TY - JOUR AB - Adult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait. AU - Slavskii, Sergei A. AU - Kuznetsov, Ivan A. AU - Shashkova, Tatiana I. AU - Bazykin, Georgii A. AU - Axenovich, Tatiana I. AU - Kondrashov, Fyodor AU - Aulchenko, Yurii S. ID - 9910 IS - 7 JF - European Journal of Human Genetics SN - 10184813 TI - The limits of normal approximation for adult height VL - 29 ER - TY - JOUR AB - In the customary random matrix model for transport in quantum dots with M internal degrees of freedom coupled to a chaotic environment via 𝑁≪𝑀 channels, the density 𝜌 of transmission eigenvalues is computed from a specific invariant ensemble for which explicit formula for the joint probability density of all eigenvalues is available. We revisit this problem in the large N regime allowing for (i) arbitrary ratio 𝜙:=𝑁/𝑀≤1; and (ii) general distributions for the matrix elements of the Hamiltonian of the quantum dot. In the limit 𝜙→0, we recover the formula for the density 𝜌 that Beenakker (Rev Mod Phys 69:731–808, 1997) has derived for a special matrix ensemble. We also prove that the inverse square root singularity of the density at zero and full transmission in Beenakker’s formula persists for any 𝜙<1 but in the borderline case 𝜙=1 an anomalous 𝜆−2/3 singularity arises at zero. To access this level of generality, we develop the theory of global and local laws on the spectral density of a large class of noncommutative rational expressions in large random matrices with i.i.d. entries. AU - Erdös, László AU - Krüger, Torben H AU - Nemish, Yuriy ID - 9912 JF - Annales Henri Poincaré SN - 1424-0637 TI - Scattering in quantum dots via noncommutative rational functions VL - 22 ER - TY - JOUR AB - Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)], we present a modified “floating crystal” trial state for jellium (also known as the classical homogeneous electron gas) with density equal to a characteristic function. This allows us to show that three definitions of the jellium energy coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache [“Equality of the Jellium and uniform electron gas next-order asymptotic terms for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized energy” studied in a series of papers by Serfaty and others, and thus, by the work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate the jellium energy to the order n term in the logarithmic energy of n points on the unit 2-sphere. We improve upon known lower bounds for this renormalized energy. Additionally, we derive formulas for the jellium energy of periodic configurations. AU - Lauritsen, Asbjørn Bækgaard ID - 9891 IS - 8 JF - Journal of Mathematical Physics KW - Mathematical Physics KW - Statistical and Nonlinear Physics SN - 0022-2488 TI - Floating Wigner crystal and periodic jellium configurations VL - 62 ER - TY - JOUR AB - Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition. AU - Zeng, Yinwei AU - Verstraeten, Inge AU - Trinh, Hoang Khai AU - Heugebaert, Thomas AU - Stevens, Christian V. AU - Garcia-Maquilon, Irene AU - Rodriguez, Pedro L. AU - Vanneste, Steffen AU - Geelen, Danny ID - 9909 IS - 8 JF - Genes TI - Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling VL - 12 ER - TY - JOUR AB - DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. AU - Labajová, Naďa AU - Baranova, Natalia S. AU - Jurásek, Miroslav AU - Vácha, Robert AU - Loose, Martin AU - Barák, Imrich ID - 9907 IS - 15 JF - International Journal of Molecular Sciences SN - 16616596 TI - Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva VL - 22 ER - TY - JOUR AB - Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period. AU - Rella, Simon AU - Kulikova, Yuliya A. AU - Dermitzakis, Emmanouil T. AU - Kondrashov, Fyodor ID - 9905 IS - 1 JF - Scientific Reports TI - Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains VL - 11 ER - TY - JOUR AB - Eigenstate thermalization in quantum many-body systems implies that eigenstates at high energy are similar to random vectors. Identifying systems where at least some eigenstates are nonthermal is an outstanding question. In this Letter we show that interacting quantum models that have a nullspace—a degenerate subspace of eigenstates at zero energy (zero modes), which corresponds to infinite temperature, provide a route to nonthermal eigenstates. We analytically show the existence of a zero mode which can be represented as a matrix product state for a certain class of local Hamiltonians. In the more general case we use a subspace disentangling algorithm to generate an orthogonal basis of zero modes characterized by increasing entanglement entropy. We show evidence for an area-law entanglement scaling of the least-entangled zero mode in the broad parameter regime, leading to a conjecture that all local Hamiltonians with the nullspace feature zero modes with area-law entanglement scaling and, as such, break the strong thermalization hypothesis. Finally, we find zero modes in constrained models and propose a setup for observing their experimental signatures. AU - Karle, Volker AU - Serbyn, Maksym AU - Michailidis, Alexios ID - 9903 IS - 6 JF - Physical Review Letters SN - 0031-9007 TI - Area-law entangled eigenstates from nullspaces of local Hamiltonians VL - 127 ER - TY - JOUR AB - Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell–cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry. AU - Chaigne, Agathe AU - Smith, Matthew B. AU - Cavestany, R. L. AU - Hannezo, Edouard B AU - Chalut, Kevin J. AU - Paluch, Ewa K. ID - 9952 IS - 14 JF - Journal of Cell Science SN - 00219533 TI - Three-dimensional geometry controls division symmetry in stem cell colonies VL - 134 ER - TY - JOUR AB - About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems. AU - Picard, Marion A L AU - Vicoso, Beatriz AU - Bertrand, Stéphanie AU - Escriva, Hector ID - 9908 IS - 8 JF - Genes TI - Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict VL - 12 ER - TY - JOUR AB - In 2020, many in-person scientific events were canceled due to the COVID-19 pandemic, creating a vacuum in networking and knowledge exchange between scientists. To fill this void in scientific communication, a group of early career nanocrystal enthusiasts launched the virtual seminar series, News in Nanocrystals, in the summer of 2020. By the end of the year, the series had attracted over 850 participants from 46 countries. In this Nano Focus, we describe the process of organizing the News in Nanocrystals seminar series; discuss its growth, emphasizing what the organizers have learned in terms of diversity and accessibility; and provide an outlook for the next steps and future opportunities. This summary and analysis of experiences and learned lessons are intended to inform the broader scientific community, especially those who are looking for avenues to continue fostering discussion and scientific engagement virtually, both during the pandemic and after. AU - Baranov, Dmitry AU - Šverko, Tara AU - Moot, Taylor AU - Keller, Helena R. AU - Klein, Megan D. AU - Vishnu, E. K. AU - Balazs, Daniel AU - Shulenberger, Katherine E. ID - 9829 IS - 7 JF - ACS Nano SN - 19360851 TI - News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience VL - 15 ER - TY - GEN AB - This dataset comprises all data shown in the figures of the submitted article "Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction". Additional raw data are available from the corresponding author on reasonable request. AU - Peruzzo, Matilda AU - Hassani, Farid AU - Szep, Grisha AU - Trioni, Andrea AU - Redchenko, Elena AU - Zemlicka, Martin AU - Fink, Johannes M ID - 13057 TI - Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction ER - TY - JOUR AB - AMPA receptor (AMPAR) abundance and positioning at excitatory synapses regulates the strength of transmission. Changes in AMPAR localisation can enact synaptic plasticity, allowing long-term information storage, and is therefore tightly controlled. Multiple mechanisms regulating AMPAR synaptic anchoring have been described, but with limited coherence or comparison between reports, our understanding of this process is unclear. Here, combining synaptic recordings from mouse hippocampal slices and super-resolution imaging in dissociated cultures, we compare the contributions of three AMPAR interaction domains controlling transmission at hippocampal CA1 synapses. We show that the AMPAR C-termini play only a modulatory role, whereas the extracellular N-terminal domain (NTD) and PDZ interactions of the auxiliary subunit TARP γ8 are both crucial, and each is sufficient to maintain transmission. Our data support a model in which γ8 accumulates AMPARs at the postsynaptic density, where the NTD further tunes their positioning. This interplay between cytosolic (TARP γ8) and synaptic cleft (NTD) interactions provides versatility to regulate synaptic transmission and plasticity. AU - Watson, Jake AU - Pinggera, Alexandra AU - Ho, Hinze AU - Greger, Ingo H. ID - 9985 IS - 1 JF - Nature Communications TI - AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions VL - 12 ER - TY - JOUR AB - The numerical simulation of dynamical phenomena in interacting quantum systems is a notoriously hard problem. Although a number of promising numerical methods exist, they often have limited applicability due to the growth of entanglement or the presence of the so-called sign problem. In this work, we develop an importance sampling scheme for the simulation of quantum spin dynamics, building on a recent approach mapping quantum spin systems to classical stochastic processes. The importance sampling scheme is based on identifying the classical trajectory that yields the largest contribution to a given quantum observable. An exact transformation is then carried out to preferentially sample trajectories that are close to the dominant one. We demonstrate that this approach is capable of reducing the temporal growth of fluctuations in the stochastic quantities, thus extending the range of accessible times and system sizes compared to direct sampling. We discuss advantages and limitations of the proposed approach, outlining directions for further developments. AU - De Nicola, Stefano ID - 9981 IS - 3 JF - SciPost Physics KW - General Physics and Astronomy SN - 2542-4653 TI - Importance sampling scheme for the stochastic simulation of quantum spin dynamics VL - 11 ER - TY - CONF AB - There has recently been a surge of interest in the computational and complexity properties of the population model, which assumes n anonymous, computationally-bounded nodes, interacting at random, with the goal of jointly computing global predicates. Significant work has gone towards investigating majority or consensus dynamics in this model: that is, assuming that every node is initially in one of two states X or Y, determine which state had higher initial count. In this paper, we consider a natural generalization of majority/consensus, which we call comparison : in its simplest formulation, we are given two baseline states, X and Y, present in any initial configuration in fixed, but possibly small counts. One of these states has higher count than the other: we will assume |X_0| > C |Y_0| for some constant C > 1. The challenge is to design a protocol by which nodes can quickly and reliably decide on which of the baseline states X_0 and Y_0 has higher initial count. We begin by analyzing a simple and general dynamics solving the above comparison problem, which uses O( log n ) states per node, and converges in O(log n) (parallel) time, with high probability, to a state where the whole population votes on opinions X or Y at rates proportional to the initial concentrations of |X_0| vs. |Y_0|. We then describe how this procedure can be bootstrapped to solve comparison, i.e. have every node in the population reach the "correct'' decision, with probability 1 - o(1), at the cost of O (log log n) additional states. Further, we prove that this dynamics is self-stabilizing, in the sense that it converges to the correct decision from arbitrary initial states, and leak-robust, in the sense that it can withstand spurious faulty reactions, which are known to occur in practical implementations of population protocols. Our analysis is based on a new martingale concentration result relating the discrete-time evolution of a population protocol to its expected (steady-state) analysis, which should be a useful tool when analyzing opinion dynamics and epidemic dissemination in the population model. AU - Alistarh, Dan-Adrian AU - Töpfer, Martin AU - Uznański, Przemysław ID - 9951 SN - 9781450385480 T2 - Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing TI - Comparison dynamics in population protocols ER - TY - JOUR AB - The control of many-body quantum dynamics in complex systems is a key challenge in the quest to reliably produce and manipulate large-scale quantum entangled states. Recently, quench experiments in Rydberg atom arrays [Bluvstein et al. Science 371, 1355 (2021)] demonstrated that coherent revivals associated with quantum many-body scars can be stabilized by periodic driving, generating stable subharmonic responses over a wide parameter regime. We analyze a simple, related model where these phenomena originate from spatiotemporal ordering in an effective Floquet unitary, corresponding to discrete time-crystalline behavior in a prethermal regime. Unlike conventional discrete time crystals, the subharmonic response exists only for Néel-like initial states, associated with quantum scars. We predict robustness to perturbations and identify emergent timescales that could be observed in future experiments. Our results suggest a route to controlling entanglement in interacting quantum systems by combining periodic driving with many-body scars. AU - Maskara, N. AU - Michailidis, Alexios AU - Ho, W. W. AU - Bluvstein, D. AU - Choi, S. AU - Lukin, M. D. AU - Serbyn, Maksym ID - 9960 IS - 9 JF - Physical Review Letters SN - 0031-9007 TI - Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving VL - 127 ER - TY - JOUR AB - The notion of Thouless energy plays a central role in the theory of Anderson localization. We investigate and compare the scaling of Thouless energy across the many-body localization (MBL) transition in a Floquet model. We use a combination of methods that are reliable on the ergodic side of the transition (e.g., spectral form factor) and methods that work on the MBL side (e.g., typical matrix elements of local operators) to obtain a complete picture of the Thouless energy behavior across the transition. On the ergodic side, Thouless energy decreases slowly with the system size, while at the transition it becomes comparable to the level spacing. Different probes yield consistent estimates of Thouless energy in their overlapping regime of applicability, giving the location of the transition point nearly free of finite-size drift. This work establishes a connection between different definitions of Thouless energy in a many-body setting and yields insights into the MBL transition in Floquet systems. AU - Sonner, Michael AU - Serbyn, Maksym AU - Papić, Zlatko AU - Abanin, Dmitry A. ID - 9961 IS - 8 JF - Physical Review B SN - 2469-9950 TI - Thouless energy across the many-body localization transition in Floquet systems VL - 104 ER - TY - CONF AB - The reflectance field of a face describes the reflectance properties responsible for complex lighting effects including diffuse, specular, inter-reflection and self shadowing. Most existing methods for estimating the face reflectance from a monocular image assume faces to be diffuse with very few approaches adding a specular component. This still leaves out important perceptual aspects of reflectance as higher-order global illumination effects and self-shadowing are not modeled. We present a new neural representation for face reflectance where we can estimate all components of the reflectance responsible for the final appearance from a single monocular image. Instead of modeling each component of the reflectance separately using parametric models, our neural representation allows us to generate a basis set of faces in a geometric deformation-invariant space, parameterized by the input light direction, viewpoint and face geometry. We learn to reconstruct this reflectance field of a face just from a monocular image, which can be used to render the face from any viewpoint in any light condition. Our method is trained on a light-stage training dataset, which captures 300 people illuminated with 150 light conditions from 8 viewpoints. We show that our method outperforms existing monocular reflectance reconstruction methods, in terms of photorealism due to better capturing of physical premitives, such as sub-surface scattering, specularities, self-shadows and other higher-order effects. AU - B R, Mallikarjun AU - Tewari, Ayush AU - Oh, Tae-Hyun AU - Weyrich, Tim AU - Bickel, Bernd AU - Seidel, Hans-Peter AU - Pfister, Hanspeter AU - Matusik, Wojciech AU - Elgharib, Mohamed AU - Theobalt, Christian ID - 9957 SN - 1063-6919 T2 - Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition TI - Monocular reconstruction of neural face reflectance fields ER - TY - JOUR AB - In this article we introduce a complete gradient estimate for symmetric quantum Markov semigroups on von Neumann algebras equipped with a normal faithful tracial state, which implies semi-convexity of the entropy with respect to the recently introduced noncommutative 2-Wasserstein distance. We show that this complete gradient estimate is stable under tensor products and free products and establish its validity for a number of examples. As an application we prove a complete modified logarithmic Sobolev inequality with optimal constant for Poisson-type semigroups on free group factors. AU - Wirth, Melchior AU - Zhang, Haonan ID - 9973 JF - Communications in Mathematical Physics KW - Mathematical Physics KW - Statistical and Nonlinear Physics SN - 0010-3616 TI - Complete gradient estimates of quantum Markov semigroups VL - 387 ER - TY - JOUR AB - Inhibition or targeted deletion of histone deacetylase 3 (HDAC3) is neuroprotective in a variety neurodegenerative conditions, including retinal ganglion cells (RGCs) after acute optic nerve damage. Consistent with this, induced HDAC3 expression in cultured cells shows selective toxicity to neurons. Despite an established role for HDAC3 in neuronal pathology, little is known regarding the mechanism of this pathology. AU - Schmitt, Heather M. AU - Fehrman, Rachel L. AU - Maes, Margaret E AU - Yang, Huan AU - Guo, Lian Wang AU - Schlamp, Cassandra L. AU - Pelzel, Heather R. AU - Nickells, Robert W. ID - 10000 IS - 10 JF - Investigative Ophthalmology and Visual Science SN - 0146-0404 TI - Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression VL - 62 ER - TY - JOUR AB - We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss type A in detail as well as its connections with quantum XXZ spin chains and trigonometric Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic version of results of Givental and Kim, connecting quantum geometry of flag varieties and Toda lattice. AU - Koroteev, Peter AU - Pushkar, Petr AU - Smirnov, Andrey V. AU - Zeitlin, Anton M. ID - 9998 IS - 5 JF - Selecta Mathematica SN - 1022-1824 TI - Quantum K-theory of quiver varieties and many-body systems VL - 27 ER -