TY - JOUR AB - Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management. AU - Viljakainen, Lumi AU - Fürst, Matthias AU - Grasse, Anna V AU - Jurvansuu, Jaana AU - Oh, Jinook AU - Tolonen, Lassi AU - Eder, Thomas AU - Rattei, Thomas AU - Cremer, Sylvia ID - 12469 JF - Frontiers in Microbiology TI - Antiviral immune response reveals host-specific virus infections in natural ant populations VL - 14 ER - TY - JOUR AB - We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use. AU - Boissonnat, Jean-Daniel AU - Dyer, Ramsay AU - Ghosh, Arijit AU - Wintraecken, Mathijs ID - 12287 JF - Discrete & Computational Geometry KW - Computational Theory and Mathematics KW - Discrete Mathematics and Combinatorics KW - Geometry and Topology KW - Theoretical Computer Science SN - 0179-5376 TI - Local criteria for triangulating general manifolds VL - 69 ER - TY - JOUR AB - It may come as a surprise that a phenomenon as ubiquitous and prominent as the transition from laminar to turbulent flow has resisted combined efforts by physicists, engineers and mathematicians, and remained unresolved for almost one and a half centuries. In recent years, various studies have proposed analogies to directed percolation, a well-known universality class in statistical mechanics, which describes a non-equilibrium phase transition from a fluctuating active phase into an absorbing state. It is this unlikely relation between the multiscale, high-dimensional dynamics that signify the transition process in virtually all flows of practical relevance, and the arguably most basic non-equilibrium phase transition, that so far has mainly been the subject of model studies, which I review in this Perspective. AU - Hof, Björn ID - 12165 JF - Nature Reviews Physics KW - General Physics and Astronomy TI - Directed percolation and the transition to turbulence VL - 5 ER - TY - JOUR AB - The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions. AU - Fäßler, Florian AU - Javoor, Manjunath AU - Schur, Florian KM ID - 12421 IS - 1 JF - Biochemical Society Transactions KW - Biochemistry SN - 0300-5127 TI - Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM VL - 51 ER - TY - JOUR AB - Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion. AU - Marensi, Elena AU - Yalniz, Gökhan AU - Hof, Björn AU - Budanur, Nazmi B ID - 12105 JF - Journal of Fluid Mechanics SN - 0022-1120 TI - Symmetry-reduced dynamic mode decomposition of near-wall turbulence VL - 954 ER - TY - JOUR AB - The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model. AU - Bolnick, Daniel I. AU - Hund, Amanda K. AU - Nosil, Patrik AU - Peng, Foen AU - Ravinet, Mark AU - Stankowski, Sean AU - Subramanian, Swapna AU - Wolf, Jochen B.W. AU - Yukilevich, Roman ID - 12514 IS - 1 JF - Evolution: International journal of organic evolution TI - A multivariate view of the speciation continuum VL - 77 ER - TY - CONF AB - The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts. AU - Forghani, Mohammad AU - Claramunt, Christophe AU - Karimipour, Farid AU - Heiler, Georg ID - 12548 T2 - 2022 IEEE International Conference on Data Mining Workshops TI - Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic ER - TY - JOUR AB - he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems. AU - Krokhin, Andrei AU - Opršal, Jakub AU - Wrochna, Marcin AU - Živný, Stanislav ID - 12563 IS - 1 JF - SIAM Journal on Computing KW - General Mathematics KW - General Computer Science SN - 0097-5397 TI - Topology and adjunction in promise constraint satisfaction VL - 52 ER - TY - JOUR AB - We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front. AU - Rojas Vega, Mauricio Nicolas AU - De Castro, Pablo AU - Soto, Rodrigo ID - 12545 IS - 1 JF - Physical Review E SN - 2470-0045 TI - Wetting dynamics by mixtures of fast and slow self-propelled particles VL - 107 ER - TY - JOUR AB - Let k be a number field and X a smooth, geometrically integral quasi-projective variety over k. For any linear algebraic group G over k and any G-torsor g : Z → X, we observe that if the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for all twists of Z by elements in H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for X. As an application, we show that any homogeneous space of the form G/H with G a connected linear algebraic group over k satisfies strong approximation off the infinite places with étale-Brauer obstruction, under some compactness assumptions when k is totally real. We also prove more refined strong approximation results for homogeneous spaces of the form G/H with G semisimple simply connected and H finite, using the theory of torsors and descent. AU - Balestrieri, Francesca ID - 12427 IS - 3 JF - Proceedings of the American Mathematical Society SN - 0002-9939 TI - Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups VL - 151 ER -