@article{7026,
abstract = {Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90% of the variation in cellular response can be decomposed into three principal components (PCs) that have clear biological interpretations. We demonstrate that the third PC captures emergent transcriptional programs that are dependent on both drugs and can predict antagonism with a third drug targeting the emergent pathway. We further show that emergent gene expression patterns are most pronounced at a drug ratio where the drug interaction is strongest, providing a guideline for future measurements. Our results provide a readily applicable recipe for uncovering emergent responses in other systems and for higher-order drug combinations. A record of this paper’s transparent peer review process is included in the Supplemental Information.},
author = {Lukacisin, Martin and Bollenbach, Tobias},
issn = {2405-4712},
journal = {Cell Systems},
number = {5},
pages = {423--433.e1--e3},
publisher = {Cell Press},
title = {{Emergent gene expression responses to drug combinations predict higher-order drug interactions}},
doi = {10.1016/j.cels.2019.10.004},
volume = {9},
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},
}
@unpublished{7083,
abstract = {Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we demonstrate that these interactions can be accounted for by “translation bottlenecks”: points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generated translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimicked antibiotic action and their interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further showed that the kinetics of drug uptake and binding together with growth laws allows direct prediction of a large fraction of observed interactions, yet fails for suppression. Simultaneously varying two translation bottlenecks in the same cell revealed how the dense traffic of ribosomes and competition for translation factors results in previously unexplained suppression. This result highlights the importance of “continuous epistasis” in bacterial physiology.},
author = {Kavcic, Bor and Tkačik, Gašper and Bollenbach, Tobias},
booktitle = {bioRxiv},
pages = {45},
publisher = {Cold Spring Harbor Laboratory},
title = {{Mechanistic origin of drug interactions between translation-inhibiting antibiotics}},
year = {2019},
}
@article{7420,
abstract = {β1-integrins mediate cell–matrix interactions and their trafficking is important in the dynamic regulation of cell adhesion, migration and malignant processes, including cancer cell invasion. Here, we employ an RNAi screen to characterize regulators of integrin traffic and identify the association of Golgi-localized gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2 limits active β1-integrin levels in focal adhesions and decreases cancer cell migration and invasion, which is in agreement with its ability to regulate the dynamics of active integrins. By using the proximity-dependent biotin identification (BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10, as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular accumulation of active β1-integrin, and reduces integrin activity in focal adhesions and cell migration similarly to GGA2 depletion, indicating that both facilitate active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are important specificity determinants for integrin activity-dependent traffic.},
author = {Sahgal, Pranshu and Alanko, Jonna H and Icha, Jaroslav and Paatero, Ilkka and Hamidi, Hellyeh and Arjonen, Antti and Pietilä, Mika and Rokka, Anne and Ivaska, Johanna},
issn = {0021-9533},
journal = {Journal of Cell Science},
number = {11},
publisher = {The Company of Biologists},
title = {{GGA2 and RAB13 promote activity-dependent β1-integrin recycling}},
doi = {10.1242/jcs.233387},
volume = {132},
year = {2019},
}
@inproceedings{7437,
abstract = {Most of today's distributed machine learning systems assume reliable networks: whenever two machines exchange information (e.g., gradients or models), the network should guarantee the delivery of the message. At the same time, recent work exhibits the impressive tolerance of machine learning algorithms to errors or noise arising from relaxed communication or synchronization. In this paper, we connect these two trends, and consider the following question: Can we design machine learning systems that are tolerant to network unreliability during training? With this motivation, we focus on a theoretical problem of independent interest-given a standard distributed parameter server architecture, if every communication between the worker and the server has a non-zero probability p of being dropped, does there exist an algorithm that still converges, and at what speed? The technical contribution of this paper is a novel theoretical analysis proving that distributed learning over unreliable network can achieve comparable convergence rate to centralized or distributed learning over reliable networks. Further, we prove that the influence of the packet drop rate diminishes with the growth of the number of parameter servers. We map this theoretical result onto a real-world scenario, training deep neural networks over an unreliable network layer, and conduct network simulation to validate the system improvement by allowing the networks to be unreliable.},
author = {Yu, Chen and Tang, Hanlin and Renggli, Cedric and Kassing, Simon and Singla, Ankit and Alistarh, Dan-Adrian and Zhang, Ce and Liu, Ji},
booktitle = {36th International Conference on Machine Learning, ICML 2019},
isbn = {9781510886988},
location = {Long Beach, CA, United States},
pages = {12481--12512},
publisher = {IMLS},
title = {{Distributed learning over unreliable networks}},
volume = {2019-June},
year = {2019},
}
@article{7413,
abstract = {We consider Bose gases consisting of N particles trapped in a box with volume one and interacting through a repulsive potential with scattering length of order N−1 (Gross–Pitaevskii regime). We determine the ground state energy and the low-energy excitation spectrum, up to errors vanishing as N→∞. Our results confirm Bogoliubov’s predictions.},
author = {Boccato, Chiara and Brennecke, Christian and Cenatiempo, Serena and Schlein, Benjamin},
issn = {0001-5962},
journal = {Acta Mathematica},
number = {2},
pages = {219--335},
publisher = {International Press of Boston},
title = {{Bogoliubov theory in the Gross–Pitaevskii limit}},
doi = {10.4310/acta.2019.v222.n2.a1},
volume = {222},
year = {2019},
}
@article{7393,
abstract = {The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.},
author = {Morales, Hernán E. and Faria, Rui and Johannesson, Kerstin and Larsson, Tomas and Panova, Marina and Westram, Anja M and Butlin, Roger K.},
issn = {2375-2548},
journal = {Science Advances},
number = {12},
publisher = {AAAS},
title = {{Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast}},
doi = {10.1126/sciadv.aav9963},
volume = {5},
year = {2019},
}
@inproceedings{7401,
abstract = {The genus g(G) of a graph G is the minimum g such that G has an embedding on the orientable surface M_g of genus g. A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z_2-genus of a graph G, denoted by g_0(G), is the minimum g such that G has an independently even drawing on M_g. By a result of Battle, Harary, Kodama and Youngs from 1962, the graph genus is additive over 2-connected blocks. In 2013, Schaefer and Stefankovic proved that the Z_2-genus of a graph is additive over 2-connected blocks as well, and asked whether this result can be extended to so-called 2-amalgamations, as an analogue of results by Decker, Glover, Huneke, and Stahl for the genus. We give the following partial answer. If G=G_1 cup G_2, G_1 and G_2 intersect in two vertices u and v, and G-u-v has k connected components (among which we count the edge uv if present), then |g_0(G)-(g_0(G_1)+g_0(G_2))|<=k+1. For complete bipartite graphs K_{m,n}, with n >= m >= 3, we prove that g_0(K_{m,n})/g(K_{m,n})=1-O(1/n). Similar results are proved also for the Euler Z_2-genus. We express the Z_2-genus of a graph using the minimum rank of partial symmetric matrices over Z_2; a problem that might be of independent interest. },
author = {Fulek, Radoslav and Kyncl, Jan},
booktitle = {35th International Symposium on Computational Geometry (SoCG 2019)},
isbn = {978-3-95977-104-7},
issn = {1868-8969},
location = {Portland, OR, United States},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Z_2-Genus of graphs and minimum rank of partial symmetric matrices}},
doi = {10.4230/LIPICS.SOCG.2019.39},
volume = {129},
year = {2019},
}
@inproceedings{6035,
abstract = {We present JuliaReach, a toolbox for set-based reachability analysis of dynamical systems. JuliaReach consists of two main packages: Reachability, containing implementations of reachability algorithms for continuous and hybrid systems, and LazySets, a standalone library that implements state-of-the-art algorithms for calculus with convex sets. The library offers both concrete and lazy set representations, where the latter stands for the ability to delay set computations until they are needed. The choice of the programming language Julia and the accompanying documentation of our toolbox allow researchers to easily translate set-based algorithms from mathematics to software in a platform-independent way, while achieving runtime performance that is comparable to statically compiled languages. Combining lazy operations in high dimensions and explicit computations in low dimensions, JuliaReach can be applied to solve complex, large-scale problems.},
author = {Bogomolov, Sergiy and Forets, Marcelo and Frehse, Goran and Potomkin, Kostiantyn and Schilling, Christian},
booktitle = {Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control},
isbn = {9781450362825},
keyword = {reachability analysis, hybrid systems, lazy computation},
location = {Montreal, QC, Canada},
pages = {39--44},
publisher = {ACM},
title = {{JuliaReach: A toolbox for set-based reachability}},
doi = {10.1145/3302504.3311804},
volume = {22},
year = {2019},
}
@article{7398,
abstract = {Transporters of the solute carrier 6 (SLC6) family translocate their cognate substrate together with Na+ and Cl−. Detailed kinetic models exist for the transporters of GABA (GAT1/SLC6A1) and the monoamines dopamine (DAT/SLC6A3) and serotonin (SERT/SLC6A4). Here, we posited that the transport cycle of individual SLC6 transporters reflects the physiological requirements they operate under. We tested this hypothesis by analyzing the transport cycle of glycine transporter 1 (GlyT1/SLC6A9) and glycine transporter 2 (GlyT2/SLC6A5). GlyT2 is the only SLC6 family member known to translocate glycine, Na+, and Cl− in a 1:3:1 stoichiometry. We analyzed partial reactions in real time by electrophysiological recordings. Contrary to monoamine transporters, both GlyTs were found to have a high transport capacity driven by rapid return of the empty transporter after release of Cl− on the intracellular side. Rapid cycling of both GlyTs was further supported by highly cooperative binding of cosubstrate ions and substrate such that their forward transport mode was maintained even under conditions of elevated intracellular Na+ or Cl−. The most important differences in the transport cycle of GlyT1 and GlyT2 arose from the kinetics of charge movement and the resulting voltage-dependent rate-limiting reactions: the kinetics of GlyT1 were governed by transition of the substrate-bound transporter from outward- to inward-facing conformations, whereas the kinetics of GlyT2 were governed by Na+ binding (or a related conformational change). Kinetic modeling showed that the kinetics of GlyT1 are ideally suited for supplying the extracellular glycine levels required for NMDA receptor activation.},
author = {Erdem, Fatma Asli and Ilic, Marija and Koppensteiner, Peter and Gołacki, Jakub and Lubec, Gert and Freissmuth, Michael and Sandtner, Walter},
issn = {0022-1295},
journal = {The Journal of General Physiology},
number = {8},
pages = {1035--1050},
publisher = {Rockefeller University Press},
title = {{A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2}},
doi = {10.1085/jgp.201912318},
volume = {151},
year = {2019},
}
@article{6186,
abstract = {We prove that the local eigenvalue statistics of real symmetric Wigner-type
matrices near the cusp points of the eigenvalue density are universal. Together
with the companion paper [arXiv:1809.03971], which proves the same result for
the complex Hermitian symmetry class, this completes the last remaining case of
the Wigner-Dyson-Mehta universality conjecture after bulk and edge
universalities have been established in the last years. We extend the recent
Dyson Brownian motion analysis at the edge [arXiv:1712.03881] to the cusp
regime using the optimal local law from [arXiv:1809.03971] and the accurate
local shape analysis of the density from [arXiv:1506.05095, arXiv:1804.07752].
We also present a PDE-based method to improve the estimate on eigenvalue
rigidity via the maximum principle of the heat flow related to the Dyson
Brownian motion.},
author = {Cipolloni, Giorgio and Erdös, László and Krüger, Torben H and Schröder, Dominik J},
issn = {2578-5885},
journal = {Pure and Applied Analysis },
number = {4},
pages = {615–707},
publisher = {MSP},
title = {{Cusp universality for random matrices, II: The real symmetric case}},
doi = {10.2140/paa.2019.1.615},
volume = {1},
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},
issn = {1521-1878},
journal = {BioEssays},
number = {11},
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},
volume = {41},
year = {2019},
}
@inproceedings{7468,
abstract = {We present a new proximal bundle method for Maximum-A-Posteriori (MAP) inference in structured energy minimization problems. The method optimizes a Lagrangean relaxation of the original energy minimization problem using a multi plane block-coordinate Frank-Wolfe method that takes advantage of the specific structure of the Lagrangean decomposition. We show empirically that our method outperforms state-of-the-art Lagrangean decomposition based algorithms on some challenging Markov Random Field, multi-label discrete tomography and graph matching problems.},
author = {Swoboda, Paul and Kolmogorov, Vladimir},
booktitle = {Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition},
isbn = {9781728132938},
issn = {10636919},
location = {Long Beach, CA, United States},
publisher = {IEEE},
title = {{Map inference via block-coordinate Frank-Wolfe algorithm}},
doi = {10.1109/CVPR.2019.01140},
volume = {2019-June},
year = {2019},
}
@article{7451,
abstract = {We prove that the observable telegraph signal accompanying the bistability in the photon-blockade-breakdown regime of the driven and lossy Jaynes–Cummings model is the finite-size precursor of what in the thermodynamic limit is a genuine first-order phase transition. We construct a finite-size scaling of the system parameters to a well-defined thermodynamic limit, in which the system remains the same microscopic system, but the telegraph signal becomes macroscopic both in its timescale and intensity. The existence of such a finite-size scaling completes and justifies the classification of the photon-blockade-breakdown effect as a first-order dissipative quantum phase transition.},
author = {Vukics, A. and Dombi, A. and Fink, Johannes M and Domokos, P.},
issn = {2521-327X},
journal = {Quantum},
publisher = {Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften},
title = {{Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition}},
doi = {10.22331/q-2019-06-03-150},
volume = {3},
year = {2019},
}
@article{5986,
abstract = {Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm (with 𝑂(𝑛8) being a crude bound on the run-time) to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of 𝑂(𝑛7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture.},
author = {Lubiw, Anna and Masárová, Zuzana and Wagner, Uli},
issn = {0179-5376},
journal = {Discrete & Computational Geometry},
number = {4},
pages = {880--898},
publisher = {Springer Nature},
title = {{A proof of the orbit conjecture for flipping edge-labelled triangulations}},
doi = {10.1007/s00454-018-0035-8},
volume = {61},
year = {2019},
}
@article{6713,
abstract = {Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.},
author = {Castro, João Pl and Yancoskie, Michelle N. and Marchini, Marta and Belohlavy, Stefanie and Hiramatsu, Layla and Kučka, Marek and Beluch, William H. and Naumann, Ronald and Skuplik, Isabella and Cobb, John and Barton, Nicholas H and Rolian, Campbell and Chan, Yingguang Frank},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice}},
doi = {10.7554/eLife.42014},
volume = {8},
year = {2019},
}
@article{151,
abstract = {We construct planar bi-Sobolev mappings whose local volume distortion is bounded from below by a given function f∈Lp with p>1. More precisely, for any 1<q<(p+1)/2 we construct W1,q-bi-Sobolev maps with identity boundary conditions; for f∈L∞, we provide bi-Lipschitz maps. The basic building block of our construction are bi-Lipschitz maps which stretch a given compact subset of the unit square by a given factor while preserving the boundary. The construction of these stretching maps relies on a slight strengthening of the celebrated covering result of Alberti, Csörnyei, and Preiss for measurable planar sets in the case of compact sets. We apply our result to a model functional in nonlinear elasticity, the integrand of which features fast blowup as the Jacobian determinant of the deformation becomes small. For such functionals, the derivation of the equilibrium equations for minimizers requires an additional regularization of test functions, which our maps provide.},
author = {Fischer, Julian L and Kneuss, Olivier},
journal = {Journal of Differential Equations},
number = {1},
pages = {257 -- 311},
publisher = {Elsevier},
title = {{Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity}},
doi = {10.1016/j.jde.2018.07.045},
volume = {266},
year = {2019},
}
@article{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 = {BioMed Central},
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{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 = {Institute of Mathematical Statistics},
title = {{Local single ring theorem on optimal scale}},
doi = {10.1214/18-AOP1284},
volume = {47},
year = {2019},
}
@unpublished{7552,
abstract = {There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests. },
author = {Bialek, William and Gregor, Thomas and Tkačik, Gašper},
booktitle = {arXiv:1912.08579},
pages = {5},
publisher = {ArXiv},
title = {{Action at a distance in transcriptional regulation}},
year = {2019},
}
@article{175,
abstract = {An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points.},
author = {Browning, Timothy D and Loughran, Daniel},
issn = {10886850},
journal = {Transactions of the American Mathematical Society},
number = {8},
pages = {5757--5785},
publisher = {American Mathematical Society},
title = {{Sieving rational points on varieties}},
doi = {10.1090/tran/7514},
volume = {371},
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 = {American Physical Society},
title = {{Colloquium: Many-body localization, thermalization, and entanglement}},
doi = {10.1103/revmodphys.91.021001},
volume = {91},
year = {2019},
}
@inproceedings{7576,
abstract = {We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.},
author = {Immler, Fabian and Althoff, Matthias and Benet, Luis and Chapoutot, Alexandre and Chen, Xin and Forets, Marcelo and Geretti, Luca and Kochdumper, Niklas and Sanders, David P. and Schilling, Christian},
booktitle = {EPiC Series in Computing},
issn = {23987340},
location = {Montreal, Canada},
pages = {41--61},
publisher = {EasyChair Publications},
title = {{ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics}},
doi = {10.29007/m75b},
volume = {61},
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{429,
abstract = {We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent.},
author = {Ajanki, Oskari H and Erdös, László and Krüger, Torben H},
issn = {14322064},
journal = {Probability Theory and Related Fields},
number = {1-2},
pages = {293–373},
publisher = {Springer},
title = {{Stability of the matrix Dyson equation and random matrices with correlations}},
doi = {10.1007/s00440-018-0835-z},
volume = {173},
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{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{6182,
abstract = {We consider large random matrices with a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent away from the spectral edges, generalizing the recent result of Ajanki et al. [‘Stability of the matrix Dyson equation and random matrices with correlations’, Probab. Theory Related Fields 173(1–2) (2019), 293–373] to allow slow correlation decay and arbitrary expectation. The main novel tool is
a systematic diagrammatic control of a multivariate cumulant expansion.},
author = {Erdös, László and Krüger, Torben H and Schröder, Dominik J},
issn = {20505094},
journal = {Forum of Mathematics, Sigma},
publisher = {Cambridge University Press},
title = {{Random matrices with slow correlation decay}},
doi = {10.1017/fms.2019.2},
volume = {7},
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{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{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},
}
@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},
number = {12},
pages = {2435–2446},
publisher = {Springer},
title = {{On a certain non-split cubic surface}},
doi = {10.1007/s11425-018-9543-8},
volume = {62},
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{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},
number = {10},
pages = {3471–3508},
publisher = {Springer Nature},
title = {{Mean-field dynamics for the Nelson model with fermions}},
doi = {10.1007/s00023-019-00828-w},
volume = {20},
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},
number = {17},
pages = {9597--9608},
publisher = {Wiley},
title = {{Green beards in the light of indirect genetic effects}},
doi = {10.1002/ece3.5484},
volume = {9},
year = {2019},
}
@article{6978,
abstract = {In pipes and channels, the onset of turbulence is initially dominated by localizedtransients, which lead to sustained turbulence through their collective dynamics. In thepresent work, we study numerically the localized turbulence in pipe flow and elucidate astate space structure that gives rise to transient chaos. Starting from the basin boundaryseparating laminar and turbulent flow, we identify transverse homoclinic orbits, thepresence of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which wasconjectured in various earlier studies. By mapping the transverse intersections between thestable and unstable manifold of a periodic orbit, we identify the gateways that promote anescape from turbulence.},
author = {Budanur, Nazmi B and Dogra, Akshunna and Hof, Björn},
journal = {Physical Review Fluids},
number = {10},
pages = {102401},
publisher = {American Physical Society},
title = {{Geometry of transient chaos in streamwise-localized pipe flow turbulence}},
doi = {10.1103/PhysRevFluids.4.102401},
volume = {4},
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},
}
@misc{7154,
author = {Guseinov, Ruslan},
publisher = {IST Austria},
title = {{Supplementary data for "Programming temporal morphing of self-actuated shells"}},
doi = {10.15479/AT:ISTA:7154},
year = {2019},
}
@unpublished{7084,
abstract = {URu2Si2 exhibits a clear phase transition at THO=17.5 K to a low-temperature phase known as "hidden order" (HO). Even the most basic information needed to construct a theory of this state---such as the number of components in the order parameter---has been lacking. Here we use resonant ultrasound spectroscopy (RUS) and machine learning to determine that the order parameter of HO is one-dimensional (singlet), ruling out a large class of theories based on two-dimensional (doublet) order parameters. This strict constraint is independent of any microscopic mechanism, and independent of other symmetries that HO may break. Our technique is general for second-order phase transitions, and can discriminate between nematic (singlet) versus loop current (doublet) order in the high-\Tc cuprates, and conventional (singlet) versus the proposed px+ipy (doublet) superconductivity in Sr2RuO4. The machine learning framework we develop should be readily adaptable to other spectroscopic techniques where missing resonances confound traditional analysis, such as NMR. },
author = {Ghosh, Sayak and Matty, Michael and Baumbach, Ryan and Bauer, Eric D. and Modic, Kimberly A and Shekhter, Arkady and Mydosh, J. A. and Kim, Eun-Ah and Ramshaw, B. J.},
booktitle = {arXiv:1903.00552},
title = {{Single-component order parameter in URu2Si2 uncovered by resonant ultrasound spectroscopy and machine learning}},
year = {2019},
}
@article{7015,
abstract = {We modify the "floating crystal" trial state for the classical homogeneous electron gas (also known as jellium), in order to suppress the boundary charge fluctuations that are known to lead to a macroscopic increase of the energy. The argument is to melt a thin layer of the crystal close to the boundary and consequently replace it by an incompressible fluid. With the aid of this trial state we show that three different definitions of the ground-state energy of jellium coincide. In the first point of view the electrons are placed in a neutralizing uniform background. In the second definition there is no background but the electrons are submitted to the constraint that their density is constant, as is appropriate in density functional theory. Finally, in the third system each electron interacts with a periodic image of itself; that is, periodic boundary conditions are imposed on the interaction potential.},
author = {Lewin, Mathieu and Lieb, Elliott H. and Seiringer, Robert},
issn = {2469-9950},
journal = {Physical Review B},
number = {3},
publisher = {APS},
title = {{Floating Wigner crystal with no boundary charge fluctuations}},
doi = {10.1103/physrevb.100.035127},
volume = {100},
year = {2019},
}
@inproceedings{6985,
abstract = {In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked contribution of individual cells to the network's output is computed by analyzing a set of interpretable metrics of their decoupled step and sinusoidal responses. As a result, our method is able to uniquely identify neurons with insightful dynamics, quantify relationships between dynamical properties and test accuracy through ablation analysis, and interpret the impact of network capacity on a network's dynamical distribution. Finally, we demonstrate the generalizability and scalability of our method by evaluating a series of different benchmark sequential datasets.},
author = {Hasani, Ramin and Amini, Alexander and Lechner, Mathias and Naser, Felix and Grosu, Radu and Rus, Daniela},
booktitle = {Proceedings of the International Joint Conference on Neural Networks},
isbn = {9781728119854},
location = {Budapest, Hungary},
publisher = {IEEE},
title = {{Response characterization for auditing cell dynamics in long short-term memory networks}},
doi = {10.1109/ijcnn.2019.8851954},
year = {2019},
}
@article{7197,
abstract = {During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This Z-ring not only organizes the division machinery, but treadmilling of FtsZ filaments was also found to play a key role in distributing proteins at the division site. What regulates the architecture, dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated proteins are known to play an important role. Here, using an in vitro reconstitution approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling and filament organization into large-scale patterns. Using high-resolution fluorescence microscopy and quantitative image analysis, we found that ZapA cooperatively increases the spatial order of the filament network, but binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Together, our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a switch-like manner.},
author = {Dos Santos Caldas, Paulo R and Lopez Pelegrin, Maria D and Pearce, Daniel J. G. and Budanur, Nazmi B and Brugués, Jan and Loose, Martin},
issn = {2041-1723},
journal = {Nature Communications},
publisher = {Springer Nature},
title = {{Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA}},
doi = {10.1038/s41467-019-13702-4},
volume = {10},
year = {2019},
}