Showing papers by "University of Connecticut published in 2016"
University of Nebraska Medical Center1, University of Connecticut2, Harvard University3, Queen's University4, University of California, San Diego5, Stony Brook University6, University of Michigan7, National Institutes of Health8, Johns Hopkins University9, University of Barcelona10, University at Buffalo11, Summa Health System12, University of Texas Health Science Center at San Antonio13, Royal Brisbane and Women's Hospital14, University of Queensland15, University of Western Australia16, University of Colorado Denver17, McMaster University18
TL;DR: These guidelines are intended for use by healthcare professionals who care for patients at risk for hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), including specialists in infectious diseases, pulmonary diseases, critical care, and surgeons, anesthesiologists, hospitalists, and any clinicians and healthcare providers caring for hospitalized patients with nosocomial pneumonia.
Abstract: It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. IDSA considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.These guidelines are intended for use by healthcare professionals who care for patients at risk for hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), including specialists in infectious diseases, pulmonary diseases, critical care, and surgeons, anesthesiologists, hospitalists, and any clinicians and healthcare providers caring for hospitalized patients with nosocomial pneumonia. The panel's recommendations for the diagnosis and treatment of HAP and VAP are based upon evidence derived from topic-specific systematic literature reviews.
2,359 citations
Oregon Health & Science University1, University of Washington2, University at Buffalo3, University of Michigan4, University of California, San Diego5, University of Iowa Hospitals and Clinics6, University of Cincinnati7, United States Department of Veterans Affairs8, Harvard University9, United States Department of the Army10, Walter Reed Army Medical Center11, University of Connecticut12, University of Colorado Denver13, Johns Hopkins University14, Veterans Health Administration15, Boston Children's Hospital16, University of Iowa17, University of Texas at Austin18, Virginia Mason Medical Center19, Thomas Jefferson University20, Seattle Children's21, Children's Hospital of Wisconsin22
TL;DR: The American Pain Society, with input from the American Society of Anesthesiologists, developed a clinical practice guideline to promote evidence-based, effective, and safer postoperative pain management in children and adults.
1,806 citations
Thomas Jefferson National Accelerator Facility1, Hampton University2, University of Paris-Sud3, University of Santiago, Chile4, Brookhaven National Laboratory5, University of Pavia6, University of Groningen7, Federico Santa María Technical University8, Shandong University9, Goethe University Frankfurt10, Stony Brook University11, Baruch College12, Duke University13, Argonne National Laboratory14, The Catholic University of America15, Old Dominion University16, Lawrence Berkeley National Laboratory17, Ohio State University18, University of Zagreb19, University of Jyväskylä20, Tel Aviv University21, CERN22, Temple University23, Massachusetts Institute of Technology24, Columbia University25, Ruhr University Bochum26, California Institute of Technology27, University of Massachusetts Amherst28, University of Buenos Aires29, University of the Basque Country30, University of Connecticut31, University of Tübingen32, Pennsylvania State University33, Stanford University34, Dalhousie University35, Central China Normal University36
TL;DR: In this article, the science case of an Electron-Ion Collider (EIC), focused on the structure and interactions of gluon-dominated matter, with the intent to articulate it to the broader nuclear science community, is presented.
Abstract: This White Paper presents the science case of an Electron-Ion Collider (EIC), focused on the structure and interactions of gluon-dominated matter, with the intent to articulate it to the broader nuclear science community. It was commissioned by the managements of Brookhaven National Laboratory (BNL) and Thomas Jefferson National Accelerator Facility (JLab) with the objective of presenting a summary of scientific opportunities and goals of the EIC as a follow-up to the 2007 NSAC Long Range plan. This document is a culmination of a community-wide effort in nuclear science following a series of workshops on EIC physics over the past decades and, in particular, the focused ten-week program on “Gluons and quark sea at high energies” at the Institute for Nuclear Theory in Fall 2010. It contains a brief description of a few golden physics measurements along with accelerator and detector concepts required to achieve them. It has been benefited profoundly from inputs by the users’ communities of BNL and JLab. This White Paper offers the promise to propel the QCD science program in the US, established with the CEBAF accelerator at JLab and the RHIC collider at BNL, to the next QCD frontier.
1,022 citations
Perimeter Institute for Theoretical Physics1, Niigata University2, CERN3, University of Connecticut4, Leiden University5, Korea Astronomy and Space Science Institute6, Federico Santa María Technical University7, University of California, Santa Barbara8, University of Maryland, College Park9, Claude Bernard University Lyon 110, University of Lyon11, Northwestern University12, University of Victoria13, University of Manchester14, University of Bonn15, Technische Universität München16, École Polytechnique Fédérale de Lausanne17, Stony Brook University18, Autonomous University of Madrid19, Centre national de la recherche scientifique20, University of Paris21, Moscow Institute of Physics and Technology22, Autonomous University of Barcelona23, University of Copenhagen24, Université libre de Bruxelles25, University of La Serena26, University of Valencia27, Taras Shevchenko National University of Kyiv28, Heidelberg University29, Yonsei University30, Princeton University31, Harvard University32, University of Geneva33, Tomsk State University34, Tomsk Polytechnic University35, University of Tübingen36, University of Washington37, University of Florida38, University of Hamburg39, TRIUMF40, University of Iowa41, University of Grenoble42, International Centre for Theoretical Physics43, Hokkai Gakuen University44, University of Illinois at Urbana–Champaign45, Durham University46, University of Melbourne47, University of Naples Federico II48, York University49, Lawrence Berkeley National Laboratory50, University of California, Berkeley51
TL;DR: It is demonstrated that the SHiP experiment has a unique potential to discover new physics and can directly probe a number of solutions of beyond the standard model puzzles, such as neutrino masses, baryon asymmetry of the Universe, dark matter, and inflation.
Abstract: This paper describes the physics case for a new fixed target facility at CERN SPS. The SHiP (search for hidden particles) experiment is intended to hunt for new physics in the largely unexplored domain of very weakly interacting particles with masses below the Fermi scale, inaccessible to the LHC experiments, and to study tau neutrino physics. The same proton beam setup can be used later to look for decays of tau-leptons with lepton flavour number non-conservation, $\tau \to 3\mu $ and to search for weakly-interacting sub-GeV dark matter candidates. We discuss the evidence for physics beyond the standard model and describe interactions between new particles and four different portals—scalars, vectors, fermions or axion-like particles. We discuss motivations for different models, manifesting themselves via these interactions, and how they can be probed with the SHiP experiment and present several case studies. The prospects to search for relatively light SUSY and composite particles at SHiP are also discussed. We demonstrate that the SHiP experiment has a unique potential to discover new physics and can directly probe a number of solutions of beyond the standard model puzzles, such as neutrino masses, baryon asymmetry of the Universe, dark matter, and inflation.
842 citations
University of Connecticut1, University of Aberdeen2, McGill University3, University of Paris4, Helmholtz Centre for Environmental Research - UFZ5, Swedish University of Agricultural Sciences6, University of Bristol7, National Marine Fisheries Service8, Katholieke Universiteit Leuven9, Lincoln University (New Zealand)10, University of Minnesota11, University of Florida12, University of Osnabrück13, Université Paris-Saclay14, University of Montpellier15, Purdue University16
TL;DR: This work identifies six biological mechanisms that commonly shape responses to climate change yet are too often missing from current predictive models and prioritize the types of information needed to inform each of these mechanisms, and suggests proxies for data that are missing or difficult to collect.
Abstract: BACKGROUND As global climate change accelerates, one of the most urgent tasks for the coming decades is to develop accurate predictions about biological responses to guide the effective protection of biodiversity. Predictive models in biology provide a means for scientists to project changes to species and ecosystems in response to disturbances such as climate change. Most current predictive models, however, exclude important biological mechanisms such as demography, dispersal, evolution, and species interactions. These biological mechanisms have been shown to be important in mediating past and present responses to climate change. Thus, current modeling efforts do not provide sufficiently accurate predictions. Despite the many complexities involved, biologists are rapidly developing tools that include the key biological processes needed to improve predictive accuracy. The biggest obstacle to applying these more realistic models is that the data needed to inform them are almost always missing. We suggest ways to fill this growing gap between model sophistication and information to predict and prevent the most damaging aspects of climate change for life on Earth. ADVANCES On the basis of empirical and theoretical evidence, we identify six biological mechanisms that commonly shape responses to climate change yet are too often missing from current predictive models: physiology; demography, life history, and phenology; species interactions; evolutionary potential and population differentiation; dispersal, colonization, and range dynamics; and responses to environmental variation. We prioritize the types of information needed to inform each of these mechanisms and suggest proxies for data that are missing or difficult to collect. We show that even for well-studied species, we often lack critical information that would be necessary to apply more realistic, mechanistic models. Consequently, data limitations likely override the potential gains in accuracy of more realistic models. Given the enormous challenge of collecting this detailed information on millions of species around the world, we highlight practical methods that promote the greatest gains in predictive accuracy. Trait-based approaches leverage sparse data to make more general inferences about unstudied species. Targeting species with high climate sensitivity and disproportionate ecological impact can yield important insights about future ecosystem change. Adaptive modeling schemes provide a means to target the most important data while simultaneously improving predictive accuracy. OUTLOOK Strategic collections of essential biological information will allow us to build generalizable insights that inform our broader ability to anticipate species’ responses to climate change and other human-caused disturbances. By increasing accuracy and making uncertainties explicit, scientists can deliver improved projections for biodiversity under climate change together with characterizations of uncertainty to support more informed decisions by policymakers and land managers. Toward this end, a globally coordinated effort to fill data gaps in advance of the growing climate-fueled biodiversity crisis offers substantial advantages in efficiency, coverage, and accuracy. Biologists can take advantage of the lessons learned from the Intergovernmental Panel on Climate Change’s development, coordination, and integration of climate change projections. Climate and weather projections were greatly improved by incorporating important mechanisms and testing predictions against global weather station data. Biology can do the same. We need to adopt this meteorological approach to predicting biological responses to climate change to enhance our ability to mitigate future changes to global biodiversity and the services it provides to humans.
755 citations
03 May 2016
TL;DR: The SAGER guidelines are designed primarily to guide authors in preparing their manuscripts, but they are also useful for editors, as gatekeepers of science, to integrate assessment of sex and gender into all manuscripts as an integral part of the editorial process.
Abstract: Sex and gender differences are often overlooked in research design, study implementation and scientific reporting, as well as in general science communication. This oversight limits the generalizability of research findings and their applicability to clinical practice, in particular for women but also for men. This article describes the rationale for an international set of guidelines to encourage a more systematic approach to the reporting of sex and gender in research across disciplines. A panel of 13 experts representing nine countries developed the guidelines through a series of teleconferences, conference presentations and a 2-day workshop. An internet survey of 716 journal editors, scientists and other members of the international publishing community was conducted as well as a literature search on sex and gender policies in scientific publishing. The Sex and Gender Equity in Research (SAGER) guidelines are a comprehensive procedure for reporting of sex and gender information in study design, data analyses, results and interpretation of findings. The SAGER guidelines are designed primarily to guide authors in preparing their manuscripts, but they are also useful for editors, as gatekeepers of science, to integrate assessment of sex and gender into all manuscripts as an integral part of the editorial process.
751 citations
Wageningen University and Research Centre1, University of Puerto Rico2, University of Alabama3, National Autonomous University of Mexico4, Brown University5, University of Connecticut6, University of São Paulo7, Smithsonian Tropical Research Institute8, Leipzig University9, Federal University of Pernambuco10, Tulane University11, University of Stirling12, Clemson University13, University of Alberta14, National Institute of Amazonian Research15, Colorado Mesa University16, State University of New York at Purchase17, World Agroforestry Centre18, University of Wisconsin-Madison19, Columbia University20, Aarhus University21, University of Minnesota22, Pedagogical and Technological University of Colombia23, University of California, Santa Barbara24, University of Maryland, College Park25, National University of Singapore26, Yale-NUS College27, Puerto Rico Department of Agriculture28, University of Amsterdam29, Museu Paraense Emílio Goeldi30, Louisiana State University31, University of Regina32
TL;DR: A biomass recovery map of Latin America is presented, which illustrates geographical and climatic variation in carbon sequestration potential during forest regrowth and will support policies to minimize forest loss in areas where biomass resilience is naturally low and promote forest regeneration and restoration in humid tropical lowland areas with high biomass resilience.
Abstract: Land-use change occurs nowhere more rapidly than in the tropics, where the imbalance between deforestation and forest regrowth has large consequences for the global carbon cycle. However, considerable uncertainty remains about the rate of biomass recovery in secondary forests, and how these rates are influenced by climate, landscape, and prior land use. Here we analyse aboveground biomass recovery during secondary succession in 45 forest sites and about 1,500 forest plots covering the major environmental gradients in the Neotropics. The studied secondary forests are highly productive and resilient. Aboveground biomass recovery after 20 years was on average 122 megagrams per hectare (Mg ha(-1)), corresponding to a net carbon uptake of 3.05 Mg C ha(-1) yr(-1), 11 times the uptake rate of old-growth forests. Aboveground biomass stocks took a median time of 66 years to recover to 90% of old-growth values. Aboveground biomass recovery after 20 years varied 11.3-fold (from 20 to 225 Mg ha(-1)) across sites, and this recovery increased with water availability (higher local rainfall and lower climatic water deficit). We present a biomass recovery map of Latin America, which illustrates geographical and climatic variation in carbon sequestration potential during forest regrowth. The map will support policies to minimize forest loss in areas where biomass resilience is naturally low (such as seasonally dry forest regions) and promote forest regeneration and restoration in humid tropical lowland areas with high biomass resilience.
724 citations
TL;DR: This paper proposed a four-phase interview protocol refinement (IPR) framework to improve the quality of qualitative interviews by ensuring interview questions align with the research questions, organizing an interview protocol to create an inquiry-based conversation, having the protocol reviewed by others, and piloting it.
Abstract: Interviews provide researchers with rich and detailed qualitative data for understanding participants' experiences, how they describe those experiences, and the meaning they make of those experiences (Rubin & Rubin, 2012). Given the centrality of interviews for qualitative research, books and articles on conducting research interviews abound. These existing resources typically focus on: the conditions fostering quality interviews, such as gaining access to and selecting participants (Rubin & Rubin, 2012; Seidman, 2013; Weiss, 1994); building trust (Rubin & Rubin, 2012); the location and length of time of the interview (Weiss, 1994); the order, quality, and clarity of questions (Patton, 2015; Rubin & Rubin, 2012); and the overall process of conducting an interview (Brinkmann & Kvale, 2015; Patton, 2015). Existing resources on conducting research interviews individually offer valuable guidance but do not come together to offer a systematic framework for developing and refining interview protocols. In this article, I present the interview protocol refinement (IPR) framework--a four-phase process to develop and fine-tune interview protocols. IPR's four-phases include ensuring interview questions align with the study's research questions, organizing an interview protocol to create an inquiry-based conversation, having the protocol reviewed by others, and piloting it. Qualitative researchers can strengthen the reliability of their interview protocols as instruments by refining them through the IPR framework presented here. By enhancing the reliability of interview protocols, researchers can increase the quality of data they obtain from research interviews. Furthermore, the IPR framework can provide qualitative researchers with a shared language for indicating the rigorous steps taken to develop interview protocols and ensure their congruency with the study at hand (Jones, Torres, & Arminio, 2014). IPR framework is most suitable for refining structured or semi-structured interviews. The IPR framework, however, may also support development of non-structured interview guides, which have topics for discussions or a small set of broad questions to facilitate the conversation. For instance, from a grounded theory perspective, piloting interview protocols/guides are unnecessary because each interview is designed to build from information learned in prior interviews (Corbin & Strauss, 2015). Yet, given the important role the first interview plays in setting the foundation for all the interviews that follow, having an initial interview protocol vetted through the recursive process I outline here may strengthen the quality of data obtained throughout the entire study. As such, I frame the IPR framework as a viable approach to developing a strong initial interview protocol so the researcher is likely to elicit rich, focused, meaningful data that captures, to the extent possible, the experiences of participants. The Four-Phase Process to Interview Protocol Refinement (IPR) The interview protocol framework is comprised of four-phases: Phase 1: Ensuring interview questions align with research questions, Phase 2: Constructing an inquiry-based conversation, Phase 3: Receiving feedback on interview protocols Phase 4: Piloting the interview protocol. Each phase helps the researcher take one step further toward developing a research instrument appropriate for their participants and congruent with the aims of the research (Jones et al., 2014). Congruency means the researchers' interviews are anchored in the purpose of the study and the research questions. Combined, these four phases offer a systematic framework for developing a well-vetted interview protocol that can help a researcher obtain robust and detailed interview data necessary to address research questions. Phase 1: Ensuring Interview Questions Align With Research Questions The first phase focuses on the alignment between interview questions and research questions. …
546 citations
01 Jan 2016
TL;DR: This chapter discusses nonparametric statistical models, function spaces and approximation theory, and the minimax paradigm, which aims to provide a model for adaptive inference oflihood-based procedures.
Abstract: 1. Nonparametric statistical models 2. Gaussian processes 3. Empirical processes 4. Function spaces and approximation theory 5. Linear nonparametric estimators 6. The minimax paradigm 7. Likelihood-based procedures 8. Adaptive inference.
534 citations
522 citations
TL;DR: Statin-associated symptoms are important because they prompt dose reduction or discontinuation of these life-saving mediations, and management of SAS requires making the possible diagnosis, altering or discontinuing the statin treatment, and using alternative lipid-lowering therapy.
TL;DR: Future directions are focused on developing innovative junction architectures, novel synthesis methods and optimizing the existing active materials to enhance charge transfer, visible light absorption, reducing the gas evolution overpotential and maintaining chemical and physical stability.
Abstract: Photocatalytic water splitting using sunlight is a promising technology capable of providing high energy yield without pollutant byproducts. Herein, we review various aspects of this technology including chemical reactions, physiochemical conditions and photocatalyst types such as metal oxides, sulfides, nitrides, nanocomposites, and doped materials followed by recent advances in computational modeling of photoactive materials. As the best-known catalyst for photocatalytic hydrogen and oxygen evolution, TiO2 is discussed in a separate section, along with its challenges such as the wide band gap, large overpotential for hydrogen evolution, and rapid recombination of produced electron-hole pairs. Various approaches are addressed to overcome these shortcomings, such as doping with different elements, heterojunction catalysts, noble metal deposition, and surface modification. Development of a photocatalytic corrosion resistant, visible light absorbing, defect-tuned material with small particle size is the key to complete the sunlight to hydrogen cycle efficiently. Computational studies have opened new avenues to understand and predict the electronic density of states and band structure of advanced materials and could pave the way for the rational design of efficient photocatalysts for water splitting. Future directions are focused on developing innovative junction architectures, novel synthesis methods and optimizing the existing active materials to enhance charge transfer, visible light absorption, reducing the gas evolution overpotential and maintaining chemical and physical stability.
Book•
01 May 2016
TL;DR: In this paper, a self-contained and authoritative analysis of the application of perturbative quantum field theory to the case of planar, maximally supersymmetric Yang-Mills theory is presented.
Abstract: Outlining a revolutionary reformulation of the foundations of perturbative quantum field theory, this book is a self-contained and authoritative analysis of the application of this new formulation to the case of planar, maximally supersymmetric Yang–Mills theory. The book begins by deriving connections between scattering amplitudes and Grassmannian geometry from first principles before introducing novel physical and mathematical ideas in a systematic manner accessible to both physicists and mathematicians. The principle players in this process are on-shell functions which are closely related to certain sub-strata of Grassmannian manifolds called positroids - in terms of which the classification of on-shell functions and their relations becomes combinatorially manifest. This is an essential introduction to the geometry and combinatorics of the positroid stratification of the Grassmannian and an ideal text for advanced students and researchers working in the areas of field theory, high energy physics, and the broader fields of mathematical physics.
TL;DR: A strategy for combining metal oxides and metal-organic frameworks is proposed to design new materials for sensing volatile organic compounds, for the first time, and shows greatly enhanced performance not only on its selectivity but also on its response, recovery behavior, and working temperature.
Abstract: A strategy for combining metal oxides and metal-organic frameworks is proposed to design new materials for sensing volatile organic compounds, for the first time. The prepared ZnO@ZIF-CoZn core-sheath nanowire arrays show greatly enhanced performance not only on its selectivity but also on its response, recovery behavior, and working temperature.
International Institute of Minnesota1, University of Connecticut2, University of Alabama3, University of Regina4, Wageningen University and Research Centre5, University of Puerto Rico6, National Autonomous University of Mexico7, Brown University8, University of São Paulo9, Leipzig University10, Smithsonian Tropical Research Institute11, Federal University of Pernambuco12, Tulane University13, University of Stirling14, Clemson University15, University of Alberta16, National Institute of Amazonian Research17, Colorado Mesa University18, State University of New York at Purchase19, World Agroforestry Centre20, Columbia University21, Aarhus University22, University of Minnesota23, Pedagogical and Technological University of Colombia24, University of California, Santa Barbara25, University of Maryland, College Park26, Yale-NUS College27, National University of Singapore28, Puerto Rico Department of Agriculture29, University of Amsterdam30, Museu Paraense Emílio Goeldi31, Louisiana State University32
TL;DR: This study estimates the age and spatial extent of lowland second-growth forests in the Latin American tropics and model their potential aboveground carbon accumulation over four decades to guide national-level forest-based carbon mitigation plans.
Abstract: Regrowth of tropical secondary forests following complete or nearly complete removal of forest vegetation actively stores carbon in aboveground biomass, partially counterbalancing carbon emissions from deforestation, forest degradation, burning of fossil fuels, and other anthropogenic sources. We estimate the age and spatial extent of lowland second-growth forests in the Latin American tropics and model their potential aboveground carbon accumulation over four decades. Our model shows that, in 2008, second-growth forests (1 to 60 years old) covered 2.4 million km2 of land (28.1% of the total study area). Over 40 years, these lands can potentially accumulate a total aboveground carbon stock of 8.48 Pg C (petagrams of carbon) in aboveground biomass via low-cost natural regeneration or assisted regeneration, corresponding to a total CO2 sequestration of 31.09 Pg CO2. This total is equivalent to carbon emissions from fossil fuel use and industrial processes in all of Latin America and the Caribbean from 1993 to 2014. Ten countries account for 95% of this carbon storage potential, led by Brazil, Colombia, Mexico, and Venezuela. We model future land-use scenarios to guide national carbon mitigation policies. Permitting natural regeneration on 40% of lowland pastures potentially stores an additional 2.0 Pg C over 40 years. Our study provides information and maps to guide national-level forest-based carbon mitigation plans on the basis of estimated rates of natural regeneration and pasture abandonment. Coupled with avoided deforestation and sustainable forest management, natural regeneration of second-growth forests provides a low-cost mechanism that yields a high carbon sequestration potential with multiple benefits for biodiversity and ecosystem services.
TL;DR: An overview of the impact that obesity and MetS parameters have on immune system function is presented, including the disruption of lymphoid tissue integrity; alterations in leukocyte development, phenotypes, and activity; and the coordination of innate and adaptive immune responses.
University of Nevada, Reno1, Purdue University2, Monsanto3, Old Dominion University4, North Carolina State University5, University College London6, Oklahoma State University–Stillwater7, Spanish National Research Council8, National Institutes of Health9, University of Cambridge10, Wellcome Trust11, J. Craig Venter Institute12, Leidos13, Broad Institute14, University of Notre Dame15, University of Nevada, Las Vegas16, University of Barcelona17, Carlos III Health Institute18, University of Massachusetts Medical School19, University of Connecticut20, University of Oxford21, University of Lausanne22, West Virginia University23, Virginia Tech24, Indiana University25, University of Maryland, Baltimore26, Kansas State University27, Texas A&M University28, University of Minnesota29, University of Manchester30, National University of Singapore31, University of California, San Francisco32, Iowa State University33, Colorado State University34, Pennsylvania State University35, Max Planck Society36, University of California, Riverside37, ANSES38, University of Santiago de Compostela39, Pompeu Fabra University40, California State Polytechnic University, Pomona41, University of Queensland42, University of the Sunshine Coast43, University of Geneva44, Swiss Institute of Bioinformatics45, University of Copenhagen46, University of Tennessee Health Science Center47, Wellcome Trust Sanger Institute48, University of Vigo49, University of Illinois at Urbana–Champaign50, Quinnipiac University51, International Livestock Research Institute52
TL;DR: Insights from genome analyses into parasitic processes unique to ticks, including host ‘questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival are reported.
Abstract: Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.
TL;DR: In this paper, the authors provide meta-analytic support for the positive relationship between shared leadership and team performance, using 50 effect sizes from both published and unpublished studies (team n = 3,198), using a random effects model, finding that the theoretical foundation and associated measurement techniques used to index shared leadership significantly moderated effect size estimates.
TL;DR: This review summarizes the current understanding of the disease pathogenesis, invasive and non-invasive animal models, imaging modalities, and pain assessment techniques in the animals.
Abstract: Osteoarthritis (OA) is one of the most commonly occurring forms of arthritis in the world today. It is a debilitating chronic illness causing pain and immense discomfort to the affected individual. Significant research is currently ongoing to understand its pathophysiology and develop successful treatment regimens based on this knowledge. Animal models have played a key role in achieving this goal. Animal models currently used to study osteoarthritis can be classified based on the etiology under investigation, primary osteoarthritis, and post-traumatic osteoarthritis, to better clarify the relationship between these models and the pathogenesis of the disease. Non-invasive animal models have shown significant promise in understanding early osteoarthritic changes. Imaging modalities play a pivotal role in understanding the pathogenesis of OA and the correlation with pain. These imaging studies would also allow in vivo surveillance of the disease as a function of time in the animal model. This review summarizes the current understanding of the disease pathogenesis, invasive and non-invasive animal models, imaging modalities, and pain assessment techniques in the animals.
TL;DR: In this paper, the authors demonstrate a systematic feature-engineering approach and a robust learning framework for efficient and accurate predictions of electronic bandgaps of double perovskites, identifying lowest occupied Kohn-Sham levels and elemental electronegativities of the constituent atomic species as the most crucial and relevant predictors.
Abstract: The ability to make rapid and accurate predictions on bandgaps of double perovskites is of much practical interest for a range of applications. While quantum mechanical computations for high-fidelity bandgaps are enormously computation-time intensive and thus impractical in high throughput studies, informatics-based statistical learning approaches can be a promising alternative. Here we demonstrate a systematic feature-engineering approach and a robust learning framework for efficient and accurate predictions of electronic bandgaps of double perovskites. After evaluating a set of more than 1.2 million features, we identify lowest occupied Kohn-Sham levels and elemental electronegativities of the constituent atomic species as the most crucial and relevant predictors. The developed models are validated and tested using the best practices of data science and further analyzed to rationalize their prediction performance.
TL;DR: HybPiper is developed as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies in Artocarpus.
Abstract: Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. Conclusions: HybPiper was designed for Linux and Mac OS X and is freely ...
TL;DR: In this largest meta-analysis of hypertensive patients, the nocturnal BP fall provided substantial prognostic information, independent of 24-hour SBP levels, and heterogeneity was low for systolic night-to-day ratio and Reverse dipping and moderate for extreme dippers.
Abstract: The prognostic importance of the nocturnal systolic blood pressure (SBP) fall, adjusted for average 24-hour SBP levels, is unclear. The Ambulatory Blood Pressure Collaboration in Patients With Hypertension (ABC-H) examined this issue in a meta-analysis of 17 312 hypertensives from 3 continents. Risks were computed for the systolic night-to-day ratio and for different dipping patterns (extreme, reduced, and reverse dippers) relative to normal dippers. ABC-H investigators provided multivariate adjusted hazard ratios (HRs), with and without adjustment for 24-hour SBP, for total cardiovascular events (CVEs), coronary events, strokes, cardiovascular mortality, and total mortality. Average 24-hour SBP varied from 131 to 140 mm Hg and systolic night-to-day ratio from 0.88 to 0.93. There were 1769 total CVEs, 916 coronary events, 698 strokes, 450 cardiovascular deaths, and 903 total deaths. After adjustment for 24-hour SBP, the systolic night-to-day ratio predicted all outcomes: from a 1-SD increase, summary HRs were 1.12 to 1.23. Reverse dipping also predicted all end points: HRs were 1.57 to 1.89. Reduced dippers, relative to normal dippers, had a significant 27% higher risk for total CVEs. Risks for extreme dippers were significantly influenced by antihypertensive treatment (P<0.001): untreated patients had increased risk of total CVEs (HR, 1.92), whereas treated patients had borderline lower risk (HR, 0.72) than normal dippers. For CVEs, heterogeneity was low for systolic night-to-day ratio and reverse/reduced dipping and moderate for extreme dippers. Quality of included studies was moderate to high, and publication bias was undetectable. In conclusion, in this largest meta-analysis of hypertensive patients, the nocturnal BP fall provided substantial prognostic information, independent of 24-hour SBP levels.
Wayne State University1, Stony Brook University2, University of Connecticut3, Harvard University4, Max Planck Society5, University of Kiel6, University College Cork7, Swarthmore College8, University of Vermont9, Indiana University10, York University11, University of Rennes12, Tel Aviv University13, Vanderbilt University14
TL;DR: Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels that constitute a wider vocabulary and framework for host biology in light of the microbiome.
Abstract: Given the complexity of host-microbiota symbioses, scientists and phi- losophers are asking questions at new biological levels of hierarchical organization— what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical dis- course is necessary in this nascent area, but productive discourse requires that skep- tics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontro- vertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but consti- tute a wider vocabulary and framework for host biology in light of the microbiome.
TL;DR: A protocol for precision nuclear run-on sequencing (PRO-seq) and its variant, PRO-cap, which map the location of active RNA polymerases or transcription start sites (TSSs) genome-wide at highresolution at high resolution is provided.
Abstract: We provide a protocol for precision nuclear run-on sequencing (PRO-seq) and its variant, PRO-cap, which map the location of active RNA polymerases (PRO-seq) or transcription start sites (TSSs) (PRO-cap) genome-wide at high resolution. The density of RNA polymerases at a particular genomic locus directly reflects the level of nascent transcription at that region. Nuclei are isolated from cells and, under nuclear run-on conditions, transcriptionally engaged RNA polymerases incorporate one or, at most, a few biotin-labeled nucleotide triphosphates (biotin-NTPs) into the 3' end of nascent RNA. The biotin-labeled nascent RNA is used to prepare sequencing libraries, which are sequenced from the 3' end to provide high-resolution positional information for the RNA polymerases. PRO-seq provides much higher sensitivity than ChIP-seq, and it generates a much larger fraction of usable sequence reads than ChIP-seq or NET-seq (native elongating transcript sequencing). Similarly to NET-seq, PRO-seq maps the RNA polymerase at up to base-pair resolution with strand specificity, but unlike NET-seq it does not require immunoprecipitation. With the protocol provided here, PRO-seq (or PRO-cap) libraries for high-throughput sequencing can be generated in 4-5 working days. The method has been applied to human, mouse, Drosophila melanogaster and Caenorhabditis elegans cells and, with slight modifications, to yeast.
TL;DR: A historical overview of forest concepts and definitions is presented, linking these changes with distinct perspectives and management objectives to illustrate how different management objectives drive the relative importance of different aspects of forest state, dynamics, and landscape context.
Abstract: We present a historical overview of forest concepts and definitions, linking these changes with distinct perspectives and management objectives. Policies dealing with a broad range of forest issues are often based on definitions created for the purpose of assessing global forest stocks, which do not distinguish between natural and planted forests or reforests, and which have not proved useful in assessing national and global rates of forest regrowth and restoration. Implementing and monitoring forest and landscape restoration requires additional approaches to defining and assessing forests that reveal the qualities and trajectories of forest patches in a spatially and temporally dynamic landscape matrix. New technologies and participatory assessment of forest states and trajectories offer the potential to operationalize such definitions. Purpose-built and contextualized definitions are needed to support policies that successfully protect, sustain, and regrow forests at national and global scales. We provide a framework to illustrate how different management objectives drive the relative importance of different aspects of forest state, dynamics, and landscape context.
University of Geneva1, New York University2, Brookhaven National Laboratory3, University of Connecticut4, Swiss Institute of Bioinformatics5, Russian Academy of Sciences6, Russian National Research Medical University7, Moscow State University8, Genentech9, Paris Diderot University10, University of Würzburg11, University Hospital of Lausanne12
TL;DR: Functional analysis of the mutations in MYCN, PTPN14 and LATS1 suggested their potential relevance in BCC tumorigenesis, and the mutational profiles, N-Myc and Hippo-YAP pathway target genes were upregulated.
Abstract: Basal cell carcinoma (BCC) of the skin is the most common malignant neoplasm in humans. BCC is primarily driven by the Sonic Hedgehog (Hh) pathway. However, its phenotypic variation remains unexplained. Our genetic profiling of 293 BCCs found the highest mutation rate in cancer (65 mutations/Mb). Eighty-five percent of the BCCs harbored mutations in Hh pathway genes (PTCH1, 73% or SMO, 20% (P = 6.6 × 10(-8)) and SUFU, 8%) and in TP53 (61%). However, 85% of the BCCs also harbored additional driver mutations in other cancer-related genes. We observed recurrent mutations in MYCN (30%), PPP6C (15%), STK19 (10%), LATS1 (8%), ERBB2 (4%), PIK3CA (2%), and NRAS, KRAS or HRAS (2%), and loss-of-function and deleterious missense mutations were present in PTPN14 (23%), RB1 (8%) and FBXW7 (5%). Consistent with the mutational profiles, N-Myc and Hippo-YAP pathway target genes were upregulated. Functional analysis of the mutations in MYCN, PTPN14 and LATS1 suggested their potential relevance in BCC tumorigenesis.
TL;DR: In this article, the conditions that favor natural regeneration within tropical forest landscapes are discussed, and the economic, social, and legal issues that challenge natural regeneration in tropical landscapes are highlighted, and a major global effort to enable cost-effective natural regeneration is needed to achieve ambitious forest and landscape restoration goals.
Abstract: A major global effort to enable cost-effective natural regeneration is needed to achieve ambitious forest and landscape restoration goals. Natural forest regeneration can potentially play a major role in large-scale landscape restoration in tropical regions. Here, we focus on the conditions that favor natural regeneration within tropical forest landscapes. We illustrate cases where large-scale natural regeneration followed forest clearing and non-forest land use, and describe the social and ecological factors that drove these local forest transitions. The self-organizing processes that create naturally regenerating forests and natural regeneration in planted forests promote local genetic adaptation, foster native species with known traditional uses, create spatial and temporal heterogeneity, and sustain local biodiversity and biotic interactions. These features confer greater ecosystem resilience in the face of future shocks and disturbances. We discuss economic, social, and legal issues that challenge natural regeneration in tropical landscapes. We conclude by suggesting ways to enable natural regeneration to become an effective tool for implementing large-scale forest and landscape restoration. Major research and policy priorities include: identifying and modeling the ecological and economic conditions where natural regeneration is a viable and favorable land-use option, developing monitoring protocols for natural regeneration that can be carried out by local communities, and developing enabling incentives, governance structures, and regulatory conditions that promote the stewardship of naturally regenerating forests. Aligning restoration goals and practices with natural regeneration can achieve the best possible outcome for achieving multiple social and environmental benefits at minimal cost.
TL;DR: In this article, a mesoporous molybdenum oxide (MoO3-x) with nanosized crystalline walls using a soft template (PEO-b-PS) synthesis method is introduced.
Abstract: A unique approach for the synthesis of nonstoichiometric, mesoporous molybdenum oxide (MoO3–x) with nanosized crystalline walls by using a soft template (PEO-b-PS) synthesis method is introduced. The as-synthesized mesoporous MoO3–x is very active and stable (durability > 12 h) for the electrochemical hydrogen evolution reaction (HER) under both acidic and alkaline conditions. The intrinsic MoO3 serves as an HER electrocatalyst without the assistance of carbon materials, noble metals, or MoS2 materials. The results from transmission electron microscopy and N2 sorption techniques show that the as-synthesized mesoporous MoO3–x has large accessible pores (20–40 nm), which are able to facilitate mass transport and charge transfer during HER. In terms of X-ray diffraction, X-ray photoelectron spectroscopy, temperature-programmed oxidation, and diffusive reflectance UV–vis spectroscopy, the mesoporous MoO3–x exhibits mixed oxidation states (Mo5+, Mo6+) and an oxygen-deficient structure. The as-synthesized MoO3–x only requires a low overpotential (≈0.14 V) to achieve a 10 mA cm−2 current density in 0.1 m KOH and the Tafel slope is as low as 56 mV dec−1. Density functional theory calculations demonstrate a change of electronic structure and the possible reaction pathway of HER. Oxygen vacancies and mesoporosity serve as key factors for excellent performance.
TL;DR: The results support the hypothesis that beliefs in moralistic, punitive and knowing gods increase impartial behaviour towards distant co-religionists, and therefore can contribute to the expansion of prosociality.
Abstract: Since the origins of agriculture, the scale of human cooperation and societal complexity has dramatically expanded. This fact challenges standard evolutionary explanations of prosociality because well-studied mechanisms of cooperation based on genetic relatedness, reciprocity and partner choice falter as people increasingly engage in fleeting transactions with genetically unrelated strangers in large anonymous groups. To explain this rapid expansion of prosociality, researchers have proposed several mechanisms. Here we focus on one key hypothesis: cognitive representations of gods as increasingly knowledgeable and punitive, and who sanction violators of interpersonal social norms, foster and sustain the expansion of cooperation, trust and fairness towards co-religionist strangers. We tested this hypothesis using extensive ethnographic interviews and two behavioural games designed to measure impartial rule-following among people (n = 591, observations = 35,400) from eight diverse communities from around the world: (1) inland Tanna, Vanuatu; (2) coastal Tanna, Vanuatu; (3) Yasawa, Fiji; (4) Lovu, Fiji; (5) Pesqueiro, Brazil; (6) Pointe aux Piments, Mauritius; (7) the Tyva Republic (Siberia), Russia; and (8) Hadzaland, Tanzania. Participants reported adherence to a wide array of world religious traditions including Christianity, Hinduism and Buddhism, as well as notably diverse local traditions, including animism and ancestor worship. Holding a range of relevant variables constant, the higher participants rated their moralistic gods as punitive and knowledgeable about human thoughts and actions, the more coins they allocated to geographically distant co-religionist strangers relative to both themselves and local co-religionists. Our results support the hypothesis that beliefs in moralistic, punitive and knowing gods increase impartial behaviour towards distant co-religionists, and therefore can contribute to the expansion of prosociality.
TL;DR: 3D scaffold fabrication methodologies with a focus on optimizing scaffold performance through the matrix pores, bioactivity and degradation rate to enable tissue regeneration are highlighted.