@misc{9704, abstract = {Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.}, author = {Mcmahon, Dino and Natsopoulou, Myrsini and Doublet, Vincent and Fürst, Matthias and Weging, Silvio and Brown, Mark and Gogol Döring, Andreas and Paxton, Robert}, publisher = {Dryad}, title = {{Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss}}, doi = {10.5061/dryad.cq7t1}, year = {2016}, } @misc{9710, abstract = {Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.}, author = {Barton, Nicholas H}, publisher = {Dryad}, title = {{Data from: How does epistasis influence the response to selection?}}, doi = {10.5061/dryad.s5s7r}, year = {2016}, } @misc{9720, abstract = {Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.}, author = {Mcmahon, Dino and Fürst, Matthias and Caspar, Jesicca and Theodorou, Panagiotis and Brown, Mark and Paxton, Robert}, publisher = {Dryad}, title = {{Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees}}, doi = {10.5061/dryad.4b565}, year = {2016}, } @article{983, abstract = {The half-filled Landau level is expected to be approximately particle-hole symmetric, which requires an extension of the Halperin-Lee-Read (HLR) theory of the compressible state observed at this filling. Recent work indicates that, when particle-hole symmetry is preserved, the composite fermions experience a quantized π-Berry phase upon winding around the composite Fermi surface, analogous to Dirac fermions at the surface of a 3D topological insulator. In contrast, the effective low-energy theory of the composite fermion liquid originally proposed by HLR lacks particle-hole symmetry and has vanishing Berry phase. In this paper, we explain how thermoelectric transport measurements can be used to test the Dirac nature of the composite fermions by quantitatively extracting this Berry phase. First, we point out that longitudinal thermopower (Seebeck effect) is nonvanishing because of the unusual nature of particle-hole symmetry in this context and is not sensitive to the Berry phase. In contrast, we find that off-diagonal thermopower (Nernst effect) is directly related to the topological structure of the composite Fermi surface, vanishing for zero Berry phase and taking its maximal value for π Berry phase. In contrast, in purely electrical transport signatures, the Berry phase contributions appear as small corrections to a large background signal, making the Nernst effect a promising diagnostic of the Dirac nature of composite fermions.}, author = {Potter, Andrew C and Maksym Serbyn and Vishwanath, Ashvin K}, journal = {Physical Review X}, number = {3}, publisher = {American Physical Society}, title = {{Thermoelectric transport signatures of Dirac composite fermions in the half-filled Landau level}}, doi = {10.1103/PhysRevX.6.031026}, volume = {6}, year = {2016}, } @article{984, abstract = {The entanglement spectrum of the reduced density matrix contains information beyond the von Neumann entropy and provides unique insights into exotic orders or critical behavior of quantum systems. Here, we show that strongly disordered systems in the many-body localized phase have power-law entanglement spectra, arising from the presence of extensively many local integrals of motion. The power-law entanglement spectrum distinguishes many-body localized systems from ergodic systems, as well as from ground states of gapped integrable models or free systems in the vicinity of scale-invariant critical points. We confirm our results using large-scale exact diagonalization. In addition, we develop a matrix-product state algorithm which allows us to access the eigenstates of large systems close to the localization transition, and discuss general implications of our results for variational studies of highly excited eigenstates in many-body localized systems.}, author = {Maksym Serbyn and Alexios Michailidis and Abanin, Dmitry A and Papić, Zlatko}, journal = {Physical Review Letters}, number = {16}, publisher = {American Physical Society}, title = {{Power-law entanglement spectrum in many-body localized phases}}, doi = {10.1103/PhysRevLett.117.160601}, volume = {117}, year = {2016}, } @article{985, abstract = {We report on magnetotransport studies of dual-gated, Bernal-stacked trilayer graphene (TLG) encapsulated in boron nitride crystals. We observe a quantum Hall effect staircase which indicates a complete lifting of the 12-fold degeneracy of the zeroth Landau level. As a function of perpendicular electric field, our data exhibit a sequence of phase transitions between all integer quantum Hall states in the filling factor interval -8<ν<0. We develop a theoretical model and argue that, in contrast to monolayer and bilayer graphene, the observed Landau level splittings and quantum Hall phase transitions can be understood within a single-particle picture, but imply the presence of a charge density imbalance between the inner and outer layers of TLG, even at charge neutrality and zero transverse electric field. Our results indicate the importance of a previously unaccounted band structure parameter which, together with a more accurate estimate of the other tight-binding parameters, results in a significantly improved determination of the electronic and Landau level structure of TLG.}, author = {Campos, Leonardo C and Taychatanapat, Thiti and Maksym Serbyn and Surakitbovorn, Kawin N and Watanabe, Kenji and Taniguchi, Takashi and Abanin, Dmitry A and Jarillo-Herrero, Pablo}, journal = {Physical Review Letters}, number = {6}, publisher = {American Physical Society}, title = {{Landau Level Splittings, Phase Transitions, and Nonuniform Charge Distribution in Trilayer Graphene}}, doi = {10.1103/PhysRevLett.117.066601}, volume = {117}, year = {2016}, } @article{986, abstract = {The many-body localization transition (MBLT) between ergodic and many-body localized phases in disordered interacting systems is a subject of much recent interest. The statistics of eigenenergies is known to be a powerful probe of crossovers between ergodic and integrable systems in simpler examples of quantum chaos. We consider the evolution of the spectral statistics across the MBLT, starting with mapping to a Brownian motion process that analytically relates the spectral properties to the statistics of matrix elements. We demonstrate that the flow from Wigner-Dyson to Poisson statistics is a two-stage process. First, a fractal enhancement of matrix elements upon approaching the MBLT from the delocalized side produces an effective power-law interaction between energy levels, and leads to a plasma model for level statistics. At the second stage, the gas of eigenvalues has local interactions and the level statistics belongs to a semi-Poisson universality class. We verify our findings numerically on the XXZ spin chain. We provide a microscopic understanding of the level statistics across the MBLT and discuss implications for the transition that are strong constraints on possible theories.}, author = {Maksym Serbyn and Moore, Joel E}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {4}, publisher = {American Physical Society}, title = {{Spectral statistics across the many-body localization transition}}, doi = {10.1103/PhysRevB.93.041424}, volume = {93}, year = {2016}, } @misc{9864, abstract = {Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.}, author = {Fernandes Redondo, Rodrigo A and de Vladar, Harold and Włodarski, Tomasz and Bollback, Jonathan P}, publisher = {The Royal Society}, title = {{Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family}}, doi = {10.6084/m9.figshare.4315652.v1}, year = {2016}, } @article{987, abstract = {In contrast to bulk FeSe, which exhibits nematic order and low temperature superconductivity, highly doped FeSe reverses the situation, having high temperature superconductivity appearing alongside a suppression of nematic order. To investigate this phenomenon, we study a minimal electronic model of FeSe, with interactions that enhance nematic fluctuations. This model is sign problem free, and is simulated using determinant quantum Monte Carlo (DQMC). We developed a DQMC algorithm with parallel tempering, which proves to be an efficient source of global updates and allows us to access the region of strong interactions. Over a wide range of intermediate couplings, we observe superconductivity with an extended s-wave order parameter, along with enhanced, but short-ranged, q=(0,0) ferro-orbital (nematic) order. These results are consistent with approximate weak-coupling treatments that predict that nematic fluctuations lead to superconducting pairing. Surprisingly, in the parameter range under study, we do not observe nematic long-range order. Instead, at stronger coupling an unusual insulating phase with q=(π,π) antiferro-orbital order appears, which is missed by weak-coupling approximations.}, author = {Dumitrescu, Philipp T and Maksym Serbyn and Scalettar, Richard T and Vishwanath, Ashvin K}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {15}, publisher = {American Physical Society}, title = {{Superconductivity and nematic fluctuations in a model of doped FeSe monolayers: Determinant quantum Monte Carlo study}}, doi = {10.1103/PhysRevB.94.155127}, volume = {94}, year = {2016}, } @article{366, abstract = {Cesium lead halide (CsPbX3, X = Cl, Br, I) nanocrystals (NCs) offer exceptional optical properties for several potential applications but their implementation is hindered by a low chemical and structural stability and limited processability. In the present work, we developed a new method to efficiently coat CsPbX3 NCs, which resulted in their increased chemical and optical stability as well as processability. The method is based on the incorporation of poly(maleic anhydride-alt-1-octadecene) (PMA) into the synthesis of the perovskite NCs. The presence of PMA in the ligand shell stabilizes the NCs by tightening the ligand binding, limiting in this way the NC surface interaction with the surrounding media. We further show that these NCs can be embedded in self-standing silicone/glass plates as down-conversion filters for the fabrication of monochromatic green and white light emitting diodes (LEDs) with narrow bandwidths and appealing color characteristics.}, author = {Meyn, Michaela and Perálvarez, Mariano and Heuer Jungemann, Amelie and Hertog, Wim and Ibanez Sabate, Maria and Nafria, Raquel and Genç, Aziz and Arbiol, Jordi and Kovalenko, Maksym and Carreras, Josep and Cabot, Andreu and Kanaras, Antonios}, journal = {ACS Applied Materials and Interfaces}, number = {30}, pages = {19579 -- 19586}, publisher = {American Chemical Society}, title = {{Polymer enhanced stability of inorganic perovskite nanocrystals and their application in color conversion LEDs}}, doi = {10.1021/acsami.6b02529}, volume = {8}, year = {2016}, } @article{389, abstract = {The coherent optical manipulation of solids is emerging as a promising way to engineer novel quantum states of matter. The strong time-periodic potential of intense laser light can be used to generate hybrid photon-electron states. Interaction of light with Bloch states leads to Floquet-Bloch states, which are essential in realizing new photo-induced quantum phases. Similarly, dressing of free-electron states near the surface of a solid generates Volkov states, which are used to study nonlinear optics in atoms and semiconductors. The interaction of these two dynamic states with each other remains an open experimental problem. Here we use time- and angle-resolved photoemission spectroscopy (Tr-ARPES) to selectively study the transition between these two states on the surface of the topological insulator Bi2Se3. We find that the coupling between the two strongly depends on the electron momentum, providing a route to enhance or inhibit it. Moreover, by controlling the light polarization we can negate Volkov states to generate pure Floquet-Bloch states. This work establishes a systematic path for the coherent manipulation of solids via light-matter interaction.}, author = {Mahmood, Fahad and Chan, Ching and Alpichshev, Zhanybek and Gardner, Dillon and Lee, Young and Lee, Patrick and Gedik, Nuh}, journal = {Nature Physics}, number = {4}, pages = {306 -- 310}, publisher = {Nature Publishing Group}, title = {{Selective scattering between Floquet Bloch and Volkov states in a topological insulator}}, doi = {10.1038/nphys3609}, volume = {12}, year = {2016}, } @article{257, abstract = {For suitable pairs of diagonal quadratic forms in eight variables we use the circle method to investigate the density of simultaneous integer solutions and relate this to the problem of estimating linear correlations among sums of two squares.}, author = {Timothy Browning and Munshi, Ritabrata}, journal = {Forum Mathematicum}, number = {4}, pages = {2025 -- 2050}, publisher = {Walter de Gruyter GmbH}, title = {{Pairs of diagonal quadratic forms and linear correlations among sums of two squares}}, doi = {10.1515/forum-2013-6024}, volume = {27}, year = {2015}, } @article{271, abstract = {We show that a non-singular integral form of degree d is soluble non-trivially over the integers if and only if it is soluble non-trivially over the reals and the p-adic numbers, provided that the form has at least (d-\sqrt{d}/2)2^d variables. This improves on a longstanding result of Birch.}, author = {Browning, Timothy D and Prendiville, Sean}, issn = {0075-4102}, journal = {Journal fur die Reine und Angewandte Mathematik}, number = {731}, pages = {203 -- 234}, publisher = {Walter de Gruyter}, title = {{Improvements in Birch's theorem on forms in many variables}}, doi = {10.1515/crelle-2014-0122}, volume = {2017}, year = {2015}, } @inproceedings{10748, abstract = {The study of fluxoid states and fluxoid dynamics in mesoscopic iron-based superconducting rings is valuable for characterizing the basic properties of the superconductor, and may also provide important insight into the superconducting paring symmetry. We report the fabrications of micron-sized rings and disks from thin films of Fe(Se, Te) grown by molecular beam epitaxy. In order to study fluxoid states in rings we developed a custom-tailored version of magnetic force microscopy (MFM). This technique has a number of qualitative advantages for working with mesoscopic superconducting samples in comparison to the conventional MFM and other imaging techniques. We observed metastable fluxoid states in rings of different sizes. Thermally activated fluxoid dynamics of these states was studied and modeled. In addition, we found different regimes of interaction between Fe(Se, Te) ring and MFM tip which are explained. Possibilities of the existence of exotic vortex states and proposals for experiments to test the symmetry of the superconducting order parameter in iron based superconductors are analyzed.}, author = {Polshyn, Hryhoriy and Zhang, Can and Naibert, Tyler and Eckstein, James and Budakian, Raffi}, booktitle = {APS March Meeting 2015}, issn = {0003-0503}, location = {San Antonio, TX, United States}, number = {1}, publisher = {American Physical Society}, title = {{Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy}}, volume = {60}, year = {2015}, } @article{10794, abstract = {Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation.}, author = {Parise, Francesca and Lygeros, John and Ruess, Jakob}, issn = {2296-665X}, journal = {Frontiers in Environmental Science}, keywords = {General Environmental Science}, publisher = {Frontiers}, title = {{Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study}}, doi = {10.3389/fenvs.2015.00042}, volume = {3}, year = {2015}, } @article{11073, abstract = {Human cancer cells bear complex chromosome rearrangements that can be potential drivers of cancer development. However, the molecular mechanisms underlying these rearrangements have been unclear. Zhang et al. use a new technique combining live-cell imaging and single-cell sequencing to demonstrate that chromosomes mis-segregated to micronuclei frequently undergo chromothripsis-like rearrangements in the subsequent cell cycle.}, author = {Hatch, Emily M. and HETZER, Martin W}, issn = {0092-8674}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {7}, pages = {1502--1504}, publisher = {Elsevier}, title = {{Linking micronuclei to chromosome fragmentation}}, doi = {10.1016/j.cell.2015.06.005}, volume = {161}, year = {2015}, } @article{11074, author = {Hatch, Emily M. and HETZER, Martin W}, issn = {0960-9822}, journal = {Current Biology}, keywords = {General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology}, number = {10}, pages = {PR397--R399}, publisher = {Elsevier}, title = {{Chromothripsis}}, doi = {10.1016/j.cub.2015.02.033}, volume = {25}, year = {2015}, } @article{11076, abstract = {Nuclear pore complexes (NPCs) are composed of several copies of ∼30 different proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE) and regulate the nucleocytoplasmic trafficking of macromolecules. Beyond this vital role, NPC components influence genome functions in a transport-independent manner. Nups play an evolutionarily conserved role in gene expression regulation that, in metazoans, extends into the nuclear interior. Additionally, in proliferative cells, Nups play a crucial role in genome integrity maintenance and mitotic progression. Here we discuss genome-related functions of Nups and their impact on essential DNA metabolism processes such as transcription, chromosome duplication, and segregation.}, author = {Ibarra, Arkaitz and HETZER, Martin W}, issn = {1549-5477}, journal = {Genes & Development}, keywords = {Developmental Biology, Genetics}, number = {4}, pages = {337--349}, publisher = {Cold Spring Harbor Laboratory}, title = {{Nuclear pore proteins and the control of genome functions}}, doi = {10.1101/gad.256495.114}, volume = {29}, year = {2015}, } @article{11077, abstract = {Nucleoporins (Nups) are a family of proteins best known as the constituent building blocks of nuclear pore complexes (NPCs), membrane-embedded channels that mediate nuclear transport across the nuclear envelope. Recent evidence suggests that several Nups have additional roles in controlling the activation and silencing of developmental genes; however, the mechanistic details of these functions remain poorly understood. Here, we show that depletion of Nup153 in mouse embryonic stem cells (mESCs) causes the derepression of developmental genes and induction of early differentiation. This loss of stem cell identity is not associated with defects in the nuclear import of key pluripotency factors. Rather, Nup153 binds around the transcriptional start site (TSS) of developmental genes and mediates the recruitment of the polycomb-repressive complex 1 (PRC1) to a subset of its target loci. Our results demonstrate a chromatin-associated role of Nup153 in maintaining stem cell pluripotency by functioning in mammalian epigenetic gene silencing.}, author = {Jacinto, Filipe V. and Benner, Chris and HETZER, Martin W}, issn = {1549-5477}, journal = {Genes & Development}, keywords = {Developmental Biology, Genetics}, number = {12}, pages = {1224--1238}, publisher = {Cold Spring Harbor Laboratory}, title = {{The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing}}, doi = {10.1101/gad.260919.115}, volume = {29}, year = {2015}, } @article{11078, abstract = {Aging is associated with the decline of protein, cell, and organ function. Here, we use an integrated approach to characterize gene expression, bulk translation, and cell biology in the brains and livers of young and old rats. We identify 468 differences in protein abundance between young and old animals. The majority are a consequence of altered translation output, that is, the combined effect of changes in transcript abundance and translation efficiency. In addition, we identify 130 proteins whose overall abundance remains unchanged but whose sub-cellular localization, phosphorylation state, or splice-form varies. While some protein-level differences appear to be a generic property of the rats’ chronological age, the majority are specific to one organ. These may be a consequence of the organ’s physiology or the chronological age of the cells within the tissue. Taken together, our study provides an initial view of the proteome at the molecular, sub-cellular, and organ level in young and old rats.}, author = {Ori, Alessandro and Toyama, Brandon H. and Harris, Michael S. and Bock, Thomas and Iskar, Murat and Bork, Peer and Ingolia, Nicholas T. and HETZER, Martin W and Beck, Martin}, issn = {2405-4712}, journal = {Cell Systems}, keywords = {Cell Biology, Histology, Pathology and Forensic Medicine}, number = {3}, pages = {P224--237}, publisher = {Elsevier}, title = {{Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats}}, doi = {10.1016/j.cels.2015.08.012}, volume = {1}, year = {2015}, }