TY - JOUR AB - We study properties of the volume of projections of the n-dimensional cross-polytope $\crosp^n = \{ x \in \R^n \mid |x_1| + \dots + |x_n| \leqslant 1\}.$ We prove that the projection of $\crosp^n$ onto a k-dimensional coordinate subspace has the maximum possible volume for k=2 and for k=3. We obtain the exact lower bound on the volume of such a projection onto a two-dimensional plane. Also, we show that there exist local maxima which are not global ones for the volume of a projection of $\crosp^n$ onto a k-dimensional subspace for any n>k⩾2. AU - Ivanov, Grigory ID - 9098 IS - 5 JF - Discrete Mathematics SN - 0012365X TI - On the volume of projections of the cross-polytope VL - 344 ER - TY - JOUR AB - Genomic imprinting is an epigenetic mechanism that results in parental allele-specific expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental regulators and play pivotal roles in many biological processes such as nutrient transfer from the mother to offspring and neuronal development. Imprinted genes are also involved in human disease, including neurodevelopmental disorders, and often occur in clusters that are regulated by a common imprint control region (ICR). In extra-embryonic tissues ICRs can act over large distances, with the largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical imprinted expression that shows near exclusive maternal or paternal expression, widespread biased imprinted expression has been identified mainly in brain. In this review we discuss recent developments mapping cell type specific imprinted expression in extra-embryonic tissues and neocortex in the mouse. We highlight the advantages of using an inducible uniparental chromosome disomy (UPD) system to generate cells carrying either two maternal or two paternal copies of a specific chromosome to analyze the functional consequences of genomic imprinting. Mosaic Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant induction of UPD sparsely in specific cell types, and thus to over-express or suppress all imprinted genes on that chromosome. To illustrate the utility of this technique, we explain how MADM-induced UPD revealed new insights about the function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs led to identification of highly cell type specific phenotypes related to perturbed imprinted expression in the mouse neocortex. Finally, we give an outlook on how MADM could be used to probe cell type specific imprinted expression in other tissues in mouse, particularly in extra-embryonic tissues. AU - Pauler, Florian AU - Hudson, Quanah AU - Laukoter, Susanne AU - Hippenmeyer, Simon ID - 9188 IS - 5 JF - Neurochemistry International KW - Cell Biology KW - Cellular and Molecular Neuroscience SN - 0197-0186 TI - Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond VL - 145 ER - TY - JOUR AB - While several tools have been developed to study the ground state of many-body quantum spin systems, the limitations of existing techniques call for the exploration of new approaches. In this manuscript we develop an alternative analytical and numerical framework for many-body quantum spin ground states, based on the disentanglement formalism. In this approach, observables are exactly expressed as Gaussian-weighted functional integrals over scalar fields. We identify the leading contribution to these integrals, given by the saddle point of a suitable effective action. Analytically, we develop a field-theoretical expansion of the functional integrals, performed by means of appropriate Feynman rules. The expansion can be truncated to a desired order to obtain analytical approximations to observables. Numerically, we show that the disentanglement approach can be used to compute ground state expectation values from classical stochastic processes. While the associated fluctuations grow exponentially with imaginary time and the system size, this growth can be mitigated by means of an importance sampling scheme based on knowledge of the saddle point configuration. We illustrate the advantages and limitations of our methods by considering the quantum Ising model in 1, 2 and 3 spatial dimensions. Our analytical and numerical approaches are applicable to a broad class of systems, bridging concepts from quantum lattice models, continuum field theory, and classical stochastic processes. AU - De Nicola, Stefano ID - 9158 IS - 1 JF - Journal of Statistical Mechanics: Theory and Experiment KW - Statistics KW - Probability and Uncertainty KW - Statistics and Probability KW - Statistical and Nonlinear Physics SN - 1742-5468 TI - Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation VL - 2021 ER - TY - JOUR AB - Cesium lead halides have intrinsically unstable crystal lattices and easily transform within perovskite and nonperovskite structures. In this work, we explore the conversion of the perovskite CsPbBr3 into Cs4PbBr6 in the presence of PbS at 450 °C to produce doped nanocrystal-based composites with embedded Cs4PbBr6 nanoprecipitates. We show that PbBr2 is extracted from CsPbBr3 and diffuses into the PbS lattice with a consequent increase in the concentration of free charge carriers. This new doping strategy enables the adjustment of the density of charge carriers between 1019 and 1020 cm–3, and it may serve as a general strategy for doping other nanocrystal-based semiconductors. AU - Calcabrini, Mariano AU - Genc, Aziz AU - Liu, Yu AU - Kleinhanns, Tobias AU - Lee, Seungho AU - Dirin, Dmitry N. AU - Akkerman, Quinten A. AU - Kovalenko, Maksym V. AU - Arbiol, Jordi AU - Ibáñez, Maria ID - 9118 IS - 2 JF - ACS Energy Letters TI - Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites VL - 6 ER - TY - JOUR AB - Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems. AU - Fraisse, Christelle AU - Sachdeva, Himani ID - 9168 IS - 2 JF - Genetics SN - 1943-2631 TI - The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes VL - 217 ER - TY - JOUR AB - “Hydrogen economy” could enable a carbon-neutral sustainable energy chain. However, issues with safety, storage, and transport of molecular hydrogen impede its realization. Alcohols as liquid H2 carriers could be enablers, but state-of-the-art reforming is difficult, requiring high temperatures >200 °C and pressures >25 bar, and the resulting H2 is carbonized beyond tolerance levels for direct use in fuel cells. Here, we demonstrate ambient temperature and pressure alcohol reforming in a fuel cell (ARFC) with a simultaneous electrical power output. The alcohol is oxidized at the alkaline anode, where the resulting CO2 is sequestrated as carbonate. Carbon-free H2 is liberated at the acidic cathode. The neutralization energy between the alkaline anode and the acidic cathode drives the process, particularly the unusually high entropy gain (1.27-fold ΔH). The significantly positive temperature coefficient of the resulting electromotive force allows us to harvest a large fraction of the output energy from the surrounding, achieving a thermodynamic efficiency as high as 2.27. MoS2 as the cathode catalyst allows alcohol reforming even under open-air conditions, a challenge that state-of-the-art alcohol reforming failed to overcome. We further show reforming of a wide range of alcohols. The ARFC offers an unprecedented route toward hydrogen economy as CO2 is simultaneously captured and pure H2 produced at mild conditions. AU - Manzoor Bhat, Zahid Manzoor AU - Thimmappa, Ravikumar AU - Dargily, Neethu Christudas AU - Raafik, Abdul AU - Kottaichamy, Alagar Raja AU - Devendrachari, Mruthyunjayachari Chattanahalli AU - Itagi, Mahesh AU - Makri Nimbegondi Kotresh, Harish AU - Freunberger, Stefan Alexander AU - Ottakam Thotiyl, Musthafa ID - 9113 IS - 8 JF - ACS Sustainable Chemistry and Engineering TI - Ambient condition alcohol reforming to hydrogen with electricity output VL - 9 ER - TY - JOUR AB - We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species. AU - Fraisse, Christelle AU - Popovic, Iva AU - Mazoyer, Clément AU - Spataro, Bruno AU - Delmotte, Stéphane AU - Romiguier, Jonathan AU - Loire, Étienne AU - Simon, Alexis AU - Galtier, Nicolas AU - Duret, Laurent AU - Bierne, Nicolas AU - Vekemans, Xavier AU - Roux, Camille ID - 9119 JF - Molecular Ecology Resources SN - 1755098X TI - DILS: Demographic inferences with linked selection by using ABC VL - 21 ER - TY - JOUR AB - We show that Hilbert schemes of points on supersingular Enriques surface in characteristic 2, Hilbn(X), for n ≥ 2 are simply connected, symplectic varieties but are not irreducible symplectic as the hodge number h2,0 > 1, even though a supersingular Enriques surface is an irreducible symplectic variety. These are the classes of varieties which appear only in characteristic 2 and they show that the hodge number formula for G¨ottsche-Soergel does not hold over haracteristic 2. It also gives examples of varieties with trivial canonical class which are neither irreducible symplectic nor Calabi-Yau, thereby showing that there are strictly more classes of simply connected varieties with trivial canonical class in characteristic 2 than over C as given by Beauville-Bogolomov decomposition theorem. AU - Srivastava, Tanya K ID - 9173 IS - 03 JF - Bulletin des Sciences Mathematiques SN - 0007-4497 TI - Pathologies of the Hilbert scheme of points of a supersingular Enriques surface VL - 167 ER - TY - CONF AB - Formal design of embedded and cyber-physical systems relies on mathematical modeling. In this paper, we consider the model class of hybrid automata whose dynamics are defined by affine differential equations. Given a set of time-series data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting behavior that is close to the data, up to a specified precision, and changes in synchrony with the data. A fundamental problem in our synthesis algorithm is to check membership of a time series in a hybrid automaton. Our solution integrates reachability and optimization techniques for affine dynamical systems to obtain both a sufficient and a necessary condition for membership, combined in a refinement framework. The algorithm processes one time series at a time and hence can be interrupted, provide an intermediate result, and be resumed. We report experimental results demonstrating the applicability of our synthesis approach. AU - Garcia Soto, Miriam AU - Henzinger, Thomas A AU - Schilling, Christian ID - 9200 KW - hybrid automaton KW - membership KW - system identification SN - 9781450383394 T2 - HSCC '21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control TI - Synthesis of hybrid automata with affine dynamics from time-series data ER - TY - JOUR AB - Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins. AU - Kampjut, Domen AU - Steiner, Julia AU - Sazanov, Leonid A ID - 9205 IS - 3 JF - iScience TI - Cryo-EM grid optimization for membrane proteins VL - 24 ER - TY - JOUR AB - In this paper we experimentally study the transitional range of Reynolds numbers in plane Couette–Poiseuille flow, focusing our attention on the localized turbulent structures triggered by a strong impulsive jet and the large-scale flow generated around these structures. We present a detailed investigation of the large-scale flow and show how its amplitude depends on Reynolds number and amplitude perturbation. In addition, we characterize the initial dynamics of the localized turbulent spot, which includes the coupling between the small and large scales, as well as the dependence of the advection speed on the large-scale flow generated around the spot. Finally, we provide the first experimental measurements of the large-scale flow around an oblique turbulent band. AU - Klotz, Lukasz AU - Pavlenko, A. M. AU - Wesfreid, J. E. ID - 9207 JF - Journal of Fluid Mechanics SN - 0022-1120 TI - Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow VL - 912 ER - TY - JOUR AB - The precise engineering of thermoelectric materials using nanocrystals as their building blocks has proven to be an excellent strategy to increase energy conversion efficiency. Here we present a synthetic route to produce Sb-doped PbS colloidal nanoparticles. These nanoparticles are then consolidated into nanocrystalline PbS:Sb using spark plasma sintering. We demonstrate that the introduction of Sb significantly influences the size, geometry, crystal lattice and especially the carrier concentration of PbS. The increase of charge carrier concentration achieved with the introduction of Sb translates into an increase of the electrical and thermal conductivities and a decrease of the Seebeck coefficient. Overall, PbS:Sb nanomaterial were characterized by two-fold higher thermoelectric figures of merit than undoped PbS. AU - Cadavid, Doris AU - Wei, Kaya AU - Liu, Yu AU - Zhang, Yu AU - Li, Mengyao AU - Genç, Aziz AU - Berestok, Taisiia AU - Ibáñez, Maria AU - Shavel, Alexey AU - Nolas, George S. AU - Cabot, Andreu ID - 9206 IS - 4 JF - Materials TI - Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks VL - 14 ER - TY - JOUR AB - 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? AU - Tkačik, Gašper AU - Gregor, Thomas ID - 9226 IS - 2 JF - Development TI - The many bits of positional information VL - 148 ER - TY - JOUR AB - 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. AU - Cornalba, Federico AU - Shardlow, Tony AU - Zimmer, Johannes ID - 9240 IS - 5 JF - Journal of Differential Equations SN - 0022-0396 TI - Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions VL - 284 ER - TY - CONF AB - 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. AU - Heiler, Georg AU - Reisch, Tobias AU - Hurt, Jan AU - Forghani, Mohammad AU - Omani, Aida AU - Hanbury, Allan AU - Karimipour, Farid ID - 9253 SN - 9781728162515 T2 - 2020 IEEE International Conference on Big Data TI - Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic ER - TY - JOUR AB - 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. AU - Achakulvisut, Titipat AU - Ruangrong, Tulakan AU - Mineault, Patrick AU - Vogels, Tim P AU - Peters, Megan A.K. AU - Poirazi, Panayiota AU - Rozell, Christopher AU - Wyble, Brad AU - Goodman, Dan F.M. AU - Kording, Konrad Paul ID - 9228 IS - 4 JF - Trends in Cognitive Sciences SN - 1364-6613 TI - Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences VL - 25 ER - TY - JOUR AB - 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. AU - Abanin, D. A. AU - Bardarson, J. H. AU - De Tomasi, G. AU - Gopalakrishnan, S. AU - Khemani, V. AU - Parameswaran, S. A. AU - Pollmann, F. AU - Potter, A. C. AU - Serbyn, Maksym AU - Vasseur, R. ID - 9224 IS - 4 JF - Annals of Physics SN - 00034916 TI - Distinguishing localization from chaos: Challenges in finite-size systems VL - 427 ER - TY - JOUR AB - 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. AU - Avni, Guy AU - Henzinger, Thomas A AU - Žikelić, Đorđe ID - 9239 IS - 8 JF - Journal of Computer and System Sciences SN - 0022-0000 TI - Bidding mechanisms in graph games VL - 119 ER - TY - JOUR AB - 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. AU - Hankeova, Simona AU - Salplachta, Jakub AU - Zikmund, Tomas AU - Kavkova, Michaela AU - Van Hul, Noémi AU - Brinek, Adam AU - Smekalova, Veronika AU - Laznovsky, Jakub AU - Dawit, Feven AU - Jaros, Josef AU - Bryja, Vítězslav AU - Lendahl, Urban AU - Ellis, Ewa AU - Nemeth, Antal AU - Fischler, Björn AU - Hannezo, Edouard B AU - Kaiser, Jozef AU - Andersson, Emma Rachel ID - 9244 JF - eLife TI - DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome VL - 10 ER - TY - JOUR AB - 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. AU - Elek, Oskar AU - Zhang, Ran AU - Sumin, Denis AU - Myszkowski, Karol AU - Bickel, Bernd AU - Wilkie, Alexander AU - Křivánek, Jaroslav AU - Weyrich, Tim ID - 9241 IS - 5 JF - Optics Express TI - Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing VL - 29 ER -