether there exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space.},
author = {Zhechev, Stephan Y},
issn = {2663-337X},
pages = {104},
publisher = {IST Austria},
title = {{Algorithmic aspects of homotopy theory and embeddability}},
doi = {10.15479/AT:ISTA:6681},
year = {2019},
}
@phdthesis{6179,
abstract = {In the first part of this thesis we consider large random matrices with arbitrary expectation and a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic control of a multivariate cumulant expansion.
In the second part we consider Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are uni- versal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner- Dyson-Mehta universality conjecture for the last remaining universality type. Our analysis holds not only for exact cusps, but approximate cusps as well, where an ex- tended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow- nian motion to the cusp regime.
In the third and final part we explore the entrywise linear statistics of Wigner ma- trices and identify the fluctuations for a large class of test functions with little regularity. This enables us to study the rectangular Young diagram obtained from the interlacing eigenvalues of the random matrix and its minor, and we find that, despite having the same limit, the fluctuations differ from those of the algebraic Young tableaux equipped with the Plancharel measure.},
author = {Schröder, Dominik J},
pages = {375},
publisher = {IST Austria},
title = {{From Dyson to Pearcey: Universal statistics in random matrix theory}},
doi = {10.15479/AT:ISTA:th6179},
year = {2019},
}
@article{6857,
abstract = {Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.
The recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop.},
author = {Giese, B and Friess, J L and Schetelig, M F and Barton, Nicholas H and Messer, Philip and Debarre, Florence and Meimberg, H and Windbichler, N and Boete, C},
journal = {BioEssays},
publisher = {Wiley},
title = {{Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna}},
doi = {10.1002/bies.201900151},
year = {2019},
}
@article{138,
abstract = {Autoregulation is the direct modulation of gene expression by the product of the corresponding gene. Autoregulation of bacterial gene expression has been mostly studied at the transcriptional level, when a protein acts as the cognate transcriptional repressor. A recent study investigating dynamics of the bacterial toxin–antitoxin MazEF system has shown how autoregulation at both the transcriptional and post-transcriptional levels affects the heterogeneity of Escherichia coli populations. Toxin–antitoxin systems hold a crucial but still elusive part in bacterial response to stress. This perspective highlights how these modules can also serve as a great model system for investigating basic concepts in gene regulation. However, as the genomic background and environmental conditions substantially influence toxin activation, it is important to study (auto)regulation of toxin–antitoxin systems in well-defined setups as well as in conditions that resemble the environmental niche.},
author = {Nikolic, Nela},
journal = {Current Genetics},
number = {1},
pages = {133--138},
publisher = {Springer},
title = {{Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system}},
doi = {10.1007/s00294-018-0879-8},
volume = {65},
year = {2019},
}
@article{405,
abstract = {We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently.},
author = {Virosztek, Daniel},
journal = {Linear Algebra and Its Applications},
pages = {67--78},
publisher = {Elsevier},
title = {{Jointly convex quantum Jensen divergences}},
doi = {10.1016/j.laa.2018.03.002},
volume = {576},
year = {2019},
}
@article{5944,
abstract = {Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10−13J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it.},
author = {Corominas-Murtra, Bernat},
issn = {20751729},
journal = {Life},
number = {1},
publisher = {MDPI},
title = {{Thermodynamics of duplication thresholds in synthetic protocell systems}},
doi = {10.3390/life9010009},
volume = {9},
year = {2019},
}
@article{5886,
abstract = {Problems involving quantum impurities, in which one or a few particles are interacting with a macroscopic environment, represent a pervasive paradigm, spanning across atomic, molecular, and condensed-matter physics. In this paper we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron–a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon–a quasiparticle formed out of a rotating molecule in a bosonic bath. We benchmark these approaches against established theories, evaluating their accuracy as a function of the impurity-bath coupling.},
author = {Li, Xiang and Bighin, Giacomo and Yakaboylu, Enderalp and Lemeshko, Mikhail},
issn = {00268976},
journal = {Molecular Physics},
publisher = {Taylor and Francis},
title = {{Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon}},
doi = {10.1080/00268976.2019.1567852},
year = {2019},
}
@article{6029,
abstract = {Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 μm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy.},
author = {Lindner, Marco and Tresztenyak, Aliz and Fülöp, Gergö and Jahr, Wiebke and Prinz, Adrian and Prinz, Iris and Danzl, Johann G and Schütz, Gerhard J. and Sevcsik, Eva},
issn = {22962646},
journal = {Frontiers in Chemistry},
publisher = {Frontiers Media S.A.},
title = {{A fast and simple contact printing approach to generate 2D protein nanopatterns}},
doi = {10.3389/fchem.2018.00655},
volume = {6},
year = {2019},
}
@article{6050,
abstract = {We answer a question of David Hilbert: given two circles it is not possible in general to construct their centers using only a straightedge. On the other hand, we give infinitely many families of pairs of circles for which such construction is possible. },
author = {Akopyan, Arseniy and Fedorov, Roman},
journal = {Proceedings of the American Mathematical Society},
pages = {91--102},
publisher = {AMS},
title = {{Two circles and only a straightedge}},
doi = {10.1090/proc/14240},
volume = {147},
year = {2019},
}
@article{6086,
abstract = {We show that linear analytic cocycles where all Lyapunov exponents are negative infinite are nilpotent. For such one-frequency cocycles we show that they can be analytically conjugated to an upper triangular cocycle or a Jordan normal form. As a consequence, an arbitrarily small analytic perturbation leads to distinct Lyapunov exponents. Moreover, in the one-frequency case where the th Lyapunov exponent is finite and the st negative infinite, we obtain a simple criterion for domination in which case there is a splitting into a nilpotent part and an invertible part.},
author = {Sadel, Christian and Xu, Disheng},
journal = {Ergodic Theory and Dynamical Systems},
number = {4},
pages = {1082--1098},
publisher = {Cambridge University Press},
title = {{Singular analytic linear cocycles with negative infinite Lyapunov exponents}},
doi = {10.1017/etds.2017.52},
volume = {39},
year = {2019},
}
@article{6093,
abstract = {Blebs are cellular protrusions observed in migrating cells and in cells undergoing spreading, cytokinesis, and apoptosis. Here we investigate the flow of cytoplasm during bleb formation and the concurrent changes in cell volume using zebrafish primordial germ cells (PGCs) as an in vivo model. We show that bleb inflation occurs concomitantly with cytoplasmic inflow into it and that during this process the total cell volume does not change. We thus show that bleb formation in primordial germ cells results primarily from redistribution of material within the cell rather than being driven by flow of water from an external source.},
author = {Goudarzi, Mohammad and Boquet-Pujadas, Aleix and Olivo-Marin, Jean Christophe and Raz, Erez},
journal = {PLOS ONE},
number = {2},
publisher = {Public Library of Science},
title = {{Fluid dynamics during bleb formation in migrating cells in vivo}},
doi = {10.1371/journal.pone.0212699},
volume = {14},
year = {2019},
}
@article{6310,
abstract = {An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariskiopen subset of an arbitrary smooth biquadratic hypersurface in sufficiently many variables. The proof uses the Hardy–Littlewood circle method.},
author = {Browning, Timothy D and Hu, L.Q.},
issn = {10902082},
journal = {Advances in Mathematics},
pages = {920--940},
publisher = {Elsevier},
title = {{ Counting rational points on biquadratic hypersurfaces}},
doi = {10.1016/j.aim.2019.04.031},
volume = {349},
year = {2019},
}
@article{6454,
abstract = {Adult neural stem cells and multiciliated ependymalcells are glial cells essential for neurological func-tions. Together, they make up the adult neurogenicniche. Using both high-throughput clonal analysisand single-cell resolution of progenitor division pat-terns and fate, we show that these two componentsof the neurogenic niche are lineally related: adult neu-ral stem cells are sister cells to ependymal cells,whereas most ependymal cells arise from the termi-nal symmetric divisions of the lineage. Unexpectedly,we found that the antagonist regulators of DNA repli-cation, GemC1 and Geminin, can tune the proportionof neural stem cells and ependymal cells. Our find-ings reveal the controlled dynamic of the neurogenicniche ontogeny and identify the Geminin familymembers as key regulators of the initial pool of adultneural stem cells.},
author = {Ortiz-Álvarez, G and Daclin, M and Shihavuddin, A and Lansade, P and Fortoul, A and Faucourt, M and Clavreul, S and Lalioti, ME and Taraviras, S and Hippenmeyer, Simon and Livet, J and Meunier, A and Genovesio, A and Spassky, N},
issn = {0896-6273},
journal = {Neuron},
number = {1},
pages = {159--172.e7},
publisher = {Elsevier},
title = {{Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members}},
doi = {10.1016/j.neuron.2019.01.051},
volume = {102},
year = {2019},
}
@article{6466,
abstract = {One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One
problem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the
study is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates.},
author = {Field, David and Fraisse, Christelle},
issn = {1365294X},
journal = {Molecular ecology},
number = {7},
pages = {1579--1581},
publisher = {Wiley},
title = {{Breaking down barriers in morning glories}},
doi = {10.1111/mec.15048},
volume = {28},
year = {2019},
}
@article{6586,
abstract = {The bottom-up assembly of colloidal nanocrystals is a versatile methodology to produce composite nanomaterials with precisely tuned electronic properties. Beyond the synthetic control over crystal domain size, shape, crystal phase, and composition, solution-processed nanocrystals allow exquisite surface engineering. This provides additional means to modulate the nanomaterial characteristics and particularly its electronic transport properties. For instance, inorganic surface ligands can be used to tune the type and concentration of majority carriers or to modify the electronic band structure. Herein, we report the thermoelectric properties of SnTe nanocomposites obtained from the consolidation of surface-engineered SnTe nanocrystals into macroscopic pellets. A CdSe-based ligand is selected to (i) converge the light and heavy bands through partial Cd alloying and (ii) generate CdSe nanoinclusions as a secondary phase within the SnTe matrix, thereby reducing the thermal conductivity. These SnTe-CdSe nanocomposites possess thermoelectric figures of merit of up to 1.3 at 850 K, which is, to the best of our knowledge, the highest thermoelectric figure of merit reported for solution-processed SnTe.},
author = {Ibáñez, Maria and Hasler, Roger and Genç, Aziz and Liu, Yu and Kuster, Beatrice and Schuster, Maximilian and Dobrozhan, Oleksandr and Cadavid, Doris and Arbiol, Jordi and Cabot, Andreu and Kovalenko, Maksym V.},
issn = {0002-7863},
journal = {Journal of the American Chemical Society},
number = {20},
pages = {8025--8029},
publisher = {ACS},
title = {{Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion}},
doi = {10.1021/jacs.9b01394},
volume = {141},
year = {2019},
}
@article{6620,
abstract = {This paper establishes an asymptotic formula with a power-saving error term for the number of rational points of bounded height on the singular cubic surface of ℙ3ℚ given by the following equation 𝑥0(𝑥21+𝑥22)−𝑥33=0 in agreement with the Manin-Peyre conjectures.
},
author = {De La Bretèche, Régis and Destagnol, Kevin N and Liu, Jianya and Wu, Jie and Zhao, Yongqiang},
issn = {16747283},
journal = {Science China Mathematics},
publisher = {Springer},
title = {{On a certain non-split cubic surface}},
doi = {10.1007/s11425-018-9543-8},
year = {2019},
}
@article{6632,
abstract = {We consider a two-component Bose gas in two dimensions at a low temperature with short-range repulsive interaction. In the coexistence phase where both components are superfluid, interspecies interactions induce a nondissipative drag between the two superfluid flows (Andreev-Bashkin effect). We show that this behavior leads to a modification of the usual Berezinskii-Kosterlitz-Thouless (BKT) transition in two dimensions. We extend the renormalization of the superfluid densities at finite temperature using the renormalization-group approach and find that the vortices of one component have a large influence on the superfluid properties of the other, mediated by the nondissipative drag. The extended BKT flow equations indicate that the occurrence of the vortex unbinding transition in one of the components can induce the breakdown of superfluidity also in the other, leading to a locking phenomenon for the critical temperatures of the two gases.},
author = {Karle, Volker and Defenu, Nicolò and Enss, Tilman},
issn = {24699934},
journal = {Physical Review A},
number = {6},
publisher = {APS},
title = {{Coupled superfluidity of binary Bose mixtures in two dimensions}},
doi = {10.1103/PhysRevA.99.063627},
volume = {99},
year = {2019},
}
@article{6637,
abstract = {The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.},
author = {Trubenova, Barbora and Krejca, Martin and Lehre, Per Kristian and Kötzing, Timo},
journal = {Evolution},
number = {7},
pages = {1356--1374},
publisher = {Wiley},
title = {{Surfing on the seascape: Adaptation in a changing environment}},
doi = {10.1111/evo.13784},
volume = {73},
year = {2019},
}
@article{6649,
abstract = {While Hartree–Fock theory is well established as a fundamental approximation for interacting fermions, it has been unclear how to describe corrections to it due to many-body correlations. In this paper we start from the Hartree–Fock state given by plane waves and introduce collective particle–hole pair excitations. These pairs can be approximately described by a bosonic quadratic Hamiltonian. We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type upper bound to the ground state energy. Our result justifies the random-phase approximation in the mean-field scaling regime, for repulsive, regular interaction potentials.
},
author = {Benedikter, Niels P and Nam, Phan Thành and Porta, Marcello and Schlein, Benjamin and Seiringer, Robert},
issn = {1432-0916},
journal = {Communications in Mathematical Physics},
publisher = {Springer},
title = {{Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime}},
doi = {10.1007/s00220-019-03505-5},
year = {2019},
}
@article{6795,
abstract = {The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations.},
author = {Trubenova, Barbora and Hager, Reinmar},
issn = {20457758},
journal = {Ecology and Evolution},
publisher = {Wiley},
title = {{Green beards in the light of indirect genetic effects}},
doi = {10.1002/ece3.5484},
year = {2019},
}
@article{6788,
abstract = {We consider the Nelson model with ultraviolet cutoff, which describes the interaction between non-relativistic particles and a positive or zero mass quantized scalar field. We take the non-relativistic particles to obey Fermi statistics and discuss the time evolution in a mean-field limit of many fermions. In this case, the limit is known to be also a semiclassical limit. We prove convergence in terms of reduced density matrices of the many-body state to a tensor product of a Slater determinant with semiclassical structure and a coherent state, which evolve according to a fermionic version of the Schrödinger–Klein–Gordon equations.},
author = {Leopold, Nikolai K and Petrat, Sören P},
issn = {1424-0661},
journal = {Annales Henri Poincare},
publisher = {Springer Nature},
title = {{Mean-field dynamics for the Nelson model with fermions}},
doi = {10.1007/s00023-019-00828-w},
year = {2019},
}
@inproceedings{6175,
abstract = {We consider the problem of expected cost analysis over nondeterministic probabilistic programs,
which aims at automated methods for analyzing the resource-usage of such programs.
Previous approaches for this problem could only handle nonnegative bounded costs.
However, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols,
both positive and negative costs are necessary and the costs are unbounded as well.
In this work, we present a sound and efficient approach to obtain polynomial bounds on the
expected accumulated cost of nondeterministic probabilistic programs.
Our approach can handle (a) general positive and negative costs with bounded updates in
variables; and (b) nonnegative costs with general updates to variables.
We show that several natural examples which could not be
handled by previous approaches are captured in our framework.
Moreover, our approach leads to an efficient polynomial-time algorithm, while no
previous approach for cost analysis of probabilistic programs could guarantee polynomial runtime.
Finally, we show the effectiveness of our approach using experimental results on a variety of programs for which we efficiently synthesize tight resource-usage bounds.},
author = {Wang, Peixin and Fu, Hongfei and Goharshady, Amir Kafshdar and Chatterjee, Krishnendu and Qin, Xudong and Shi, Wenjun},
booktitle = {40th ACM Conference on Programming Language Design and Implementation (PLDI 2019)},
keyword = {Program Cost Analysis, Program Termination, Probabilistic Programs, Martingales},
location = {Phoenix, AZ, United States},
pages = {204--220},
publisher = {Association for Computing Machinery},
title = {{Cost analysis of nondeterministic probabilistic programs}},
doi = {10.1145/3314221.3314581},
year = {2019},
}
@article{6442,
abstract = {This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples.},
author = {Schreck, Camille and Hafner, Christian and Wojtan, Christopher J},
journal = {ACM Transactions on Graphics},
number = {4},
publisher = {ACM},
title = {{Fundamental solutions for water wave animation}},
doi = {10.1145/3306346.3323002},
volume = {38},
year = {2019},
}
@article{6187,
abstract = {Aberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify a key conserved regulator that orchestrates O-glycosylation on a protein subset to activate a program governing migration steps important for both development and cancer metastasis.},
author = {Valosková, Katarina and Biebl, Julia and Roblek, Marko and Emtenani, Shamsi and György, Attila and Misova, Michaela and Ratheesh, Aparna and Rodrigues, Patricia and Shkarina, Katerina and Larsen, Ida Signe Bohse and Vakhrushev, Sergey Y and Clausen, Henrik and Siekhaus, Daria E},
issn = {2050-084X},
journal = {eLife},
publisher = {eLife Sciences Publications, Ltd},
title = {{A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion}},
doi = {10.7554/elife.41801},
volume = {8},
year = {2019},
}
@article{5949,
abstract = {Aberrant proteostasis of protein aggregation may lead to behavior disorders including chronic mental illnesses (CMI). Furthermore, the neuronal activity alterations that underlie CMI are not well understood. We recorded the local field potential and single-unit activity of the hippocampal CA1 region in vivo in rats transgenically overexpressing the Disrupted-in-Schizophrenia 1 (DISC1) gene (tgDISC1), modeling sporadic CMI. These tgDISC1 rats have previously been shown to exhibit DISC1 protein aggregation, disturbances in the dopaminergic system and attention-related deficits. Recordings were performed during exploration of familiar and novel open field environments and during sleep, allowing investigation of neuronal abnormalities in unconstrained behavior. Compared to controls, tgDISC1 place cells exhibited smaller place fields and decreased speed-modulation of their firing rates, demonstrating altered spatial coding and deficits in encoding location-independent sensory inputs. Oscillation analyses showed that tgDISC1 pyramidal neurons had higher theta phase locking strength during novelty, limiting their phase coding ability. However, their mean theta phases were more variable at the population level, reducing oscillatory network synchronization. Finally, tgDISC1 pyramidal neurons showed a lack of novelty-induced shift in their preferred theta and gamma firing phases, indicating deficits in coding of novel environments with oscillatory firing. By combining single cell and neuronal population analyses, we link DISC1 protein pathology with abnormal hippocampal neural coding and network synchrony, and thereby gain a more comprehensive understanding of CMI mechanisms.},
author = {Käfer, Karola and Malagon-Vina, Hugo and Dickerson, Desiree and O'Neill, Joseph and Trossbach, Svenja V. and Korth, Carsten and Csicsvari, Jozsef L},
journal = {Hippocampus},
publisher = {Wiley},
title = {{Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization}},
doi = {10.1002/hipo.23076},
year = {2019},
}
@article{6240,
abstract = {For a general class of large non-Hermitian random block matrices X we prove that there are no eigenvalues away from a deterministic set with very high probability. This set is obtained from the Dyson equation of the Hermitization of X as the self-consistent approximation of the pseudospectrum. We demonstrate that the analysis of the matrix Dyson equation from (Probab. Theory Related Fields (2018)) offers a unified treatment of many structured matrix ensembles.},
author = {Alt, Johannes and Erdös, László and Krüger, Torben H and Nemish, Yuriy},
issn = {02460203},
journal = {Annales de l'institut Henri Poincare},
number = {2},
pages = {661--696},
title = {{Location of the spectrum of Kronecker random matrices}},
doi = {10.1214/18-AIHP894},
volume = {55},
year = {2019},
}
@inproceedings{6884,
abstract = {In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the "bank" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding. },
author = {Avni, Guy and Henzinger, Thomas A and Zikelic, Dorde},
location = {Aachen, Germany},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Bidding mechanisms in graph games}},
doi = {10.4230/LIPICS.MFCS.2019.11},
volume = {138},
year = {2019},
}
@inproceedings{6889,
abstract = {We study Markov decision processes and turn-based stochastic games with parity conditions. There are three qualitative winning criteria, namely, sure winning, which requires all paths to satisfy the condition, almost-sure winning, which requires the condition to be satisfied with probability 1, and limit-sure winning, which requires the condition to be satisfied with probability arbitrarily close to 1. We study the combination of two of these criteria for parity conditions, e.g., there are two parity conditions one of which must be won surely, and the other almost-surely. The problem has been studied recently by Berthon et al. for MDPs with combination of sure and almost-sure winning, under infinite-memory strategies, and the problem has been established to be in NP cap co-NP. Even in MDPs there is a difference between finite-memory and infinite-memory strategies. Our main results for combination of sure and almost-sure winning are as follows: (a) we show that for MDPs with finite-memory strategies the problem is in NP cap co-NP; (b) we show that for turn-based stochastic games the problem is co-NP-complete, both for finite-memory and infinite-memory strategies; and (c) we present algorithmic results for the finite-memory case, both for MDPs and turn-based stochastic games, by reduction to non-stochastic parity games. In addition we show that all the above complexity results also carry over to combination of sure and limit-sure winning, and results for all other combinations can be derived from existing results in the literature. Thus we present a complete picture for the study of combinations of two qualitative winning criteria for parity conditions in MDPs and turn-based stochastic games. },
author = {Chatterjee, Krishnendu and Piterman, Nir},
location = {Amsterdam, Netherlands},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Combinations of Qualitative Winning for Stochastic Parity Games}},
doi = {10.4230/LIPICS.CONCUR.2019.6},
volume = {140},
year = {2019},
}
@article{6593,
abstract = {We consider the monotone variational inequality problem in a Hilbert space and describe a projection-type method with inertial terms under the following properties: (a) The method generates a strongly convergent iteration sequence; (b) The method requires, at each iteration, only one projection onto the feasible set and two evaluations of the operator; (c) The method is designed for variational inequality for which the underline operator is monotone and uniformly continuous; (d) The method includes an inertial term. The latter is also shown to speed up the convergence in our numerical results. A comparison with some related methods is given and indicates that the new method is promising.},
author = {Shehu, Yekini and Li, Xiao-Huan and Dong, Qiao-Li},
issn = {1017-1398},
journal = {Numerical Algorithms},
pages = {1--24},
publisher = {Springer Nature},
title = {{An efficient projection-type method for monotone variational inequalities in Hilbert spaces}},
doi = {10.1007/s11075-019-00758-y},
year = {2019},
}
@inproceedings{6935,
abstract = {This paper investigates the power of preprocessing in the CONGEST model. Schmid and Suomela (ACM HotSDN 2013) introduced the SUPPORTED CONGEST model to study the application of distributed algorithms in Software-Defined Networks (SDNs). In this paper, we show that a large class of lower bounds in the CONGEST model still hold in the SUPPORTED model, highlighting the robustness of these bounds. This also raises the question how much does
preprocessing help in the CONGEST model.},
author = {Foerster, Klaus-Tycho and Korhonen, Janne and Rybicki, Joel and Schmid, Stefan},
booktitle = {Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing},
isbn = {9781450362177},
location = {Toronto, ON, Canada},
pages = {259--261},
publisher = {ACM},
title = {{Does preprocessing help under congestion?}},
doi = {10.1145/3293611.3331581},
year = {2019},
}
@inproceedings{6822,
abstract = {In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the qualitative winner or quantitative payoff of the game. In bidding games, in each turn, we hold an auction between the two players to determine which player moves the token. Bidding games have largely been studied with concrete bidding mechanisms that are variants of a first-price auction: in each turn both players simultaneously submit bids, the higher
bidder moves the token, and pays his bid to the lower bidder in Richman bidding, to the bank in poorman bidding, and in taxman bidding, the bid is split between the other player and the bank according to a predefined constant factor. Bidding games are deterministic games. They have an intriguing connection with a fragment of stochastic games called
randomturn games. We study, for the first time, a combination of bidding games with probabilistic behavior; namely, we study bidding games that are played on Markov decision processes, where the players bid for the right to choose the next action, which determines the probability distribution according to which the next vertex is chosen. We study parity and meanpayoff bidding games on MDPs and extend results from the deterministic bidding setting to the probabilistic one.},
author = {Avni, Guy and Henzinger, Thomas A and Ibsen-Jensen, Rasmus and Novotny, Petr},
booktitle = { Proceedings of the 13th International Conference of Reachability Problems},
isbn = {978-303030805-6},
issn = {0302-9743},
location = {Brussels, Belgium},
pages = {1--12},
publisher = {Springer},
title = {{Bidding games on Markov decision processes}},
doi = {10.1007/978-3-030-30806-3_1},
volume = {11674},
year = {2019},
}
@inproceedings{6942,
abstract = {Graph games and Markov decision processes (MDPs) are standard models in reactive synthesis and verification of probabilistic systems with nondeterminism. The class of 𝜔 -regular winning conditions; e.g., safety, reachability, liveness, parity conditions; provides a robust and expressive specification formalism for properties that arise in analysis of reactive systems. The resolutions of nondeterminism in games and MDPs are represented as strategies, and we consider succinct representation of such strategies. The decision-tree data structure from machine learning retains the flavor of decisions of strategies and allows entropy-based minimization to obtain succinct trees. However, in contrast to traditional machine-learning problems where small errors are allowed, for winning strategies in graph games and MDPs no error is allowed, and the decision tree must represent the entire strategy. In this work we propose decision trees with linear classifiers for representation of strategies in graph games and MDPs. We have implemented strategy representation using this data structure and we present experimental results for problems on graph games and MDPs, which show that this new data structure presents a much more efficient strategy representation as compared to standard decision trees.},
author = {Ashok, Pranav and Brázdil, Tomáš and Chatterjee, Krishnendu and Křetínský, Jan and Lampert, Christoph and Toman, Viktor},
booktitle = {16th International Conference on Quantitative Evaluation of Systems},
isbn = {9783030302801},
issn = {0302-9743},
location = {Glasgow, United Kingdom},
pages = {109--128},
publisher = {Springer Nature},
title = {{Strategy representation by decision trees with linear classifiers}},
doi = {10.1007/978-3-030-30281-8_7},
volume = {11785},
year = {2019},
}
@article{5907,
abstract = {Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins.},
author = {Mócsai, Réka and Figl, Rudolf and Troschl, Clemens and Strasser, Richard and Svehla, Elisabeth and Windwarder, Markus and Thader, Andreas and Altmann, Friedrich},
journal = {Scientific Reports},
number = {1},
publisher = {Nature Publishing Group},
title = {{N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated}},
doi = {10.1038/s41598-018-36884-1},
volume = {9},
year = {2019},
}
@article{6102,
abstract = {Light is a union of electric and magnetic fields, and nowhere is the complex relationship between these fields more evident than in the near fields of nanophotonic structures. There, complicated electric and magnetic fields varying over subwavelength scales are generally present, which results in photonic phenomena such as extraordinary optical momentum, superchiral fields, and a complex spatial evolution of optical singularities. An understanding of such phenomena requires nanoscale measurements of the complete optical field vector. Although the sensitivity of near- field scanning optical microscopy to the complete electromagnetic field was recently demonstrated, a separation of different components required a priori knowledge of the sample. Here, we introduce a robust algorithm that can disentangle all six electric and magnetic field components from a single near-field measurement without any numerical modeling of the structure. As examples, we unravel the fields of two prototypical nanophotonic structures: a photonic crystal waveguide and a plasmonic nanowire. These results pave the way for new studies of complex photonic phenomena at the nanoscale and for the design of structures that optimize their optical behavior.},
author = {Le Feber, B. and Sipe, J. E. and Wulf, Matthias and Kuipers, L. and Rotenberg, N.},
issn = {20477538},
journal = {Light: Science and Applications},
number = {1},
publisher = {Springer Nature},
title = {{A full vectorial mapping of nanophotonic light fields}},
doi = {10.1038/s41377-019-0124-3},
volume = {8},
year = {2019},
}
@article{6025,
abstract = {Non-canonical Wnt signaling plays a central role for coordinated cell polarization and directed migration in metazoan development. While spatiotemporally restricted activation of non-canonical Wnt-signaling drives cell polarization in epithelial tissues, it remains unclear whether such instructive activity is also critical for directed mesenchymal cell migration. Here, we developed a light-activated version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm (prechordal plate, ppl) cell migration within the zebrafish gastrula. We found that Fz7 signaling is required for ppl cell protrusion formation and migration and that spatiotemporally restricted ectopic activation is capable of redirecting their migration. Finally, we show that uniform activation of Fz7 signaling in ppl cells fully rescues defective directed cell migration in fz7 mutant embryos. Together, our findings reveal that in contrast to the situation in epithelial cells, non-canonical Wnt signaling functions permissively rather than instructively in directed mesenchymal cell migration during gastrulation.},
author = {Capek, Daniel and Smutny, Michael and Tichy, Alexandra Madelaine and Morri, Maurizio and Janovjak, Harald L and Heisenberg, Carl-Philipp J},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration}},
doi = {10.7554/eLife.42093},
volume = {8},
year = {2019},
}
@article{6032,
abstract = {The main result of this article is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Using a reduction to even Δ-matroids, we then extend the tractability result to larger classes of Δ-matroids that we call efficiently coverable. It properly includes classes that were known to be tractable before, namely, co-independent, compact, local, linear, and binary, with the following caveat:We represent Δ-matroids by lists of tuples, while the last two use a representation by matrices. Since an n ×n matrix can represent exponentially many tuples, our tractability result is not strictly stronger than the known algorithm for linear and binary Δ-matroids.},
author = {Kazda, Alexandr and Kolmogorov, Vladimir and Rolinek, Michal},
journal = {ACM Transactions on Algorithms},
number = {2},
publisher = {ACM},
title = {{Even delta-matroids and the complexity of planar boolean CSPs}},
doi = {10.1145/3230649},
volume = {15},
year = {2019},
}
@article{6049,
abstract = {In this article it is shown that large systems with many interacting units endowing multiple phases display self-oscillations in the presence of linear feedback between the control and order parameters, where an Andronov–Hopf bifurcation takes over the phase transition. This is simply illustrated through the mean field Landau theory whose feedback dynamics turn out to be described by the Van der Pol equation and it is then validated for the fully connected Ising model following heat bath dynamics. Despite its simplicity, this theory accounts potentially for a rich range of phenomena: here it is applied to describe in a stylized way (i) excess demand-price cycles due to strong herding in a simple agent-based market model; (ii) congestion waves in queuing networks triggered by user feedback to delays in overloaded conditions; and (iii) metabolic network oscillations resulting from cell growth control in a bistable phenotypic landscape.},
author = {De Martino, Daniele},
journal = {Journal of Physics A: Mathematical and Theoretical},
number = {4},
publisher = {IOP Publishing},
title = {{Feedback-induced self-oscillations in large interacting systems subjected to phase transitions}},
doi = {10.1088/1751-8121/aaf2dd},
volume = {52},
year = {2019},
}
@article{6260,
abstract = {Polar auxin transport plays a pivotal role in plant growth and development. PIN auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport.},
author = {Oochi, A and Hajny, Jakub and Fukui, K and Nakao, Y and Gallei, Michelle C and Quareshy, M and Takahashi, K and Kinoshita, T and Harborough, SR and Kepinski, S and Kasahara, H and Napier, RM and Friml, Jiří and Hayashi, KI},
issn = {0032-0889},
journal = {Plant Physiology},
number = {2},
pages = {1152--1165},
publisher = {ASPB},
title = {{Pinstatic acid promotes auxin transport by inhibiting PIN internalization}},
doi = {10.1104/pp.19.00201},
volume = {180},
year = {2019},
}
@article{6412,
abstract = {Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.},
author = {Moussa, Hagar F. and Bsteh, Daniel and Yelagandula, Ramesh and Pribitzer, Carina and Stecher, Karin and Bartalska, Katarina and Michetti, Luca and Wang, Jingkui and Zepeda-Martinez, Jorge A. and Elling, Ulrich and Stuckey, Jacob I. and James, Lindsey I. and Frye, Stephen V. and Bell, Oliver},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Springer Nature},
title = {{Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing}},
doi = {10.1038/s41467-019-09628-6},
volume = {10},
year = {2019},
}
@article{6486,
abstract = {Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow.},
author = {Kühnen, Jakob and Scarselli, Davide and Hof, Björn},
issn = {1528901X},
journal = {Journal of Fluids Engineering},
number = {11},
publisher = {ASME},
title = {{Relaminarization of pipe flow by means of 3D-printed shaped honeycombs}},
doi = {10.1115/1.4043494},
volume = {141},
year = {2019},
}
@article{6366,
abstract = {Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl.},
author = {Bellstaedt, Julia and Trenner, Jana and Lippmann, Rebecca and Poeschl, Yvonne and Zhang, Xixi and Friml, Jiří and Quint, Marcel and Delker, Carolin},
issn = {0032-0889},
journal = {Plant Physiology},
number = {2},
pages = {757--766},
publisher = {ASPB},
title = {{A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls}},
doi = {10.1104/pp.18.01377},
volume = {180},
year = {2019},
}