Showing papers by "Colorado State University published in 2019"
Northern Arizona University1, National Institutes of Health2, University of Minnesota3, Woods Hole Oceanographic Institution4, University of California, Davis5, Massachusetts Institute of Technology6, University of Copenhagen7, University of Trento8, Chinese Academy of Sciences9, University of California, San Francisco10, University of Pennsylvania11, Pacific Northwest National Laboratory12, North Carolina State University13, University of California, San Diego14, Institute for Systems Biology15, Dalhousie University16, University of British Columbia17, Statens Serum Institut18, Anschutz Medical Campus19, University of Washington20, Michigan State University21, Stanford University22, Harvard University23, Broad Institute24, Australian National University25, University of Düsseldorf26, University of New South Wales27, Sookmyung Women's University28, San Diego State University29, Howard Hughes Medical Institute30, Cornell University31, Max Planck Society32, Colorado State University33, Google34, Syracuse University35, Webster University36, United States Department of Agriculture37, University of Arkansas for Medical Sciences38, Colorado School of Mines39, National Oceanic and Atmospheric Administration40, University of Southern Mississippi41, University of California, Merced42, Wageningen University and Research Centre43, University of Arizona44, Environment Agency45, University of Florida46, Merck & Co.47
TL;DR: QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and R.K.P. and partial support was also provided by the following: grants NIH U54CA143925 and U54MD012388.
Abstract: QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and U54MD012388 (J.G.C. and T.P.); grants from the Alfred P. Sloan Foundation (J.G.C. and R.K.); ERCSTG project MetaPG (N.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences QYZDB-SSW-SMC021 (Y.B.); the Australian National Health and Medical Research Council APP1085372 (G.A.H., J.G.C., Von Bing Yap and R.K.); the Natural Sciences and Engineering Research Council (NSERC) to D.L.G.; and the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. All NCI coauthors were supported by the Intramural Research Program of the National Cancer Institute. S.M.G. and C. Diener were supported by the Washington Research Foundation Distinguished Investigator Award.
8,821 citations
TL;DR: It is suggested that future studies should primarily focus on using new observation tools to improve the understanding of tropical plant phenology, on improving process-based phenology modeling, and on the scaling of phenology from species to landscape-level.
Abstract: Plant phenology, the annually recurring sequence of plant developmental stages, is important for plant functioning and ecosystem services and their biophysical and biogeochemical feedbacks to the climate system. Plant phenology depends on temperature, and the current rapid climate change has revived interest in understanding and modeling the responses of plant phenology to the warming trend and the consequences thereof for ecosystems. Here, we review recent progresses in plant phenology and its interactions with climate change. Focusing on the start (leaf unfolding) and end (leaf coloring) of plant growing seasons, we show that the recent rapid expansion in ground- and remote sensing- based phenology data acquisition has been highly beneficial and has supported major advances in plant phenology research. Studies using multiple data sources and methods generally agree on the trends of advanced leaf unfolding and delayed leaf coloring due to climate change, yet these trends appear to have decelerated or even reversed in recent years. Our understanding of the mechanisms underlying the plant phenology responses to climate warming is still limited. The interactions between multiple drivers complicate the modeling and prediction of plant phenology changes. Furthermore, changes in plant phenology have important implications for ecosystem carbon cycles and ecosystem feedbacks to climate, yet the quantification of such impacts remains challenging. We suggest that future studies should primarily focus on using new observation tools to improve the understanding of tropical plant phenology, on improving process-based phenology modeling, and on the scaling of phenology from species to landscape-level.
750 citations
University of Melbourne1, Australian National University2, Ghent University3, Pontifical Catholic University of Chile4, University of Pamplona5, University of Puerto Rico6, State University of Campinas7, Florida International University8, Spanish National Research Council9, Imperial College London10, Alexander von Humboldt Biological Resources Research Institute11, University of Los Andes12, Zoological Society of London13, North-West University14, Smithsonian Institution15, Colorado State University16, Universidad San Francisco de Quito17, Museum für Naturkunde18, Massey University19, University of Maryland, College Park20, University of Florida21, University of the Republic22, Cornell University23, Georgia Institute of Technology24, National Autonomous University of Mexico25, University of Pittsburgh26, Instituto Politécnico Nacional27, Andrés Bello National University28, University of Nevada, Reno29, Zoo Miami30, Natural History Museum31
TL;DR: A global, quantitative assessment of the amphibian chytridiomycosis panzootic demonstrates its role in the decline of at least 501 amphibian species over the past half-century and represents the greatest recorded loss of biodiversity attributable to a disease.
Abstract: Anthropogenic trade and development have broken down dispersal barriers, facilitating the spread of diseases that threaten Earth's biodiversity. We present a global, quantitative assessment of the amphibian chytridiomycosis panzootic, one of the most impactful examples of disease spread, and demonstrate its role in the decline of at least 501 amphibian species over the past half-century, including 90 presumed extinctions. The effects of chytridiomycosis have been greatest in large-bodied, range-restricted anurans in wet climates in the Americas and Australia. Declines peaked in the 1980s, and only 12% of declined species show signs of recovery, whereas 39% are experiencing ongoing decline. There is risk of further chytridiomycosis outbreaks in new areas. The chytridiomycosis panzootic represents the greatest recorded loss of biodiversity attributable to a disease.
680 citations
University of Oxford1, Harvard University2, Boston Children's Hospital3, University of Washington4, University of London5, Université libre de Bruxelles6, RTI International7, University of Nottingham8, University of Notre Dame9, Fudan University10, University of Southampton11, Southwestern University of Finance and Economics12, National University of Defense Technology13, Central South University14, Pan American Health Organization15, European Centre for Disease Prevention and Control16, Institute of Tropical Medicine Antwerp17, Colorado State University18, ETH Zurich19, Karolinska Institutet20, Stockholm School of Economics21, Pasteur Institute22, Université de Namur23, University of California, Davis24, University of Melbourne25
TL;DR: It is shown that human movement patterns explain the spread of both Aedes aegypti and Aedes albopictus in Europe and the United States following their introduction and predicted the future distributions of both species in response to accelerating urbanization, connectivity and climate change.
Abstract: The global population at risk from mosquito-borne diseases-including dengue, yellow fever, chikungunya and Zika-is expanding in concert with changes in the distribution of two key vectors: Aedes aegypti and Aedes albopictus. The distribution of these species is largely driven by both human movement and the presence of suitable climate. Using statistical mapping techniques, we show that human movement patterns explain the spread of both species in Europe and the United States following their introduction. We find that the spread of Ae. aegypti is characterized by long distance importations, while Ae. albopictus has expanded more along the fringes of its distribution. We describe these processes and predict the future distributions of both species in response to accelerating urbanization, connectivity and climate change. Global surveillance and control efforts that aim to mitigate the spread of chikungunya, dengue, yellow fever and Zika viruses must consider the so far unabated spread of these mosquitos. Our maps and predictions offer an opportunity to strategically target surveillance and control programmes and thereby augment efforts to reduce arbovirus burden in human populations globally.
605 citations
Lawrence Livermore National Laboratory1, University of Rochester2, Rutherford Appleton Laboratory3, École Polytechnique4, Ohio State University5, University of Michigan6, University of Jena7, Russian Academy of Sciences8, Osaka University9, Academy of Sciences of the Czech Republic10, Chinese Academy of Sciences11, Shanghai Jiao Tong University12, Gwangju Institute of Science and Technology13, Colorado State University14, University of Szeged15
TL;DR: In this paper, the authors provide a comprehensive update of the current status of ultra-high-power lasers and demonstrate how the technology has developed, and what technologies are to be deployed to get to these new regimes, and some critical issues facing their development.
Abstract: In the 2015 review paper 'Petawatt Class Lasers Worldwide' a comprehensive overview of the current status of highpower facilities of >200 TW was presented. This was largely based on facility specifications, with some description of their uses, for instance in fundamental ultra-high-intensity interactions, secondary source generation, and inertial confinement fusion (ICF). With the 2018 Nobel Prize in Physics being awarded to Professors Donna Strickland and Gerard Mourou for the development of the technique of chirped pulse amplification (CPA), which made these lasers possible, we celebrate by providing a comprehensive update of the current status of ultra-high-power lasers and demonstrate how the technology has developed. We are now in the era of multi-petawatt facilities coming online, with 100 PW lasers being proposed and even under construction. In addition to this there is a pull towards development of industrial and multidisciplinary applications, which demands much higher repetition rates, delivering high-average powers with higher efficiencies and the use of alternative wavelengths: mid-IR facilities. So apart from a comprehensive update of the current global status, we want to look at what technologies are to be deployed to get to these new regimes, and some of the critical issues facing their development.
559 citations
ETH Zurich1, University of California, Davis2, Bielefeld University3, Nanyang Technological University4, Wageningen University and Research Centre5, Brigham Young University6, Aligarh Muslim University7, Colorado State University8, University of Manchester9, University of Cologne10, University of La Rioja11, University of Brasília12, Queen's University Belfast13, Nanjing Agricultural University14, University of Minho15, Empresa Brasileira de Pesquisa Agropecuária16, Zealand Institute of Business and Technology17, Spanish National Research Council18, Scotland's Rural College19, American Museum of Natural History20, Russian Academy of Sciences21, Swedish University of Agricultural Sciences22, University of Göttingen23, Chinese Academy of Sciences24, University of Catania25, University of Nebraska–Lincoln26, James Hutton Institute27, Vietnam Academy of Science and Technology28, University of Sydney29, Bulgarian Academy of Sciences30, Universidade Federal de Lavras31, University of Helsinki32, University of Montpellier33, Aarhus University34, Lancaster University35, National Taiwan University36
TL;DR: High-resolution spatial maps of the global abundance of soil nematodes and the composition of functional groups show that soil nematode are found in higher abundances in sub-Arctic regions, than in temperate or tropical regions.
Abstract: Soil organisms are a crucial part of the terrestrial biosphere. Despite their importance for ecosystem functioning, few quantitative, spatially explicit models of the active belowground community currently exist. In particular, nematodes are the most abundant animals on Earth, filling all trophic levels in the soil food web. Here we use 6,759 georeferenced samples to generate a mechanistic understanding of the patterns of the global abundance of nematodes in the soil and the composition of their functional groups. The resulting maps show that 4.4 ± 0.64 × 1020 nematodes (with a total biomass of approximately 0.3 gigatonnes) inhabit surface soils across the world, with higher abundances in sub-Arctic regions (38% of total) than in temperate (24%) or tropical (21%) regions. Regional variations in these global trends also provide insights into local patterns of soil fertility and functioning. These high-resolution models provide the first steps towards representing soil ecological processes in global biogeochemical models and will enable the prediction of elemental cycling under current and future climate scenarios.
552 citations
University of Virginia1, Cornell University2, University of Texas Health Science Center at San Antonio3, University of Illinois at Chicago4, University of Pennsylvania5, Stanford University6, Colorado State University7, Providence Portland Medical Center8, Johns Hopkins University9, University of California, San Diego10, Brown University11, Northwestern University12, University of California, Davis13, Harvard University14, University of Bonn15, International University, Cambodia16, University of Washington17, Mayo Clinic18, Rush University Medical Center19, Keio University20, University of Texas Medical Branch21, Baylor College of Medicine22
TL;DR: Given that the majority of the biological and human health variables remained stable, or returned to baseline, after a 340-day space mission, these data suggest that human health can be mostly sustained over this duration of spaceflight.
Abstract: INTRODUCTION To date, 559 humans have been flown into space, but long-duration (>300 days) missions are rare (n = 8 total). Long-duration missions that will take humans to Mars and beyond are planned by public and private entities for the 2020s and 2030s; therefore, comprehensive studies are needed now to assess the impact of long-duration spaceflight on the human body, brain, and overall physiology. The space environment is made harsh and challenging by multiple factors, including confinement, isolation, and exposure to environmental stressors such as microgravity, radiation, and noise. The selection of one of a pair of monozygotic (identical) twin astronauts for NASA’s first 1-year mission enabled us to compare the impact of the spaceflight environment on one twin to the simultaneous impact of the Earth environment on a genetically matched subject. RATIONALE The known impacts of the spaceflight environment on human health and performance, physiology, and cellular and molecular processes are numerous and include bone density loss, effects on cognitive performance, microbial shifts, and alterations in gene regulation. However, previous studies collected very limited data, did not integrate simultaneous effects on multiple systems and data types in the same subject, or were restricted to 6-month missions. Measurement of the same variables in an astronaut on a year-long mission and in his Earth-bound twin indicated the biological measures that might be used to determine the effects of spaceflight. Presented here is an integrated longitudinal, multidimensional description of the effects of a 340-day mission onboard the International Space Station. RESULTS Physiological, telomeric, transcriptomic, epigenetic, proteomic, metabolomic, immune, microbiomic, cardiovascular, vision-related, and cognitive data were collected over 25 months. Some biological functions were not significantly affected by spaceflight, including the immune response (T cell receptor repertoire) to the first test of a vaccination in flight. However, significant changes in multiple data types were observed in association with the spaceflight period; the majority of these eventually returned to a preflight state within the time period of the study. These included changes in telomere length, gene regulation measured in both epigenetic and transcriptional data, gut microbiome composition, body weight, carotid artery dimensions, subfoveal choroidal thickness and peripapillary total retinal thickness, and serum metabolites. In addition, some factors were significantly affected by the stress of returning to Earth, including inflammation cytokines and immune response gene networks, as well as cognitive performance. For a few measures, persistent changes were observed even after 6 months on Earth, including some genes’ expression levels, increased DNA damage from chromosomal inversions, increased numbers of short telomeres, and attenuated cognitive function. CONCLUSION Given that the majority of the biological and human health variables remained stable, or returned to baseline, after a 340-day space mission, these data suggest that human health can be mostly sustained over this duration of spaceflight. The persistence of the molecular changes (e.g., gene expression) and the extrapolation of the identified risk factors for longer missions (>1 year) remain estimates and should be demonstrated with these measures in future astronauts. Finally, changes described in this study highlight pathways and mechanisms that may be vulnerable to spaceflight and may require safeguards for longer space missions; thus, they serve as a guide for targeted countermeasures or monitoring during future missions.
538 citations
TL;DR: In this paper, the mass, spin, and redshift distributions of binary black hole (BBH) mergers with LIGO and Advanced Virgo observations were analyzed using phenomenological population models.
Abstract: We present results on the mass, spin, and redshift distributions with phenomenological population models using the 10 binary black hole (BBH) mergers detected in the first and second observing runs completed by Advanced LIGO and Advanced Virgo. We constrain properties of the BBH mass spectrum using models with a range of parameterizations of the BBH mass and spin distributions. We find that the mass distribution of the more massive BH in such binaries is well approximated by models with no more than 1% of BHs more massive than 45 M and a power-law index of (90% credibility). We also show that BBHs are unlikely to be composed of BHs with large spins aligned to the orbital angular momentum. Modeling the evolution of the BBH merger rate with redshift, we show that it is flat or increasing with redshift with 93% probability. Marginalizing over uncertainties in the BBH population, we find robust estimates of the BBH merger rate density of R= (90% credibility). As the BBH catalog grows in future observing runs, we expect that uncertainties in the population model parameters will shrink, potentially providing insights into the formation of BHs via supernovae, binary interactions of massive stars, stellar cluster dynamics, and the formation history of BHs across cosmic time.
464 citations
TL;DR: In this article, the authors present coupling of European-wide databases with soil organic matter physical fractionation to determine continental-scale forest and grassland topsoil carbon and nitrogen stocks and their distribution between mineral-associated and particulate organic matter pools.
Abstract: Effective land-based solutions to climate change mitigation require actions that maximize soil carbon storage without generating surplus nitrogen. Land management for carbon sequestration is most often informed by bulk soil carbon inventories, without considering the form in which carbon is stored, its capacity, persistency and nitrogen demand. Here, we present coupling of European-wide databases with soil organic matter physical fractionation to determine continental-scale forest and grassland topsoil carbon and nitrogen stocks and their distribution between mineral-associated and particulate organic matter pools. Grasslands and arbuscular mycorrhizal forests store more soil carbon in mineral-associated organic carbon, which is more persistent but has a higher nitrogen demand and saturates. Ectomycorrhizal forests store more carbon in particulate organic matter, which is more vulnerable to disturbance but has a lower nitrogen demand and can potentially accumulate indefinitely. The share of carbon between mineral-associated and particulate organic matter and the ratio between carbon and nitrogen affect soil carbon stocks and mediate the effects of other variables on soil carbon stocks. Understanding the physical distribution of organic matter in pools of mineral-associated versus particulate organic matter can inform land management for nitrogen-efficient carbon sequestration, which should be driven by the inherent soil carbon capacity and nitrogen availability in ecosystems. Land management strategies for enhancing soil carbon sequestration need to be tailored to different soil types, depending on how much organic matter is stored in pools of mineral-associated and particulate organic matter, suggests an analysis of soil organic matter across Europe.
455 citations
TL;DR: In this paper, the authors place constraints on the dipole radiation and possible deviations from GR in the post-Newtonian coefficients that govern the inspiral regime of a binary neutron star inspiral.
Abstract: The recent discovery by Advanced LIGO and Advanced Virgo of a gravitational wave signal from a binary neutron star inspiral has enabled tests of general relativity (GR) with this new type of source. This source, for the first time, permits tests of strong-field dynamics of compact binaries in the presence of matter. In this Letter, we place constraints on the dipole radiation and possible deviations from GR in the post-Newtonian coefficients that govern the inspiral regime. Bounds on modified dispersion of gravitational waves are obtained; in combination with information from the observed electromagnetic counterpart we can also constrain effects due to large extra dimensions. Finally, the polarization content of the gravitational wave signal is studied. The results of all tests performed here show good agreement with GR.
430 citations
University of Minnesota1, George Mason University2, University of California, Santa Barbara3, Zoological Society of London4, Arizona State University5, World Conservation Monitoring Centre6, Leonardo7, Kunming Institute of Zoology8, Woods Hole Research Center9, Google10, Colorado State University11, Microsoft12
TL;DR: Freshwater and marine targets included here extend the GDN to all realms and provide a pathway to ensuring a more livable biosphere.
Abstract: The Global Deal for Nature (GDN) is a time-bound, science-driven plan to save the diversity and abundance of life on Earth. Pairing the GDN and the Paris Climate Agreement would avoid catastrophic climate change, conserve species, and secure essential ecosystem services. New findings give urgency to this union: Less than half of the terrestrial realm is intact, yet conserving all native ecosystems—coupled with energy transition measures—will be required to remain below a 1.5°C rise in average global temperature. The GDN targets 30% of Earth to be formally protected and an additional 20% designated as climate stabilization areas, by 2030, to stay below 1.5°C. We highlight the 67% of terrestrial ecoregions that can meet 30% protection, thereby reducing extinction threats and carbon emissions from natural reservoirs. Freshwater and marine targets included here extend the GDN to all realms and provide a pathway to ensuring a more livable biosphere.
University of California, Santa Barbara1, Colorado School of Mines2, University of Illinois at Urbana–Champaign3, National Center for Supercomputing Applications4, Johns Hopkins University5, Gdańsk University of Technology6, Colorado State University7, University of Maryland, College Park8, National Institute of Standards and Technology9
TL;DR: In this paper, a new kagome prototype structure is presented, which is based on vanadium, with the Fermi level in close proximity to several Dirac points.
Abstract: In this work, we present our discovery and characterization of a new kagome prototype structure, ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$. We also present the discovery of the isostructural compounds ${\mathrm{RbV}}_{3}{\mathrm{Sb}}_{5}$ and ${\mathrm{CsV}}_{3}{\mathrm{Sb}}_{5}$. All materials exhibit a structurally perfect two-dimensional kagome net of vanadium. Density-functional theory calculations indicate that the materials are metallic, with the Fermi level in close proximity to several Dirac points. Powder and single-crystal syntheses are presented, with postsynthetic treatments shown to deintercalate potassium from single crystals of ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$. Considering the proximity to Dirac points, deintercalation provides a convenient means to tune the Fermi level. Magnetization measurements indicate that ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$ exhibits behavior consistent with a the Curie-Weiss model at high temperatures, although the effective moment is low $(0.22{\ensuremath{\mu}}_{\text{B}}$ per vanadium ion). An anomaly is observed in both magnetization and heat capacity measurements at 80 K, below which the moment is largely quenched. Elastic neutron scattering measurements find no obvious evidence of long-range or short-range magnetic ordering below 80 K. The possibility of an orbital-ordering event is considered. Single-crystal resistivity measurements show the effect of deintercalation on the electron transport and allow estimation of the Kadowaki-Woods ratio in ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$. We find that $A/{\ensuremath{\gamma}}^{2}\ensuremath{\sim}61\phantom{\rule{4pt}{0ex}}\ensuremath{\mu}\mathrm{Ohm}$ cm ${\mathrm{mol}}_{\text{FU}}^{2}\phantom{\rule{4pt}{0ex}}{\mathrm{K}}^{2}\phantom{\rule{4pt}{0ex}}{\mathrm{J}}^{\ensuremath{-}2}$, suggesting that correlated electron transport may be possible. ${\mathrm{KV}}_{3}{\mathrm{Sb}}_{5}$ and its cogeners ${\mathrm{RbV}}_{3}{\mathrm{Sb}}_{5}$ and ${\mathrm{CsV}}_{3}{\mathrm{Sb}}_{5}$ represent a new family of kagome metals, and our results demonstrate that they deserve further study as potential model systems.
International Rice Research Institute1, University of Missouri2, University of the Philippines Los Baños3, University of Florida4, University of Montpellier5, Colorado State University6, Iowa State University7, Max Planck Society8, Frankfurt University of Applied Sciences9, Nagoya University10, Donald Danforth Plant Science Center11
TL;DR: Paddy trials showed that genome-edited SWEET promoters endow rice lines with robust, broad-spectrum resistance to all Xanthomonas bacterial blight strains tested.
Abstract: Bacterial blight of rice is an important disease in Asia and Africa. The pathogen, Xanthomonas oryzae pv. oryzae (Xoo), secretes one or more of six known transcription-activator-like effectors (TALes) that bind specific promoter sequences and induce, at minimum, one of the three host sucrose transporter genes SWEET11, SWEET13 and SWEET14, the expression of which is required for disease susceptibility. We used CRISPR-Cas9-mediated genome editing to introduce mutations in all three SWEET gene promoters. Editing was further informed by sequence analyses of TALe genes in 63 Xoo strains, which revealed multiple TALe variants for SWEET13 alleles. Mutations were also created in SWEET14, which is also targeted by two TALes from an African Xoo lineage. A total of five promoter mutations were simultaneously introduced into the rice line Kitaake and the elite mega varieties IR64 and Ciherang-Sub1. Paddy trials showed that genome-edited SWEET promoters endow rice lines with robust, broad-spectrum resistance.
Joint Genome Institute1, University of Liverpool2, Radboud University Nijmegen3, University of Guelph4, Catholic University of Leuven5, Arizona State University6, University of Cape Town7, European Bioinformatics Institute8, Cairo University9, Vanderbilt University10, University of South Florida11, Colorado State University12, University of Michigan13, University of California, Davis14, University of Auvergne15, University of Southern California16, University of Queensland17, University of Arizona18, Texas A&M University19, National Institute of Genetics20, University of Alicante21, Kyoto University22, Université Paris-Saclay23, University of Chicago24, University of Los Andes25, Universidad Miguel Hernández de Elche26, University of Maryland, Baltimore27, University of Hawaii at Manoa28, Ohio State University29, École Polytechnique Fédérale de Lausanne30, University of British Columbia31, University of Exeter32, Oregon State University33, Australian Institute of Marine Science34, University of California, Irvine35, University of Tennessee36, University of Delaware37, Max Planck Society38, Montana State University39, J. Craig Venter Institute40, University of California, San Diego41
TL;DR: The MIUViG (Minimum Information about an Uncultivated Virus Genome) as mentioned in this paper standard was developed within the Genomic Standards Consortium framework and includes virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction.
Abstract: We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.
TL;DR: It is demonstrated that plant Toll/interleukin-1 receptor (TIR) domains of NLRs are enzymes capable of degrading nicotinamide adenine dinucleotide in its oxidized form (NAD+); both cell death induction and NAD+ cleavage activity of plant TIR domains require known self-association interfaces.
Abstract: Plant nucleotide-binding leucine-rich repeat (NLR) immune receptors activate cell death and confer disease resistance by unknown mechanisms. We demonstrate that plant Toll/interleukin-1 receptor (TIR) domains of NLRs are enzymes capable of degrading nicotinamide adenine dinucleotide in its oxidized form (NAD+). Both cell death induction and NAD+ cleavage activity of plant TIR domains require known self-association interfaces and a putative catalytic glutamic acid that is conserved in both bacterial TIR NAD+-cleaving enzymes (NADases) and the mammalian SARM1 (sterile alpha and TIR motif containing 1) NADase. We identify a variant of cyclic adenosine diphosphate ribose as a biomarker of TIR enzymatic activity. TIR enzymatic activity is induced by pathogen recognition and functions upstream of the genes enhanced disease susceptibility 1 (EDS1) and N requirement gene 1 (NRG1), which encode regulators required for TIR immune function. Thus, plant TIR-NLR receptors require NADase function to transduce recognition of pathogens into a cell death response.
Northern Arizona University1, National Institutes of Health2, University of Minnesota3, Woods Hole Oceanographic Institution4, University of California, Davis5, Massachusetts Institute of Technology6, University of Copenhagen7, University of Trento8, Chinese Academy of Sciences9, University of California, San Francisco10, University of Pennsylvania11, Pacific Northwest National Laboratory12, North Carolina State University13, University of Montana14, Institute for Systems Biology15, Dalhousie University16, University of British Columbia17, Statens Serum Institut18, Anschutz Medical Campus19, University of Washington20, University of California, San Diego21, Michigan State University22, Stanford University23, Harvard University24, Broad Institute25, Australian National University26, University of Düsseldorf27, University of New South Wales28, Sookmyung Women's University29, San Diego State University30, Howard Hughes Medical Institute31, Max Planck Society32, Cornell University33, Colorado State University34, Google35, Syracuse University36, Webster University37, United States Department of Agriculture38, University of Arkansas for Medical Sciences39, Colorado School of Mines40, National Oceanic and Atmospheric Administration41, University of Southern Mississippi42, University of California, Merced43, Wageningen University and Research Centre44, University of Arizona45, Environment Agency46, University of Florida47, Merck & Co.48
TL;DR: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Abstract: In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al. instead of Schloss et al. The reference to mothur should have cited Schloss et al. instead of McMurdie & Holmes. The reference to phyloseq should have cited McMurdie & Holmes instead of Huber et al. The reference to Bioconductor should have cited Huber et al. instead of Franzosa et al. And the reference to the biobakery suite should have cited Franzosa et al. instead of Kluyver et al. The errors have been corrected in the HTML and PDF versions of the article.
TL;DR: Testing biochar's impact on cumulative N2O emissions, soil NO3- concentrations and leaching in temperate, semi-arid, sub-tropical, and tropical climate provided a valuable starting point for future biochar-based N loss mitigation studies.
TL;DR: Some of the cross-cutting research themes in machine learning that are applicable across several geoscience problems, and the importance of a deep collaboration between machine learning and geosciences for synergistic advancements in both disciplines are discussed.
Abstract: Geosciences is a field of great societal relevance that requires solutions to several urgent problems facing our humanity and the planet. As geosciences enters the era of big data, machine learning (ML)—that has been widely successful in commercial domains—offers immense potential to contribute to problems in geosciences. However, geoscience applications introduce novel challenges for ML due to combinations of geoscience properties encountered in every problem, requiring novel research in machine learning. This article introduces researchers in the machine learning (ML) community to these challenges offered by geoscience problems and the opportunities that exist for advancing both machine learning and geosciences. We first highlight typical sources of geoscience data and describe their common properties. We then describe some of the common categories of geoscience problems where machine learning can play a role, discussing the challenges faced by existing ML methods and opportunities for novel ML research. We conclude by discussing some of the cross-cutting research themes in machine learning that are applicable across several geoscience problems, and the importance of a deep collaboration between machine learning and geosciences for synergistic advancements in both disciplines.
TL;DR: It is shown that antiferromagnets have richer spin Hall properties than do non-magnetic materials, and a magnetic contribution to the spin Hall effect is observed in the non-collinearantiferromagnet Mn3Sn, which is attributed to momentum-dependent spin splitting produced by non- Collinear magnetic order.
Abstract: The spin Hall effect (SHE)1–5 achieves coupling between charge currents and collective spin dynamics in magnetically ordered systems and is a key element of modern spintronics6–9. However, previous research has focused mainly on non-magnetic materials, so the magnetic contribution to the SHE is not well understood. Here we show that antiferromagnets have richer spin Hall properties than do non-magnetic materials. We find that in the non-collinear antiferromagnet10 Mn3Sn, the SHE has an anomalous sign change when its triangularly ordered moments switch orientation. We observe contributions to the SHE (which we call the magnetic SHE) and the inverse SHE (the magnetic inverse SHE) that are absent in non-magnetic materials and that can be dominant in some magnetic materials, including antiferromagnets. We attribute the dominance of this magnetic mechanism in Mn3Sn to the momentum-dependent spin splitting that is produced by non-collinear magnetic order. This discovery expands the horizons of antiferromagnet spintronics and spin–charge coupling mechanisms. A magnetic contribution to the spin Hall effect is observed in the non-collinear antiferromagnet Mn3Sn, which is attributed to momentum-dependent spin splitting produced by non-collinear magnetic order.
TL;DR: A large retrospective case series involving clinical application of CBD for anxiety and sleep complaints as an adjunct to usual treatment found CBD was well tolerated in all but 3 patients.
Abstract: Context
Cannabidiol (CBD) is one of many cannabinoid compounds found in cannabis. It does not appear to alter consciousness or trigger a “high.” A recent surge in scientific publications has found preclinical and clinical evidence documenting value for CBD in some neuropsychiatric disorders, including epilepsy, anxiety, and schizophrenia. Evidence points toward a calming effect for CBD in the central nervous system. Interest in CBD as a treatment of a wide range of disorders has exploded, yet few clinical studies of CBD exist in the psychiatric literature.
TL;DR: An approach to assess the impacts of global climate change on biodiversity that takes into account adaptive genetic variation and evolutionary potential is presented, showing that considering local climatic adaptations reduces range loss projections but increases the potential for competition between species.
Abstract: Local adaptations can determine the potential of populations to respond to environmental changes, yet adaptive genetic variation is commonly ignored in models forecasting species vulnerability and biogeographical shifts under future climate change. Here we integrate genomic and ecological modeling approaches to identify genetic adaptations associated with climate in two cryptic forest bats. We then incorporate this information directly into forecasts of range changes under future climate change and assessment of population persistence through the spread of climate-adaptive genetic variation (evolutionary rescue potential). Considering climate-adaptive potential reduced range loss projections, suggesting that failure to account for intraspecific variability can result in overestimation of future losses. On the other hand, range overlap between species was projected to increase, indicating that interspecific competition is likely to play an important role in limiting species' future ranges. We show that although evolutionary rescue is possible, it depends on a population's adaptive capacity and connectivity. Hence, we stress the importance of incorporating genomic data and landscape connectivity in climate change vulnerability assessments and conservation management.
Henan University1, Hebei University2, Peking University3, Chinese Academy of Sciences4, Colorado State University5, University of Vermont6, University of Antwerp7, University of Tasmania8, Auckland University of Technology9, University of Copenhagen10, Swedish University of Agricultural Sciences11, East China Normal University12, Northern Arizona University13, Villanova University14, ETH Zurich15, University of Bern16, Purdue University17, Marine Biological Laboratory18, Michigan State University19, Environmental Molecular Sciences Laboratory20, Iowa State University21, Lawrence Berkeley National Laboratory22, University of California, Berkeley23, United States Department of Agriculture24, Boston University25, Virginia Tech26, Oak Ridge National Laboratory27, Indiana University28, Commonwealth Scientific and Industrial Research Organisation29, Binzhou University30
TL;DR: There is an urgent need to explore the interactions among multiple global change drivers in underrepresented regions such as semi-arid ecosystems, forests in the tropics and subtropics, and Arctic tundra when forecasting future terrestrial carbon-climate feedback.
Abstract: Direct quantification of terrestrial biosphere responses to global change is crucial for projections of future climate change in Earth system models. Here, we synthesized ecosystem carbon-cycling data from 1,119 experiments performed over the past four decades concerning changes in temperature, precipitation, CO2 and nitrogen across major terrestrial vegetation types of the world. Most experiments manipulated single rather than multiple global change drivers in temperate ecosystems of the USA, Europe and China. The magnitudes of warming and elevated CO2 treatments were consistent with the ranges of future projections, whereas those of precipitation changes and nitrogen inputs often exceeded the projected ranges. Increases in global change drivers consistently accelerated, but decreased precipitation slowed down carbon-cycle processes. Nonlinear (including synergistic and antagonistic) effects among global change drivers were rare. Belowground carbon allocation responded negatively to increased precipitation and nitrogen addition and positively to decreased precipitation and elevated CO2. The sensitivities of carbon variables to multiple global change drivers depended on the background climate and ecosystem condition, suggesting that Earth system models should be evaluated using site-specific conditions for best uses of this large dataset. Together, this synthesis underscores an urgent need to explore the interactions among multiple global change drivers in underrepresented regions such as semi-arid ecosystems, forests in the tropics and subtropics, and Arctic tundra when forecasting future terrestrial carbon-climate feedback.
Washington University in St. Louis1, Technical University of Madrid2, Beijing Institute of Genomics3, Georgia State University4, United States Army Medical Research Institute of Infectious Diseases5, Commonwealth Scientific and Industrial Research Organisation6, Columbia University7, University of Texas Medical Branch8, Friedrich Loeffler Institute9, National Institutes of Health10, Instituto Biológico11, Albert Einstein College of Medicine12, Erasmus University Rotterdam13, University of Queensland14, University of Marburg15, Humboldt University of Berlin16, Robert Koch Institute17, International Atomic Energy Agency18, University of Pittsburgh19, University of Warwick20, World Health Organization21, Empresa Brasileira de Pesquisa Agropecuária22, Boston University23, Public Health England24, Kyoto University25, Murdoch University26, Huazhong Agricultural University27, University of São Paulo28, Laval University29, Okayama University30, United States Geological Survey31, United States Department of Agriculture32, Northwestern University33, Icahn School of Medicine at Mount Sinai34, Institut de recherche pour le développement35, Ohio State University36, Katholieke Universiteit Leuven37, South Dakota State University38, Novosibirsk State University39, University of Medicine and Health Sciences40, University of Veterinary Medicine Vienna41, University of Bergen42, Texas A&M University43, Queen's University Belfast44, Centers for Disease Control and Prevention45, University of Sydney46, University of Oxford47, Defence Science and Technology Laboratory48, Queensland University of Technology49, Colorado State University50, Hokkaido University51, Pasteur Institute52, National University of Singapore53, North Carolina State University54, Universidade Federal de Viçosa55, Chinese Center for Disease Control and Prevention56, Fudan University57
TL;DR: The updated taxonomy of the order Mononegavirales is presented as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Abstract: In February 2019, following the annual taxon ratification vote, the order Mononegavirales was amended by the addition of four new subfamilies and 12 new genera and the creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Centers for Disease Control and Prevention1, United States Department of Agriculture2, University of Naples Federico II3, University of Ljubljana4, Mississippi State University5, University of Texas Medical Branch6, Friedrich Loeffler Institute7, Colorado State University8, Columbia University9, University of California, Irvine10, University of the Free State11, Xinjiang University12, Aix-Marseille University13, International Rice Research Institute14, Scripps Research Institute15, Public Health Agency of Canada16, Mayo Clinic17, Hacettepe University18, United States Army Medical Research Institute of Infectious Diseases19, Chinese Center for Disease Control and Prevention20, Kansas State University21, Bernhard Nocht Institute for Tropical Medicine22, Paris Diderot University23, University of Queensland24, University of Zurich25, University of Helsinki26, Public Health England27, Seoul National University28, Charité29, Slovak Academy of Sciences30, Karolinska Institutet31, Katholieke Universiteit Leuven32, University of Washington33, Wuhan University of Science and Technology34, University of Louisville35, University of São Paulo36, University of Bari37, Hokkaido University38, University of Hamburg39, Public Health Agency of Sweden40, Washington State University41, Aristotle University of Thessaloniki42, Oswaldo Cruz Foundation43, University of Brasília44, National University of La Plata45, Pasteur Institute46, University of Maryland, Baltimore47, National Agriculture and Food Research Organization48, University of Glasgow49, University of Tokyo50, University of Oxford51, Korea University52, National Research Council53, Fujian Agriculture and Forestry University54, North Carolina State University55, Universidade Federal de Viçosa56, Fudan University57, National Institutes of Health58
TL;DR: The updated taxonomy of the order Bunyavirales now accepted by the International Committee on Taxonomy of Viruses (ICTV) is presented.
Abstract: In February 2019, following the annual taxon ratification vote, the order Bunyavirales was amended by creation of two new families, four new subfamilies, 11 new genera and 77 new species, merging of two species, and deletion of one species. This article presents the updated taxonomy of the order Bunyavirales now accepted by the International Committee on Taxonomy of Viruses (ICTV).
TL;DR: The results reveal that PcG condensates assemble through liquid–liquid phase separation (LLPS) and suggest that phase-separated condensate can organize Pcg-bound chromatin, and reveal a mechanism underlying the assembly of CBX2–PRC1 condensating.
TL;DR: The third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed, concluded that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not.
Abstract: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.
TL;DR: This study defines a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing, and charts NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains.
TL;DR: What is currently known about sex differences in the neuroendocrine response to stress, as well as outstanding questions regarding this sex bias, are examined in the rodent literature.
Leipzig University1, Martin Luther University of Halle-Wittenberg2, Universidade Positivo3, University of Vigo4, Empresa Brasileira de Pesquisa Agropecuária5, ETH Zurich6, Moscow State University7, University of Freiburg8, University of Jena9, University of Catania10, Wageningen University and Research Centre11, Free University of Berlin12, Senckenberg Museum13, Colorado State University14, National Agriculture and Food Research Organization15, University of Nairobi16, Commonwealth Scientific and Industrial Research Organisation17, National Scientific and Technical Research Council18, Brandenburg University of Technology19, Cornell University20, University College Dublin21, United States Forest Service22, University of Toronto23, Aberystwyth University24, State University of New York at Cortland25, National University of Luján26, University of Trier27, University of the Philippines Mindanao28, Razi University29, Josip Juraj Strossmayer University of Osijek30, Kyushu University31, Minnesota Pollution Control Agency32, Aarhus University33, Northern Kentucky University34, Lincoln University (Missouri)35, University of Agricultural Sciences, Dharwad36, Fukushima University37, Matej Bel University38, Lancaster University39, Université d'Abobo-Adjamé40, Tarbiat Modares University41, Pachhunga University College42, University of São Paulo43, University of Hawaii at Hilo44, College of Tropical Agriculture and Human Resources45, Oklahoma State University–Stillwater46, Forest Research Institute47, University of Extremadura48, Katholieke Universiteit Leuven49, Research Institute for Nature and Forest50, Natural Resources Institute Finland51, University of Alcalá52, COMSATS Institute of Information Technology53, King Abdulaziz University54, University of Minnesota55, Federal University of Maranhão56, Jagiellonian University57, Technical University of Berlin58, University of Wisconsin-Madison59, Leibniz Association60, Braunschweig University of Technology61, University of Innsbruck62, Keldysh Institute of Applied Mathematics63, Russian Academy of Sciences64, Khalsa College, Amritsar65, University of La Laguna66, Kōchi University67, Universidad Pública de Navarra68, McGill University69, The Nature Conservancy70, University of Giessen71, Henan University72, University of Saint Mary73
TL;DR: It was found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms, which suggest that climate change may have serious implications for earthworm communities and for the functions they provide.
Abstract: Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.
Colorado State University1, University of Auckland2, New Mexico Institute of Mining and Technology3, University of Hull4, Macquarie University5, United States Forest Service6, Durham University7, University of Lausanne8, Dartmouth College9, Texas State University10, University of Texas at Austin11, University of Vienna12, Concordia University Wisconsin13
TL;DR: The value in evaluating boundaries between components of geomorphic systems as transition zones and examining the fluxes across them to understand landscape functioning is emphasized.
Abstract: Connectivity describes the efficiency of material transfer between geomorphic system components such as hillslopes and rivers or longitudinal segments within a river network. Representations of geomorphic systems as networks should recognize that the compartments, links, and nodes exhibit connectivity at differing scales. The historical underpinnings of connectivity in geomorphology involve management of geomorphic systems and observations linking surface processes to landform dynamics. Current work in geomorphic connectivity emphasizes hydrological, sediment, or landscape connectivity. Signatures of connectivity can be detected using diverse indicators that vary from contemporary processes to stratigraphic records or a spatial metric such as sediment yield that encompasses geomorphic processes operate over time and space. One approach to measuring connectivity is to determine the fundamental temporal and spatial scales for the phenomenon of interest and to make measurements at a sufficiently large multiple of the fundamental scales to capture reliably a representative sample. Another approach seeks to characterize how connectivity varies with scale, by applying the same metric over a wide range of scales or using statistical measures that characterize the frequency distributions of connectivity across scales. Identifying and measuring connectivity is useful in basic and applied geomorphic research and we explore the implications of connectivity for river management. Common themes and ideas that merit further research include; increased understanding of the importance of capturing landscape heterogeneity and connectivity patterns; the potential to use graph and network theory metrics in analyzing connectivity; the need to understand which metrics best represent the physical system and its connectivity pathways, and to apply these metrics to the validation of numerical models; and the need to recognize the importance of low levels of connectivity in some situations. We emphasize the value in evaluating boundaries between components of geomorphic systems as transition zones and examining the fluxes across them to understand landscape functioning.