Showing papers by "University of Florida published in 2018"
TL;DR: This guidance provides a data-supported approach to the diagnostic, therapeutic, and preventive aspects of NAFLD care.
4,431 citations
TL;DR: This analysis expands upon previous analyses by working under the hypothesis that both bodies were neutron stars that are described by the same equation of state and have spins within the range observed in Galactic binary neutron stars.
Abstract: On 17 August 2017, the LIGO and Virgo observatories made the first direct detection of gravitational waves from the coalescence of a neutron star binary system. The detection of this gravitational-wave signal, GW170817, offers a novel opportunity to directly probe the properties of matter at the extreme conditions found in the interior of these stars. The initial, minimal-assumption analysis of the LIGO and Virgo data placed constraints on the tidal effects of the coalescing bodies, which were then translated to constraints on neutron star radii. Here, we expand upon previous analyses by working under the hypothesis that both bodies were neutron stars that are described by the same equation of state and have spins within the range observed in Galactic binary neutron stars. Our analysis employs two methods: the use of equation-of-state-insensitive relations between various macroscopic properties of the neutron stars and the use of an efficient parametrization of the defining function pðρÞ of the equation of state itself. From the LIGO and Virgo data alone and the first method, we measure the two neutron star radii as R1 ¼ 10.8 þ2.0 −1.7 km for the heavier star and R2 ¼ 10.7 þ2.1 −1.5 km for the lighter star at the 90% credible level. If we additionally require that the equation of state supports neutron stars with masses larger than 1.97 M⊙ as required from electromagnetic observations and employ the equation-of-state parametrization, we further constrain R1 ¼ 11.9 þ1.4 −1.4 km and R2 ¼ 11.9 þ1.4 −1.4 km at the 90% credible level. Finally, we obtain constraints on pðρÞ at supranuclear densities, with pressure at twice nuclear saturation density measured at 3.5 þ2.7 −1.7 × 1034 dyn cm−2 at the 90% level.
1,595 citations
TL;DR: The role of defects and impurities on the transport and optical properties of bulk, epitaxial, and nanostructures material, the difficulty in p-type doping, and the development of processing techniques like etching, contact formation, dielectrics for gate formation, and passivation are discussed in this article.
Abstract: Gallium oxide (Ga2O3) is emerging as a viable candidate for certain classes of power electronics, solar blind UV photodetectors, solar cells, and sensors with capabilities beyond existing technologies due to its large bandgap. It is usually reported that there are five different polymorphs of Ga2O3, namely, the monoclinic (β-Ga2O3), rhombohedral (α), defective spinel (γ), cubic (δ), or orthorhombic (e) structures. Of these, the β-polymorph is the stable form under normal conditions and has been the most widely studied and utilized. Since melt growth techniques can be used to grow bulk crystals of β-GaO3, the cost of producing larger area, uniform substrates is potentially lower compared to the vapor growth techniques used to manufacture bulk crystals of GaN and SiC. The performance of technologically important high voltage rectifiers and enhancement-mode Metal-Oxide Field Effect Transistors benefit from the larger critical electric field of β-Ga2O3 relative to either SiC or GaN. However, the absence of clear demonstrations of p-type doping in Ga2O3, which may be a fundamental issue resulting from the band structure, makes it very difficult to simultaneously achieve low turn-on voltages and ultra-high breakdown. The purpose of this review is to summarize recent advances in the growth, processing, and device performance of the most widely studied polymorph, β-Ga2O3. The role of defects and impurities on the transport and optical properties of bulk, epitaxial, and nanostructures material, the difficulty in p-type doping, and the development of processing techniques like etching, contact formation, dielectrics for gate formation, and passivation are discussed. Areas where continued development is needed to fully exploit the properties of Ga2O3 are identified.
1,535 citations
University of Hawaii at Manoa1, University of Pennsylvania2, University of Michigan3, Harvard University4, GlaxoSmithKline5, Imperial College London6, University of Toronto7, Princess Margaret Cancer Centre8, Vanderbilt University9, Drexel University10, Carnegie Mellon University11, Stanford University12, University of Virginia13, Broad Institute14, Toyota Technological Institute at Chicago15, Trinity University16, Princeton University17, National Institutes of Health18, Howard Hughes Medical Institute19, University of Florida20, University of Colorado Denver21, University of Münster22, Georgetown University Medical Center23, Washington University in St. Louis24, Brown University25, Morgridge Institute for Research26, University of Wisconsin-Madison27
TL;DR: It is found that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art.
Abstract: Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.
1,491 citations
Verneri Anttila1, Verneri Anttila2, Brendan Bulik-Sullivan2, Brendan Bulik-Sullivan1 +717 more•Institutions (270)
TL;DR: It is demonstrated that, in the general population, the personality trait neuroticism is significantly correlated with almost every psychiatric disorder and migraine, and it is shown that both psychiatric and neurological disorders have robust correlations with cognitive and personality measures.
Abstract: Disorders of the brain can exhibit considerable epidemiological comorbidity and often share symptoms, provoking debate about their etiologic overlap. We quantified the genetic sharing of 25 brain disorders from genome-wide association studies of 265,218 patients and 784,643 control participants and assessed their relationship to 17 phenotypes from 1,191,588 individuals. Psychiatric disorders share common variant risk, whereas neurological disorders appear more distinct from one another and from the psychiatric disorders. We also identified significant sharing between disorders and a number of brain phenotypes, including cognitive measures. Further, we conducted simulations to explore how statistical power, diagnostic misclassification, and phenotypic heterogeneity affect genetic correlations. These results highlight the importance of common genetic variation as a risk factor for brain disorders and the value of heritability-based methods in understanding their etiology.
1,357 citations
TL;DR: In the current database version of MODOMICS, the following new features and data are included: extended mass spectrometry and liquid chromatography data for modified nucleosides; links between human tRNA sequences and MINTbase - a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments.
Abstract: MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. In the current database version, we included the following new features and data: extended mass spectrometry and liquid chromatography data for modified nucleosides; links between human tRNA sequences and MINTbase - a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments; new, machine-friendly system of unified abbreviations for modified nucleoside names; sets of modified tRNA sequences for two bacterial species, updated collection of mammalian tRNA modifications, 19 newly identified modified ribonucleosides and 66 functionally characterized proteins involved in RNA modification. Data from MODOMICS have been linked to the RNAcentral database of RNA sequences. MODOMICS is available at http://modomics.genesilico.pl.
1,292 citations
University of Zurich1, Johns Hopkins University2, Mayo Clinic3, St. Marianna University School of Medicine4, Catholic University of the Sacred Heart5, Katholieke Universiteit Leuven6, University of Ferrara7, University of Lübeck8, Yokohama City University9, University of Giessen10, Wakayama Medical University11, University of Padua12, Hiroshima University13, University of Florida14, Imperial College London15, University of Gothenburg16, Leiden University17, Karolinska Institutet18, University of Adelaide19, Tohoku University20
TL;DR: The clinical expert consensus document part I summarizes the current state of knowledge on clinical presentation and characteristics of TTS and agrees on controversies surrounding TTS such as nomenclature, different TTS types, role of coronary artery disease, and etiology.
Abstract: Takotsubo syndrome (TTS) is a poorly recognized heart disease that was initially regarded as a benign condition. Recently, it has been shown that TTS may be associated with severe clinical complications including death and that its prevalence is probably underestimated. Since current guidelines on TTS are lacking, it appears timely and important to provide an expert consensus statement on TTS. The clinical expert consensus document part I summarizes the current state of knowledge on clinical presentation and characteristics of TTS and agrees on controversies surrounding TTS such as nomenclature, different TTS types, role of coronary artery disease, and etiology. This consensus also proposes new diagnostic criteria based on current knowledge to improve diagnostic accuracy.
903 citations
TL;DR: This review sums up recent theoretical and experimental approaches for understanding the underlying photophysical processes in hot electron generation and discusses various electron-transfer models on both plasmonic metal nanostructures and plasMonic metal/semiconductor heterostructure.
Abstract: Visible-light-driven photochemistry has continued to attract heightened interest due to its capacity to efficiently harvest solar energy and its potential to solve the global energy crisis. Plasmonic nanostructures boast broadly tunable optical properties coupled with catalytically active surfaces that offer a unique opportunity for solar photochemistry. Resonant optical excitation of surface plasmons produces energetic hot electrons that can be collected to facilitate chemical reactions. This review sums up recent theoretical and experimental approaches for understanding the underlying photophysical processes in hot electron generation and discusses various electron-transfer models on both plasmonic metal nanostructures and plasmonic metal/semiconductor heterostructures. Following that are highlights of recent examples of plasmon-driven hot electron photochemical reactions within the context of both cases. The review concludes with a discussion about the remaining challenges in the field and future oppor...
891 citations
Northern Arizona University1, University of Minnesota2, Woods Hole Oceanographic Institution3, University of California, Davis4, Massachusetts Institute of Technology5, University of Copenhagen6, University of Trento7, Chinese Academy of Sciences8, University of California, San Francisco9, Children's Hospital of Philadelphia10, Pacific Northwest National Laboratory11, North Carolina State University12, University of Montana13, Dalhousie University14, University of British Columbia15, Shedd Aquarium16, University of Colorado Denver17, University of California, San Diego18, Michigan State University19, Stanford University20, Broad Institute21, Harvard University22, Australian National University23, University of Düsseldorf24, Sookmyung Women's University25, San Diego State University26, Howard Hughes Medical Institute27, Max Planck Society28, Cornell University29, University of Washington30, Colorado State University31, Google32, Syracuse University33, Webster University34, United States Department of Agriculture35, University of Arkansas for Medical Sciences36, Colorado School of Mines37, University of Southern Mississippi38, Atlantic Oceanographic and Meteorological Laboratory39, University of California, Merced40, Wageningen University and Research Centre41, University of Arizona42, Environment Agency43, University of Florida44, Merck & Co.45
TL;DR: QIIME 2 provides new features that will drive the next generation of microbiome research, including interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.
Abstract: We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.
875 citations
TL;DR: In this article, the authors present possible observing scenarios for the Advanced LIGO, Advanced Virgo and KAGRA gravitational-wave detectors over the next decade, with the intention of providing information to the astronomy community to facilitate planning for multi-messenger astronomy with gravitational waves.
Abstract: We present possible observing scenarios for the Advanced LIGO, Advanced Virgo and KAGRA gravitational-wave detectors over the next decade, with the intention of providing information to the astronomy community to facilitate planning for multi-messenger astronomy with gravitational waves. We estimate the sensitivity of the network to transient gravitational-wave signals, and study the capability of the network to determine the sky location of the source. We report our findings for gravitational-wave transients, with particular focus on gravitational-wave signals from the inspiral of binary neutron star systems, which are the most promising targets for multi-messenger astronomy. The ability to localize the sources of the detected signals depends on the geographical distribution of the detectors and their relative sensitivity, and 90% credible regions can be as large as thousands of square degrees when only two sensitive detectors are operational. Determining the sky position of a significant fraction of detected signals to areas of 5– 20 deg2 requires at least three detectors of sensitivity within a factor of ∼2 of each other and with a broad frequency bandwidth. When all detectors, including KAGRA and the third LIGO detector in India, reach design sensitivity, a significant fraction of gravitational-wave signals will be localized to a few square degrees by gravitational-wave observations alone.
804 citations
Oregon Health & Science University1, Howard Hughes Medical Institute2, Oregon State University3, University of Florida4, University of Texas Southwestern Medical Center5, Fox Chase Cancer Center6, University of Utah7, National Institutes of Health8, University of Colorado Denver9, University of Kansas10, University of Miami11, Stanford University12
TL;DR: Analyses of samples from patients with acute myeloid leukaemia reveal that drug response is associated with mutational status and gene expression; the generated dataset provides a basis for future clinical and functional studies of this disease.
Abstract: The implementation of targeted therapies for acute myeloid leukaemia (AML) has been challenging because of the complex mutational patterns within and across patients as well as a dearth of pharmacologic agents for most mutational events. Here we report initial findings from the Beat AML programme on a cohort of 672 tumour specimens collected from 562 patients. We assessed these specimens using whole-exome sequencing, RNA sequencing and analyses of ex vivo drug sensitivity. Our data reveal mutational events that have not previously been detected in AML. We show that the response to drugs is associated with mutational status, including instances of drug sensitivity that are specific to combinatorial mutational events. Integration with RNA sequencing also revealed gene expression signatures, which predict a role for specific gene networks in the drug response. Collectively, we have generated a dataset—accessible through the Beat AML data viewer (Vizome)—that can be leveraged to address clinical, genomic, transcriptomic and functional analyses of the biology of AML. Analyses of samples from patients with acute myeloid leukaemia reveal that drug response is associated with mutational status and gene expression; the generated dataset provides a basis for future clinical and functional studies of this disease.
TL;DR: In this paper, the authors survey the current research on applying deep learning to clinical tasks based on EHR data, where they find a variety of deep learning techniques and frameworks being applied to several types of clinical applications including information extraction, representation learning, outcome prediction, phenotyping, and deidentification.
Abstract: The past decade has seen an explosion in the amount of digital information stored in electronic health records (EHRs). While primarily designed for archiving patient information and performing administrative healthcare tasks like billing, many researchers have found secondary use of these records for various clinical informatics applications. Over the same period, the machine learning community has seen widespread advances in the field of deep learning. In this review, we survey the current research on applying deep learning to clinical tasks based on EHR data, where we find a variety of deep learning techniques and frameworks being applied to several types of clinical applications including information extraction, representation learning, outcome prediction, phenotyping, and deidentification. We identify several limitations of current research involving topics such as model interpretability, data heterogeneity, and lack of universal benchmarks. We conclude by summarizing the state of the field and identifying avenues of future deep EHR research.
California Institute of Technology1, Carnegie Institution for Science2, University of California, Davis3, University of California, San Diego4, Northwestern University5, University of Texas at Austin6, University of Toronto7, University of Zurich8, University of California, Berkeley9, Massachusetts Institute of Technology10, Stanford University11, University of California, Irvine12, University of Florida13
TL;DR: The Feedback In Realistic Environments (FIRE) project explores feedback in cosmological galaxy formation simulations as mentioned in this paper, which has been used to explore new physics (e.g. magnetic fields).
Abstract: The Feedback In Realistic Environments (FIRE) project explores feedback in cosmological galaxy formation simulations. Previous FIRE simulations used an identical source code (“FIRE-1”) for consistency. Motivated by the development of more accurate numerics – including hydrodynamic solvers, gravitational softening, and supernova coupling algorithms – and exploration of new physics (e.g. magnetic fields), we introduce “FIRE-2”, an updated numerical implementation of FIRE physics for the GIZMO code. We run a suite of simulations and compare against FIRE-1: overall, FIRE-2 improvements do not qualitatively change galaxy-scale properties. We pursue an extensive study of numerics versus physics. Details of the star-formation algorithm, cooling physics, and chemistry have weak effects, provided that we include metal-line cooling and star formation occurs at higher-than-mean densities. We present new resolution criteria for high-resolution galaxy simulations. Most galaxy-scale properties are robust to numerics we test, provided: (1) Toomre masses are resolved; (2) feedback coupling ensures conservation, and (3) individual supernovae are time-resolved. Stellar masses and profiles are most robust to resolution, followed by metal abundances and morphologies, followed by properties of winds and circum-galactic media (CGM). Central (∼kpc) mass concentrations in massive (>L*) galaxies are sensitive to numerics (via trapping/recycling of winds in hot halos). Multiple feedback mechanisms play key roles: supernovae regulate stellar masses/winds; stellar mass-loss fuels late star formation; radiative feedback suppresses accretion onto dwarfs and instantaneous star formation in disks. We provide all initial conditions and numerical algorithms used.
TL;DR: The world is facing a Parkinson pandemic that will require heightened activism, focused planning, and novel approaches, and additional factors, including increasing longevity, declining smoking rates, and increasing industrialization could raise the burden to over 17 million.
Abstract: Neurological disorders are now the leading source of disability globally, and the fastest growing neurological disorder in the world is Parkinson disease. From 1990 to 2015, the number of people with Parkinson disease doubled to over 6 million. Driven principally by aging, this number is projected to double again to over 12 million by 2040. Additional factors, including increasing longevity, declining smoking rates, and increasing industrialization, could raise the burden to over 17 million. For most of human history, Parkinson has been a rare disorder. However, demography and the by-products of industrialization have now created a Parkinson pandemic that will require heightened activism, focused planning, and novel approaches.
TL;DR: A new comprehensive and updated host plant list will improve the understanding of pest biology and management, as well as facilitate future studies on this pest.
Abstract: The fall armyworm, Spodoptera frugiperda (J.E. Smith, 1797) (Lepidoptera: Noctuidae), is the most important noctuid pest in the Americas and has recently become an invasive pest in Africa. A detailed record of S. frugiperda's host plants is essential to better understand the biology and ecology of this pest, conduct future studies, and develop Integrated Pest Management programmes. In this study, we collected and systematically arranged the fragmented bibliographic information on S. frugiperda feeding records. Furthermore, we registered new records of host plants for S. frugiperda based on eight years of surveys in Brazil. The literature review and surveys resulted in a total of 353 S. frugiperda larval host plant records belonging to 76 plant families, principally Poaceae (106), Asteraceae (31) and Fabaceae (31). The literature search revealed 274 (77 % of total) bibliographic records, while 82 (23 %) are new records from surveys in Brazil. The new comprehensive and updated host plant list will improve our understanding of pest biology and management, as well as facilitate future studies on this pest.
TL;DR: It is hypothesized that the selection pressure for glyphosate-resistance in bacteria could lead to shifts in microbiome composition and increases in antibiotic resistance to clinically important antimicrobial agents, which would have an impact on plant, animal and human health.
University of California1, University of Illinois at Urbana–Champaign2, Smithsonian Institution3, Royal Botanic Gardens4, George Washington University5, University of Cambridge6, Wellcome Trust Sanger Institute7, Harvard University8, University of Science and Technology9, University of Copenhagen10, United States Department of Energy11, University of California, Berkeley12, United States Department of Agriculture13, Rockefeller University14, Baylor College of Medicine15, World Economic Forum16, University of São Paulo17, University of Florida18, Chinese Academy of Sciences19
TL;DR: A perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of 10 years, is presented.
Abstract: Increasing our understanding of Earth’s biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet’s organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project’s goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.
TL;DR: The study reveals a multi-omics view of the metabolic breeding history of tomato, as well as provides insights into metabolome-assisted breeding and plant biology.
Richard A. Klein1, Michelangelo Vianello2, Fred Hasselman3, Byron G. Adams4 +187 more•Institutions (118)
TL;DR: This paper conducted preregistered replications of 28 classic and contemporary published findings, with protocols that were peer reviewed in advance, to examine variation in effect magnitudes across samples and settings, and found that very little heterogeneity was attributable to the order in which the tasks were performed or whether the task were administered in lab versus online.
Abstract: We conducted preregistered replications of 28 classic and contemporary published findings, with protocols that were peer reviewed in advance, to examine variation in effect magnitudes across samples and settings. Each protocol was administered to approximately half of 125 samples that comprised 15,305 participants from 36 countries and territories. Using the conventional criterion of statistical significance (p < .05), we found that 15 (54%) of the replications provided evidence of a statistically significant effect in the same direction as the original finding. With a strict significance criterion (p < .0001), 14 (50%) of the replications still provided such evidence, a reflection of the extremely high-powered design. Seven (25%) of the replications yielded effect sizes larger than the original ones, and 21 (75%) yielded effect sizes smaller than the original ones. The median comparable Cohen’s ds were 0.60 for the original findings and 0.15 for the replications. The effect sizes were small (< 0.20) in 16 of the replications (57%), and 9 effects (32%) were in the direction opposite the direction of the original effect. Across settings, the Q statistic indicated significant heterogeneity in 11 (39%) of the replication effects, and most of those were among the findings with the largest overall effect sizes; only 1 effect that was near zero in the aggregate showed significant heterogeneity according to this measure. Only 1 effect had a tau value greater than .20, an indication of moderate heterogeneity. Eight others had tau values near or slightly above .10, an indication of slight heterogeneity. Moderation tests indicated that very little heterogeneity was attributable to the order in which the tasks were performed or whether the tasks were administered in lab versus online. Exploratory comparisons revealed little heterogeneity between Western, educated, industrialized, rich, and democratic (WEIRD) cultures and less WEIRD cultures (i.e., cultures with relatively high and low WEIRDness scores, respectively). Cumulatively, variability in the observed effect sizes was attributable more to the effect being studied than to the sample or setting in which it was studied.
National Autonomous University of Mexico1, Fermilab2, Massachusetts Institute of Technology3, Columbia University4, New Mexico State University5, Los Alamos National Laboratory6, Argonne National Laboratory7, University of Alabama8, University of Florida9, University of Cincinnati10, Queen Mary University of London11, Virginia Tech12, Royal Holloway, University of London13, University of Michigan14, University of Minnesota15, Lancaster University16, Indiana University17, Louisiana State University18, University of Colorado Boulder19
TL;DR: The MiniBooNE data are consistent in energy and magnitude with the excess of events reported by the Liquid Scintillator Neutrino Detector (LSND), and the significance of the combined LSND and Mini BooNE excesses is 6.0σ.
Abstract: The MiniBooNE experiment at Fermilab reports results from an analysis of ν_{e} appearance data from 12.84×10^{20} protons on target in neutrino mode, an increase of approximately a factor of 2 over previously reported results. A ν_{e} charged-current quasielastic event excess of 381.2±85.2 events (4.5σ) is observed in the energy range 200
University of Washington1, Lawrence Livermore National Laboratory2, Fermilab3, Pacific Northwest National Laboratory4, National Radio Astronomy Observatory5, University of Sheffield6, University of Illinois at Chicago7, University of California, Berkeley8, University of Florida9, National Institute of Standards and Technology10
TL;DR: This Letter reports the results from a haloscope search for dark matter axions with masses between 2.66 and 2.81 μeV, achieving unprecedented sensitivity by operating a large-volume haloscope at subkelvin temperatures, thereby reducing thermal noise as well as the excess noise from the ultralow-noise superconducting quantum interference device amplifier used for the signal power readout.
Abstract: This Letter reports the results from a haloscope search for dark matter axions with masses between 2.66 and 2.81 μ eV . The search excludes the range of axion-photon couplings predicted by plausible models of the invisible axion. This unprecedented sensitivity is achieved by operating a large-volume haloscope at subkelvin temperatures, thereby reducing thermal noise as well as the excess noise from the ultralow-noise superconducting quantum interference device amplifier used for the signal power readout. Ongoing searches will provide nearly definitive tests of the invisible axion model over a wide range of axion masses.
University of Zurich1, Johns Hopkins University2, Mayo Clinic3, St. Marianna University School of Medicine4, Catholic University of the Sacred Heart5, Katholieke Universiteit Leuven6, University of Ferrara7, University of Lübeck8, Yokohama City University9, University of Giessen10, Wakayama Medical University11, University of Padua12, Hiroshima University13, University of Florida14, Imperial College London15, University of Gothenburg16, Leiden University17, Karolinska Institutet18, University of Adelaide19, Tohoku University20
TL;DR: The clinical expert consensus statement on takotsubo syndrome (TTS) part II focuses on the diagnostic workup, outcome, and management and summarizes the diagnostic approach, which may facilitate correct and timely diagnosis.
Abstract: The clinical expert consensus statement on takotsubo syndrome (TTS) part II focuses on the diagnostic workup, outcome, and management. The recommendations are based on interpretation of the limited clinical trial data currently available and experience of international TTS experts. It summarizes the diagnostic approach, which may facilitate correct and timely diagnosis. Furthermore, the document covers areas where controversies still exist in risk stratification and management of TTS. Based on available data the document provides recommendations on optimal care of such patients for practising physicians.
The Heart Research Institute1, Saint Louis University2, Wake Forest University3, University of Maryland, Baltimore4, Heidelberg University5, University of Florida6, University of Milan7, University of Miami8, University of Erlangen-Nuremberg9, Université du Québec à Montréal10, University of Otago11, University of Adelaide12, Agostino Gemelli University Polyclinic13, United States Department of Veterans Affairs14, Tufts University15, Kyung Hee University16, Dalhousie University17, King's College London18, Sichuan University19, The Chinese University of Hong Kong20, University of Western Australia21, National Institutes of Health22, National University of Singapore23, Uppsala University24, University of São Paulo25, Memorial Hospital of South Bend26, Vrije Universiteit Brussel27, Maastricht University28, Universidad Pública de Navarra29, Centre Hospitalier Universitaire de Toulouse30
TL;DR: Evidence-based clinical practice guidelines for screening, diagnosis and management of sarcopenia from the task force of the International Conference on Sarcopenia and Frailty Research (ICSFR) are presented.
Abstract: Sarcopenia, defined as an age-associated loss of skeletal muscle function and muscle mass, occurs in approximately 6 - 22 % of older adults. This paper presents evidence-based clinical practice guidelines for screening, diagnosis and management of sarcopenia from the task force of the International Conference on Sarcopenia and Frailty Research (ICSFR). To develop the guidelines, we drew upon the best available evidence from two systematic reviews paired with consensus statements by international working groups on sarcopenia. Eight topics were selected for the recommendations: (i) defining sarcopenia; (ii) screening and diagnosis; (iii) physical activity prescription; (iv) protein supplementation; (v) vitamin D supplementation; (vi) anabolic hormone prescription; (vii) medications under development; and (viii) research. The ICSFR task force evaluated the evidence behind each topic including the quality of evidence, the benefitharm balance of treatment, patient preferences/values, and cost-effectiveness. Recommendations were graded as either strong or conditional (weak) as per the GRADE (Grading of Recommendations Assessment, Development and Evaluation) approach. Consensus was achieved via one face-to-face workshop and a modified Delphi process. We make a conditional recommendation for the use of an internationally accepted measurement tool for the diagnosis of sarcopenia including the EWGSOP and FNIH definitions, and advocate for rapid screening using gait speed or the SARC-F. To treat sarcopenia, we strongly recommend the prescription of resistance-based physical activity, and conditionally recommend protein supplementation/a protein-rich diet. No recommendation is given for Vitamin D supplementation or for anabolic hormone prescription. There is a lack of robust evidence to assess the strength of other treatment options.
TL;DR: In this paper, the discriminating variables and the algorithms used for heavy-flavour jet identification during the first years of operation of the CMS experiment in proton-proton collisions at a centre-of-mass energy of 13 TeV, are presented.
Abstract: Many measurements and searches for physics beyond the standard model at the LHC rely on the efficient identification of heavy-flavour jets, i.e. jets originating from bottom or charm quarks. In this paper, the discriminating variables and the algorithms used for heavy-flavour jet identification during the first years of operation of the CMS experiment in proton-proton collisions at a centre-of-mass energy of 13 TeV, are presented. Heavy-flavour jet identification algorithms have been improved compared to those used previously at centre-of-mass energies of 7 and 8 TeV. For jets with transverse momenta in the range expected in simulated events, these new developments result in an efficiency of 68% for the correct identification of a b jet for a probability of 1% of misidentifying a light-flavour jet. The improvement in relative efficiency at this misidentification probability is about 15%, compared to previous CMS algorithms. In addition, for the first time algorithms have been developed to identify jets containing two b hadrons in Lorentz-boosted event topologies, as well as to tag c jets. The large data sample recorded in 2016 at a centre-of-mass energy of 13 TeV has also allowed the development of new methods to measure the efficiency and misidentification probability of heavy-flavour jet identification algorithms. The b jet identification efficiency is measured with a precision of a few per cent at moderate jet transverse momenta (between 30 and 300 GeV) and about 5% at the highest jet transverse momenta (between 500 and 1000 GeV).
United States Department of Energy1, Institut national de la recherche agronomique2, University of Florida3, Centre de coopération internationale en recherche agronomique pour le développement4, University of California, Riverside5, University of California, Berkeley6, Okinawa Institute of Science and Technology7
TL;DR: Ten natural citrus species are described, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and it is proposed that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons.
Abstract: The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins This work provides a new evolutionary framework for the genus Citrus The origin, evolution and domestication of Citrus and the genealogy of the most important wild and cultivated citrus varieties Citrus fruits are one of the most cultivated crops worldwide, yet the evolutionary relationships among citrus species remain uncertain Daniel Rokhsar, Manuel Talon and colleagues analyse the genomes of 60 accessions that represent a diverse range of citrus species, including 30 newly sequenced citrus genomes They characterize the diversity and evolution of citrus at the species level and identify interspecific citrus hybrids and admixtures—genetic mixing between previously isolated populations—that could be the result of human activities such as migration and agriculture The authors identify 10 progenitor species and suggest that citrus originated in southeast Asia, diversifying during the late Miocene epoch through a rapid southeast Asian radiation that correlated with a changing climate, including the weakening of the monsoons They also find extensive relatedness among mandarins and sweet oranges, showing a complex history of admixture during the domestication of these groups
National Center for Atmospheric Research1, Lawrence Berkeley National Laboratory2, University of Utah3, Los Alamos National Laboratory4, Boston University5, University of Texas at Austin6, University of Maryland, College Park7, University of Florida8, Empresa Brasileira de Pesquisa Agropecuária9, University of Notre Dame10, Smithsonian Tropical Research Institute11, Brookhaven National Laboratory12, Japan Agency for Marine-Earth Science and Technology13, Lund University14, Princeton University15, Ghent University16, Columbia University17, Harvard University18
TL;DR: It is argued that stronger and more innovative connections to data are required to address gaps in understanding, and that constrained predictions at ecologically relevant spatial and temporal scales will require a similar investment of effort and intensified inter-disciplinary communication.
Abstract: Numerous current efforts seek to improve the representation of ecosystem ecology and vegetation demographic processes within Earth System Models (ESMs). These developments are widely viewed as an important step in developing greater realism in predictions of future ecosystem states and fluxes. Increased realism, however, leads to increased model complexity, with new features raising a suite of ecological questions that require empirical constraints. Here, we review the developments that permit the representation of plant demographics in ESMs, and identify issues raised by these developments that highlight important gaps in ecological understanding. These issues inevitably translate into uncertainty in model projections but also allow models to be applied to new processes and questions concerning the dynamics of real-world ecosystems. We argue that stronger and more innovative connections to data, across the range of scales considered, are required to address these gaps in understanding. The development of first-generation land surface models as a unifying framework for ecophysiological understanding stimulated much research into plant physiological traits and gas exchange. Constraining predictions at ecologically relevant spatial and temporal scales will require a similar investment of effort and intensified inter-disciplinary communication.
12 Jul 2018
TL;DR: Vibrio spp.
Abstract: Vibrio is a genus of ubiquitous bacteria found in a wide variety of aquatic and marine habitats; of the >100 described Vibrio spp., ~12 cause infections in humans. Vibrio cholerae can cause cholera, a severe diarrhoeal disease that can be quickly fatal if untreated and is typically transmitted via contaminated water and person-to-person contact. Non-cholera Vibrio spp. (for example, Vibrio parahaemolyticus, Vibrio alginolyticus and Vibrio vulnificus) cause vibriosis - infections normally acquired through exposure to sea water or through consumption of raw or undercooked contaminated seafood. Non-cholera bacteria can lead to several clinical manifestations, most commonly mild, self-limiting gastroenteritis, with the exception of V. vulnificus, an opportunistic pathogen with a high mortality that causes wound infections that can rapidly lead to septicaemia. Treatment for Vibrio spp. infection largely depends on the causative pathogen: for example, rehydration therapy for V. cholerae infection and debridement of infected tissues for V. vulnificus-associated wound infections, with antibiotic therapy for severe cholera and systemic infections. Although cholera is preventable and effective oral cholera vaccines are available, outbreaks can be triggered by natural or man-made events that contaminate drinking water or compromise access to safe water and sanitation. The incidence of vibriosis is rising, perhaps owing in part to the spread of Vibrio spp. favoured by climate change and rising sea water temperature.
TL;DR: The data from this study suggest that duration of the prescription rather than dosage is more strongly associated with ultimate misuse in the early postsurgical period, and each refill and week of opioid prescription is associated with a large increase in opioid misuse among opioid naive patients.
Abstract: Objective To quantify the effects of varying opioid prescribing patterns after surgery on dependence, overdose, or abuse in an opioid naive population. Design Retrospective cohort study. Setting Surgical claims from a linked medical and pharmacy administrative database of 37 651 619 commercially insured patients between 2008 and 2016. Participants 1 015 116 opioid naive patients undergoing surgery. Main outcome measures Use of oral opioids after discharge as defined by refills and total dosage and duration of use. The primary outcome was a composite of misuse identified by a diagnostic code for opioid dependence, abuse, or overdose. Results 568 612 (56.0%) patients received postoperative opioids, and a code for abuse was identified for 5906 patients (0.6%, 183 per 100 000 person years). Total duration of opioid use was the strongest predictor of misuse, with each refill and additional week of opioid use associated with an adjusted increase in the rate of misuse of 44.0% (95% confidence interval 40.8% to 47.2%, P Conclusions Each refill and week of opioid prescription is associated with a large increase in opioid misuse among opioid naive patients. The data from this study suggest that duration of the prescription rather than dosage is more strongly associated with ultimate misuse in the early postsurgical period. The analysis quantifies the association of prescribing choices on opioid misuse and identifies levers for possible impact.
TL;DR: The working group recommends that ‘perioperative neurocognitive disorders’ be used as an overarching term for cognitive impairment identified in the preoperative or postoperative period as well as two major classification guidelines used outside of anaesthesia and surgery.
Abstract: Cognitive change affecting patients after anaesthesia and surgery has been recognised for more than 100 yr. Research into cognitive change after anaesthesia and surgery accelerated in the 1980s when multiple studies utilised detailed neuropsychological testing for assessment of cognitive change after cardiac surgery. This body of work consistently documented decline in cognitive function in elderly patients after anaesthesia and surgery, and cognitive changes have been identified up to 7.5 yr afterwards. Importantly, other studies have identified that the incidence of cognitive change is similar after non-cardiac surgery. Other than the inclusion of non-surgical control groups to calculate postoperative cognitive dysfunction, research into these cognitive changes in the perioperative period has been undertaken in isolation from cognitive studies in the general population. The aim of this work is to develop similar terminology to that used in cognitive classifications of the general population for use in investigations of cognitive changes after anaesthesia and surgery. A multispecialty working group followed a modified Delphi procedure with no prespecified number of rounds comprised of three face-to-face meetings followed by online editing of draft versions.Two major classification guidelines (Diagnostic and Statistical Manual for Mental Disorders, fifth edition [DSM-5] and National Institute for Aging and the Alzheimer Association [NIA-AA]) are used outside of anaesthesia and surgery, and may be useful for inclusion of biomarkers in research. For clinical purposes, it is recommended to use the DSM-5 nomenclature. The working group recommends that 'perioperative neurocognitive disorders' be used as an overarching term for cognitive impairment identified in the preoperative or postoperative period. This includes cognitive decline diagnosed before operation (described as neurocognitive disorder); any form of acute event (postoperative delirium) and cognitive decline diagnosed up to 30 days after the procedure (delayed neurocognitive recovery) and up to 12 months (postoperative neurocognitive disorder).
St. Vincent's Health System1, University of Melbourne2, Mayo Clinic3, University of Florida4, University of Copenhagen5, Johns Hopkins University School of Medicine6, Brigham and Women's Hospital7, Duke University8, University of Pennsylvania9, Rutgers University10, Harvard University11, Icahn School of Medicine at Mount Sinai12, Utrecht University13, Karolinska University Hospital14, University of California, San Diego15, University of Wisconsin-Madison16, Beth Israel Deaconess Medical Center17, Johns Hopkins University18, University of California, San Francisco19, Sunnybrook Health Sciences Centre20, University of Florida College of Public Health and Health Professions21, University of New South Wales22, Oregon Health & Science University23, Johns Hopkins Bayview Medical Center24, Indiana University25, Columbia University26
TL;DR: The working group recommends that ‘perioperative neurocognitive disorders’ be used as an overarching term for cognitive impairment identified in the preoperative or postoperative period as well as two major classification guidelines used outside of anaesthesia and surgery.
Abstract: Cognitive change affecting patients after anaesthesia and surgery has been recognised for more than 100 yr. Research into cognitive change after anaesthesia and surgery accelerated in the 1980s when multiple studies utilised detailed neuropsychological testing for assessment of cognitive change after cardiac surgery. This body of work consistently documented decline in cognitive function in elderly patients after anaesthesia and surgery, and cognitive changes have been identified up to 7.5 yr afterwards. Importantly, other studies have identified that the incidence of cognitive change is similar after non-cardiac surgery. Other than the inclusion of non-surgical control groups to calculate postoperative cognitive dysfunction, research into these cognitive changes in the perioperative period has been undertaken in isolation from cognitive studies in the general population. The aim of this work is to develop similar terminology to that used in cognitive classifications of the general population for use in investigations of cognitive changes after anaesthesia and surgery. A multispecialty working group followed a modified Delphi procedure with no prespecified number of rounds comprised of three face-to-face meetings followed by online editing of draft versions. Two major classification guidelines [Diagnostic and Statistical Manual for Mental Disorders, fifth edition (DSM-5) and National Institute for Aging and the Alzheimer Association (NIA-AA)] are used outside of anaesthesia and surgery, and may be useful for inclusion of biomarkers in research. For clinical purposes, it is recommended to use the DSM-5 nomenclature. The working group recommends that 'perioperative neurocognitive disorders' be used as an overarching term for cognitive impairment identified in the preoperative or postoperative period. This includes cognitive decline diagnosed before operation (described as neurocognitive disorder); any form of acute event (postoperative delirium) and cognitive decline diagnosed up to 30 days after the procedure (delayed neurocognitive recovery) and up to 12 months (postoperative neurocognitive disorder).