@article{9226, abstract = {Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?}, author = {Tkačik, Gašper and Gregor, Thomas}, issn = {1477-9129}, journal = {Development}, number = {2}, publisher = {The Company of Biologists}, title = {{The many bits of positional information}}, doi = {10.1242/dev.176065}, volume = {148}, year = {2021}, } @article{9240, abstract = {A stochastic PDE, describing mesoscopic fluctuations in systems of weakly interacting inertial particles of finite volume, is proposed and analysed in any finite dimension . It is a regularised and inertial version of the Dean–Kawasaki model. A high-probability well-posedness theory for this model is developed. This theory improves significantly on the spatial scaling restrictions imposed in an earlier work of the same authors, which applied only to significantly larger particles in one dimension. The well-posedness theory now applies in d-dimensions when the particle-width ϵ is proportional to for and N is the number of particles. This scaling is optimal in a certain Sobolev norm. Key tools of the analysis are fractional Sobolev spaces, sharp bounds on Bessel functions, separability of the regularisation in the d-spatial dimensions, and use of the Faà di Bruno's formula.}, author = {Cornalba, Federico and Shardlow, Tony and Zimmer, Johannes}, issn = {1090-2732}, journal = {Journal of Differential Equations}, number = {5}, pages = {253--283}, publisher = {Elsevier}, title = {{Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions}}, doi = {10.1016/j.jde.2021.02.048}, volume = {284}, year = {2021}, } @inproceedings{9253, abstract = {In March 2020, the Austrian government introduced a widespread lock-down in response to the COVID-19 pandemic. Based on subjective impressions and anecdotal evidence, Austrian public and private life came to a sudden halt. Here we assess the effect of the lock-down quantitatively for all regions in Austria and present an analysis of daily changes of human mobility throughout Austria using near-real-time anonymized mobile phone data. We describe an efficient data aggregation pipeline and analyze the mobility by quantifying mobile-phone traffic at specific point of interests (POIs), analyzing individual trajectories and investigating the cluster structure of the origin-destination graph. We found a reduction of commuters at Viennese metro stations of over 80% and the number of devices with a radius of gyration of less than 500 m almost doubled. The results of studying crowd-movement behavior highlight considerable changes in the structure of mobility networks, revealed by a higher modularity and an increase from 12 to 20 detected communities. We demonstrate the relevance of mobility data for epidemiological studies by showing a significant correlation of the outflow from the town of Ischgl (an early COVID-19 hotspot) and the reported COVID-19 cases with an 8-day time lag. This research indicates that mobile phone usage data permits the moment-by-moment quantification of mobility behavior for a whole country. We emphasize the need to improve the availability of such data in anonymized form to empower rapid response to combat COVID-19 and future pandemics.}, author = {Heiler, Georg and Reisch, Tobias and Hurt, Jan and Forghani, Mohammad and Omani, Aida and Hanbury, Allan and Karimipour, Farid}, booktitle = {2020 IEEE International Conference on Big Data}, isbn = {9781728162515}, location = {Atlanta, GA, United States}, pages = {3123--3132}, publisher = {IEEE}, title = {{Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic}}, doi = {10.1109/bigdata50022.2020.9378374}, year = {2021}, } @article{9228, abstract = {Legacy conferences are costly and time consuming, and exclude scientists lacking various resources or abilities. During the 2020 pandemic, we created an online conference platform, Neuromatch Conferences (NMC), aimed at developing technological and cultural changes to make conferences more democratic, scalable, and accessible. We discuss the lessons we learned.}, author = {Achakulvisut, Titipat and Ruangrong, Tulakan and Mineault, Patrick and Vogels, Tim P and Peters, Megan A.K. and Poirazi, Panayiota and Rozell, Christopher and Wyble, Brad and Goodman, Dan F.M. and Kording, Konrad Paul}, issn = {1879-307X}, journal = {Trends in Cognitive Sciences}, number = {4}, pages = {265--268}, publisher = {Elsevier}, title = {{Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences}}, doi = {10.1016/j.tics.2021.01.007}, volume = {25}, year = {2021}, } @article{9224, abstract = {We re-examine attempts to study the many-body localization transition using measures that are physically natural on the ergodic/quantum chaotic regime of the phase diagram. Using simple scaling arguments and an analysis of various models for which rigorous results are available, we find that these measures can be particularly adversely affected by the strong finite-size effects observed in nearly all numerical studies of many-body localization. This severely impacts their utility in probing the transition and the localized phase. In light of this analysis, we discuss a recent study (Šuntajs et al., 2020) of the behaviour of the Thouless energy and level repulsion in disordered spin chains, and its implications for the question of whether MBL is a true phase of matter.}, author = {Abanin, D. A. and Bardarson, J. H. and De Tomasi, G. and Gopalakrishnan, S. and Khemani, V. and Parameswaran, S. A. and Pollmann, F. and Potter, A. C. and Serbyn, Maksym and Vasseur, R.}, issn = {1096035X}, journal = {Annals of Physics}, number = {4}, publisher = {Elsevier}, title = {{Distinguishing localization from chaos: Challenges in finite-size systems}}, doi = {10.1016/j.aop.2021.168415}, volume = {427}, year = {2021}, } @article{9239, abstract = {A graph game proceeds as follows: two players move a token through a graph to produce a finite or infinite path, which determines the payoff of the game. We study bidding games in which in each turn, an auction determines which player moves the token. Bidding games were largely studied in combination with two variants of first-price auctions called “Richman” and “poorman” bidding. We study taxman bidding, which span the spectrum between the two. The game is parameterized by a constant : portion τ of the winning bid is paid to the other player, and portion 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: we unify, generalize, and simplify previous equivalences between bidding games and a class of stochastic games called random-turn games.}, author = {Avni, Guy and Henzinger, Thomas A and Žikelić, Đorđe}, issn = {1090-2724}, journal = {Journal of Computer and System Sciences}, number = {8}, pages = {133--144}, publisher = {Elsevier}, title = {{Bidding mechanisms in graph games}}, doi = {10.1016/j.jcss.2021.02.008}, volume = {119}, year = {2021}, } @article{9244, abstract = {Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models.}, author = {Hankeova, Simona and Salplachta, Jakub and Zikmund, Tomas and Kavkova, Michaela and Van Hul, Noémi and Brinek, Adam and Smekalova, Veronika and Laznovsky, Jakub and Dawit, Feven and Jaros, Josef and Bryja, Vítězslav and Lendahl, Urban and Ellis, Ewa and Nemeth, Antal and Fischler, Björn and Hannezo, Edouard B and Kaiser, Jozef and Andersson, Emma Rachel}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome}}, doi = {10.7554/eLife.60916}, volume = {10}, year = {2021}, } @article{9241, abstract = {Volumetric light transport is a pervasive physical phenomenon, and therefore its accurate simulation is important for a broad array of disciplines. While suitable mathematical models for computing the transport are now available, obtaining the necessary material parameters needed to drive such simulations is a challenging task: direct measurements of these parameters from material samples are seldom possible. Building on the inverse scattering paradigm, we present a novel measurement approach which indirectly infers the transport parameters from extrinsic observations of multiple-scattered radiance. The novelty of the proposed approach lies in replacing structured illumination with a structured reflector bonded to the sample, and a robust fitting procedure that largely compensates for potential systematic errors in the calibration of the setup. We show the feasibility of our approach by validating simulations of complex 3D compositions of the measured materials against physical prints, using photo-polymer resins. As presented in this paper, our technique yields colorspace data suitable for accurate appearance reproduction in the area of 3D printing. Beyond that, and without fundamental changes to the basic measurement methodology, it could equally well be used to obtain spectral measurements that are useful for other application areas.}, author = {Elek, Oskar and Zhang, Ran and Sumin, Denis and Myszkowski, Karol and Bickel, Bernd and Wilkie, Alexander and Křivánek, Jaroslav and Weyrich, Tim}, issn = {1094-4087}, journal = {Optics Express}, number = {5}, pages = {7568--7588}, publisher = {The Optical Society}, title = {{Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing}}, doi = {10.1364/OE.406095}, volume = {29}, year = {2021}, } @article{9243, abstract = {Peptidoglycan is an essential component of the bacterial cell envelope that surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis. Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan synthases that polymerize glycan chains and connect adjacent stem peptides by transpeptidation. How these enzymes work in their physiological membrane environment is poorly understood. Here, we developed a novel Förster resonance energy transfer-based assay to follow in real time both reactions of class A PBPs reconstituted in liposomes or supported lipid bilayers and applied this assay with PBP1B homologues from Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence or absence of their cognate lipoprotein activator. Our assay will allow unravelling the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can be further developed to be used for high-throughput screening for new antimicrobials.}, author = {Hernández-Rocamora, Víctor M. and Baranova, Natalia S. and Peters, Katharina and Breukink, Eefjan and Loose, Martin and Vollmer, Waldemar}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins}}, doi = {10.7554/eLife.61525}, volume = {10}, year = {2021}, } @article{9246, abstract = {We consider the Fröhlich Hamiltonian in a mean-field limit where many bosonic particles weakly couple to the quantized phonon field. For large particle numbers and a suitably small coupling, we show that the dynamics of the system is approximately described by the Landau–Pekar equations. These describe a Bose–Einstein condensate interacting with a classical polarization field, whose dynamics is effected by the condensate, i.e., the back-reaction of the phonons that are created by the particles during the time evolution is of leading order.}, author = {Leopold, Nikolai K and Mitrouskas, David Johannes and Seiringer, Robert}, issn = {14320673}, journal = {Archive for Rational Mechanics and Analysis}, pages = {383--417}, publisher = {Springer Nature}, title = {{Derivation of the Landau–Pekar equations in a many-body mean-field limit}}, doi = {10.1007/s00205-021-01616-9}, volume = {240}, year = {2021}, }