Showing papers by "Colorado State University published in 2020"
TL;DR: In 2019, the LIGO Livingston detector observed a compact binary coalescence with signal-to-noise ratio 12.9 and the Virgo detector was also taking data that did not contribute to detection due to a low SINR but were used for subsequent parameter estimation as discussed by the authors.
Abstract: On 2019 April 25, the LIGO Livingston detector observed a compact binary coalescence with signal-to-noise ratio 12.9. The Virgo detector was also taking data that did not contribute to detection due to a low signal-to-noise ratio, but were used for subsequent parameter estimation. The 90% credible intervals for the component masses range from to if we restrict the dimensionless component spin magnitudes to be smaller than 0.05). These mass parameters are consistent with the individual binary components being neutron stars. However, both the source-frame chirp mass and the total mass of this system are significantly larger than those of any other known binary neutron star (BNS) system. The possibility that one or both binary components of the system are black holes cannot be ruled out from gravitational-wave data. We discuss possible origins of the system based on its inconsistency with the known Galactic BNS population. Under the assumption that the signal was produced by a BNS coalescence, the local rate of neutron star mergers is updated to 250-2810.
1,189 citations
TL;DR: This Review explores how plant microbiome research has unravelled the complex network of genetic, biochemical, physical and metabolic interactions among the plant, the associated microbial communities and the environment and how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits.
Abstract: Healthy plants host diverse but taxonomically structured communities of microorganisms, the plant microbiota, that colonize every accessible plant tissue. Plant-associated microbiomes confer fitness advantages to the plant host, including growth promotion, nutrient uptake, stress tolerance and resistance to pathogens. In this Review, we explore how plant microbiome research has unravelled the complex network of genetic, biochemical, physical and metabolic interactions among the plant, the associated microbial communities and the environment. We also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits, such as nutrient acquisition and plant health, in addition to highlighting knowledge gaps and future directions. In this Review, Trivedi and colleagues explore the interactions between plants, their associated microbial communities and the environment, and also discuss how those interactions shape the assembly of plant-associated microbiomes and modulate their beneficial traits.
999 citations
TL;DR: In this paper, the authors reported the observation of a compact binary coalescence involving a 222 −243 M ⊙ black hole and a compact object with a mass of 250 −267 M ⋆ (all measurements quoted at the 90% credible level) The gravitational-wave signal, GW190814, was observed during LIGO's and Virgo's third observing run on 2019 August 14 at 21:10:39 UTC and has a signal-to-noise ratio of 25 in the three-detector network.
Abstract: We report the observation of a compact binary coalescence involving a 222–243 M ⊙ black hole and a compact object with a mass of 250–267 M ⊙ (all measurements quoted at the 90% credible level) The gravitational-wave signal, GW190814, was observed during LIGO's and Virgo's third observing run on 2019 August 14 at 21:10:39 UTC and has a signal-to-noise ratio of 25 in the three-detector network The source was localized to 185 deg2 at a distance of ${241}_{-45}^{+41}$ Mpc; no electromagnetic counterpart has been confirmed to date The source has the most unequal mass ratio yet measured with gravitational waves, ${0112}_{-0009}^{+0008}$, and its secondary component is either the lightest black hole or the heaviest neutron star ever discovered in a double compact-object system The dimensionless spin of the primary black hole is tightly constrained to ≤007 Tests of general relativity reveal no measurable deviations from the theory, and its prediction of higher-multipole emission is confirmed at high confidence We estimate a merger rate density of 1–23 Gpc−3 yr−1 for the new class of binary coalescence sources that GW190814 represents Astrophysical models predict that binaries with mass ratios similar to this event can form through several channels, but are unlikely to have formed in globular clusters However, the combination of mass ratio, component masses, and the inferred merger rate for this event challenges all current models of the formation and mass distribution of compact-object binaries
913 citations
TL;DR: The extent of the trait data compiled in TRY is evaluated and emerging patterns of data coverage and representativeness are analyzed to conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements.
Abstract: Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
882 citations
TL;DR: It is inferred that the primary black hole mass lies within the gap produced by (pulsational) pair-instability supernova processes, with only a 0.32% probability of being below 65 M⊙, which can be considered an intermediate mass black hole (IMBH).
Abstract: On May 21, 2019 at 03:02:29 UTC Advanced LIGO and Advanced Virgo observed a short duration gravitational-wave signal, GW190521, with a three-detector network signal-to-noise ratio of 14.7, and an estimated false-alarm rate of 1 in 4900 yr using a search sensitive to generic transients. If GW190521 is from a quasicircular binary inspiral, then the detected signal is consistent with the merger of two black holes with masses of 85_{-14}^{+21} M_{⊙} and 66_{-18}^{+17} M_{⊙} (90% credible intervals). We infer that the primary black hole mass lies within the gap produced by (pulsational) pair-instability supernova processes, with only a 0.32% probability of being below 65 M_{⊙}. We calculate the mass of the remnant to be 142_{-16}^{+28} M_{⊙}, which can be considered an intermediate mass black hole (IMBH). The luminosity distance of the source is 5.3_{-2.6}^{+2.4} Gpc, corresponding to a redshift of 0.82_{-0.34}^{+0.28}. The inferred rate of mergers similar to GW190521 is 0.13_{-0.11}^{+0.30} Gpc^{-3} yr^{-1}.
876 citations
TL;DR: Findings suggest that although families experience elevated stressors from COVID-19, providing parental support and increasing perceived control may be promising intervention targets.
767 citations
01 Jan 2020
TL;DR: In this article, the authors examined the detection of the greening signal, its causes and its consequences, and showed that greening is pronounced over intensively farmed or afforested areas, such as in China and India, reflecting human activities.
Abstract: Vegetation greenness has been increasing globally since at least 1981, when satellite technology enabled large-scale vegetation monitoring. The greening phenomenon, together with warming, sea-level rise and sea-ice decline, represents highly credible evidence of anthropogenic climate change. In this Review, we examine the detection of the greening signal, its causes and its consequences. Greening is pronounced over intensively farmed or afforested areas, such as in China and India, reflecting human activities. However, strong greening also occurs in biomes with low human footprint, such as the Arctic, where global change drivers play a dominant role. Vegetation models suggest that CO2 fertilization is the main driver of greening on the global scale, with other factors being notable at the regional scale. Modelling indicates that greening could mitigate global warming by increasing the carbon sink on land and altering biogeophysical processes, mainly evaporative cooling. Coupling high temporal and fine spatial resolution remote-sensing observations with ground measurements, increasing sampling in the tropics and Arctic, and modelling Earth systems in more detail will further our insights into the greening of Earth. Vegetation on Earth is increasing, potentially leading to a larger terrestrial carbon sink. In this Review, we discuss the occurrence of this global greening phenomenon, its drivers and how it might impact carbon cycling and land-atmosphere heat and water fluxes.
722 citations
TL;DR: Microbial nucleic acids are detected in samples of tissues and blood from more than 10,000 patients with cancer, and machine learning is used to show that these can be used to discriminate between and among different types of cancer, suggesting a new microbiome-based diagnostic approach.
Abstract: Systematic characterization of the cancer microbiome provides the opportunity to develop techniques that exploit non-human, microorganism-derived molecules in the diagnosis of a major human disease. Following recent demonstrations that some types of cancer show substantial microbial contributions1–10, we re-examined whole-genome and whole-transcriptome sequencing studies in The Cancer Genome Atlas11 (TCGA) of 33 types of cancer from treatment-naive patients (a total of 18,116 samples) for microbial reads, and found unique microbial signatures in tissue and blood within and between most major types of cancer. These TCGA blood signatures remained predictive when applied to patients with stage Ia–IIc cancer and cancers lacking any genomic alterations currently measured on two commercial-grade cell-free tumour DNA platforms, despite the use of very stringent decontamination analyses that discarded up to 92.3% of total sequence data. In addition, we could discriminate among samples from healthy, cancer-free individuals (n = 69) and those from patients with multiple types of cancer (prostate, lung, and melanoma; 100 samples in total) solely using plasma-derived, cell-free microbial nucleic acids. This potential microbiome-based oncology diagnostic tool warrants further exploration. Microbial nucleic acids are detected in samples of tissues and blood from more than 10,000 patients with cancer, and machine learning is used to show that these can be used to discriminate between and among different types of cancer, suggesting a new microbiome-based diagnostic approach.
524 citations
TL;DR: Conceptualizing SOM into POM versus MAOM is a feasible, well-supported, and useful framework that will allow scientists to move beyond studies of bulk SOM, but also use a consistent separation scheme across studies.
Abstract: Managing soil organic matter (SOM) stocks to address global change challenges requires well-substantiated knowledge of SOM behavior that can be clearly communicated between scientists, management practitioners, and policy makers. However, SOM is incredibly complex and requires separation into multiple components with contrasting behavior in order to study and predict its dynamics. Numerous diverse SOM separation schemes are currently used, making cross-study comparisons difficult and hindering broad-scale generalizations. Here, we recommend separating SOM into particulate (POM) and mineral-associated (MAOM) forms, two SOM components that are fundamentally different in terms of their formation, persistence, and functioning. We provide evidence of their highly contrasting physical and chemical properties, mean residence times in soil, and responses to land use change, plant litter inputs, warming, CO2 enrichment, and N fertilization. Conceptualizing SOM into POM versus MAOM is a feasible, well-supported, and useful framework that will allow scientists to move beyond studies of bulk SOM, but also use a consistent separation scheme across studies. Ultimately, we propose the POM versus MAOM framework as the best way forward to understand and predict broad-scale SOM dynamics in the context of global change challenges and provide necessary recommendations to managers and policy makers.
521 citations
TL;DR: In this article, the authors reported the observation of gravitational waves from a binary-black-hole coalescence during the first two weeks of LIGO and Virgo's third observing run.
Abstract: We report the observation of gravitational waves from a binary-black-hole coalescence during the first two weeks of LIGO’s and Virgo’s third observing run. The signal was recorded on April 12, 2019 at 05∶30∶44 UTC with a network signal-to-noise ratio of 19. The binary is different from observations during the first two observing runs most notably due to its asymmetric masses: a ∼30 M⊙ black hole merged with a ∼8 M⊙ black hole companion. The more massive black hole rotated with a dimensionless spin magnitude between 0.22 and 0.60 (90% probability). Asymmetric systems are predicted to emit gravitational waves with stronger contributions from higher multipoles, and indeed we find strong evidence for gravitational radiation beyond the leading quadrupolar order in the observed signal. A suite of tests performed on GW190412 indicates consistency with Einstein’s general theory of relativity. While the mass ratio of this system differs from all previous detections, we show that it is consistent with the population model of stellar binary black holes inferred from the first two observing runs.
507 citations
Aarhus University1, King Abdullah University of Science and Technology2, Colorado State University3, Massachusetts Institute of Technology4, Pontifical Catholic University of Chile5, Sciences Po6, Prince Albert II of Monaco Foundation7, University of Paris8, Boston University9, James Cook University10, National Museum of Natural History11, University of Queensland12, Dalhousie University13, University of York14
TL;DR: Recovery rates across studies suggest that substantial recovery of the abundance, structure and function of marine life could be achieved by 2050 if major pressures, including climate change, are mitigated.
Abstract: Sustainable Development Goal 14 of the United Nations aims to "conserve and sustainably use the oceans, seas and marine resources for sustainable development". Achieving this goal will require rebuilding the marine life-support systems that deliver the many benefits that society receives from a healthy ocean. Here we document the recovery of marine populations, habitats and ecosystems following past conservation interventions. Recovery rates across studies suggest that substantial recovery of the abundance, structure and function of marine life could be achieved by 2050, if major pressures-including climate change-are mitigated. Rebuilding marine life represents a doable Grand Challenge for humanity, an ethical obligation and a smart economic objective to achieve a sustainable future.
Pablo de Olavide University1, University of Sydney2, University of Alicante3, University of Minnesota4, University of New South Wales5, Universidad Mayor6, Spanish National Research Council7, University of California, Merced8, Newcastle University9, University of Western Australia10, Fujian Normal University11, University of Melbourne12, National Taiwan University13, University of Innsbruck14, University of Chile15, United States Geological Survey16, University of Nevada, Reno17, Colorado State University18, Arizona State University19, Virginia Tech20
TL;DR: Evidence is provided that soil biodiversity (bacteria, fungi, protists and invertebrates) is significantly and positively associated with multiple ecosystem functions including nutrient cycling, decomposition, plant production, and reduced potential for pathogenicity and belowground biological warfare.
Abstract: The role of soil biodiversity in regulating multiple ecosystem functions is poorly understood, limiting our ability to predict how soil biodiversity loss might affect human wellbeing and ecosystem sustainability. Here, combining a global observational study with an experimental microcosm study, we provide evidence that soil biodiversity (bacteria, fungi, protists and invertebrates) is significantly and positively associated with multiple ecosystem functions. These functions include nutrient cycling, decomposition, plant production, and reduced potential for pathogenicity and belowground biological warfare. Our findings also reveal the context dependency of such relationships and the importance of the connectedness, biodiversity and nature of the globally distributed dominant phylotypes within the soil network in maintaining multiple functions. Moreover, our results suggest that the positive association between plant diversity and multifunctionality across biomes is indirectly driven by soil biodiversity. Together, our results provide insights into the importance of soil biodiversity for maintaining soil functionality locally and across biomes, as well as providing strong support for the inclusion of soil biodiversity in conservation and management programmes.
Washington University in St. Louis1, Dalhousie University2, University of California, Berkeley3, Goddard Space Flight Center4, Universities Space Research Association5, California Institute of Technology6, University of British Columbia7, Institute for Health Metrics and Evaluation8, University of Texas at Austin9, University of Colorado Boulder10, Earth System Research Laboratory11, Tsinghua University12, Colorado State University13, Harvard University14
TL;DR: Global estimates of annual PM2.5 concentrations and trends for 1998-2018 are developed using advances in satellite observations, chemical transport modeling, and ground-based monitoring, identifying significant trends for eastern North America, Europe, and globally.
Abstract: Exposure to outdoor fine particulate matter (PM2.5) is a leading risk factor for mortality. We develop global estimates of annual PM2.5 concentrations and trends for 1998-2018 using advances in satellite observations, chemical transport modeling, and ground-based monitoring. Aerosol optical depths (AODs) from advanced satellite products including finer resolution, increased global coverage, and improved long-term stability are combined and related to surface PM2.5 concentrations using geophysical relationships between surface PM2.5 and AOD simulated by the GEOS-Chem chemical transport model with updated algorithms. The resultant annual mean geophysical PM2.5 estimates are highly consistent with globally distributed ground monitors (R2 = 0.81; slope = 0.90). Geographically weighted regression is applied to the geophysical PM2.5 estimates to predict and account for the residual bias with PM2.5 monitors, yielding even higher cross validated agreement (R2 = 0.90-0.92; slope = 0.90-0.97) with ground monitors and improved agreement compared to all earlier global estimates. The consistent long-term satellite AOD and simulation enable trend assessment over a 21 year period, identifying significant trends for eastern North America (-0.28 ± 0.03 μg/m3/yr), Europe (-0.15 ± 0.03 μg/m3/yr), India (1.13 ± 0.15 μg/m3/yr), and globally (0.04 ± 0.02 μg/m3/yr). The positive trend (2.44 ± 0.44 μg/m3/yr) for India over 2005-2013 and the negative trend (-3.37 ± 0.38 μg/m3/yr) for China over 2011-2018 are remarkable, with implications for the health of billions of people.
TL;DR: The GW190521 signal is consistent with a binary black hole (BBH) merger source at redshift 0.13-0.30 Gpc-3 yr-1.8 as discussed by the authors.
Abstract: The gravitational-wave signal GW190521 is consistent with a binary black hole (BBH) merger source at redshift 0.8 with unusually high component masses, 85-14+21 M o˙ and 66-18+17 M o˙, compared to previously reported events, and shows mild evidence for spin-induced orbital precession. The primary falls in the mass gap predicted by (pulsational) pair-instability supernova theory, in the approximate range 65-120 M o˙. The probability that at least one of the black holes in GW190521 is in that range is 99.0%. The final mass of the merger (142-16+28 M o˙) classifies it as an intermediate-mass black hole. Under the assumption of a quasi-circular BBH coalescence, we detail the physical properties of GW190521's source binary and its post-merger remnant, including component masses and spin vectors. Three different waveform models, as well as direct comparison to numerical solutions of general relativity, yield consistent estimates of these properties. Tests of strong-field general relativity targeting the merger-ringdown stages of the coalescence indicate consistency of the observed signal with theoretical predictions. We estimate the merger rate of similar systems to be 0.13-0.11+0.30 Gpc-3 yr-1. We discuss the astrophysical implications of GW190521 for stellar collapse and for the possible formation of black holes in the pair-instability mass gap through various channels: via (multiple) stellar coalescences, or via hierarchical mergers of lower-mass black holes in star clusters or in active galactic nuclei. We find it to be unlikely that GW190521 is a strongly lensed signal of a lower-mass black hole binary merger. We also discuss more exotic possible sources for GW190521, including a highly eccentric black hole binary, or a primordial black hole binary.
Sun Yat-sen University1, Iowa State University2, East China Normal University3, Centre national de la recherche scientifique4, Princeton University5, Colorado State University6, Tsinghua University7, University of Tennessee8, Yale University9, Clark University10, Southern University of Science and Technology11
TL;DR: In this article, the authors map global annual urban dynamics from 1985 to 2015 at a 30'm resolution using numerous surface reflectance data from Landsat satellites and find that global urban extent has expanded by 9,687'km2 per year.
Abstract: High-resolution global maps of annual urban land coverage provide fundamental information of global environmental change and contribute to applications related to climate mitigation and urban planning for sustainable development. Here we map global annual urban dynamics from 1985 to 2015 at a 30 m resolution using numerous surface reflectance data from Landsat satellites. We find that global urban extent has expanded by 9,687 km2 per year. This rate is four times greater than previous reputable estimates from worldwide individual cities, suggesting an unprecedented rate of global urbanization. The rate of urban expansion is notably faster than that of population growth, indicating that the urban land area already exceeds what is needed to sustain population growth. Looking ahead, using these maps in conjunction with integrated assessment models can facilitate greater understanding of the complex environmental impacts of urbanization and help urban planners avoid natural hazards; for example, by limiting new development in flood risk zones. The world keeps urbanizing. This study finds that since 1985 global urban lands have expanded four times faster than previously recognized and faster than population is growing.
TL;DR: The junctions appear to provide a major site for microglia-neuron communication and may help to mediate the neuroprotective effects ofmicroglia after acute brain injury, and microglial processes at these junctions could potentially monitor and protect neuronal functions.
Abstract: Microglia are the main immune cells in the brain and have roles in brain homeostasis and neurological diseases. Mechanisms underlying microglia–neuron communication remain elusive. Here, we identified an interaction site between neuronal cell bodies and microglial processes in mouse and human brain. Somatic microglia–neuron junctions have a specialized nanoarchitecture optimized for purinergic signaling. Activity of neuronal mitochondria was linked with microglial junction formation, which was induced rapidly in response to neuronal activation and blocked by inhibition of P2Y12 receptors. Brain injury–induced changes at somatic junctions triggered P2Y12 receptor–dependent microglial neuroprotection, regulating neuronal calcium load and functional connectivity. Thus, microglial processes at these junctions could potentially monitor and protect neuronal functions.
Research Triangle Park1, Foundation for Research & Technology – Hellas2, University of Washington3, University of Michigan4, National Center for Atmospheric Research5, University of East Anglia6, Colorado State University7, University of Maryland, Baltimore County8, Leibniz Association9, University of Crete10, Columbia University11, University of Illinois at Urbana–Champaign12, Nankai University13, Georgia Institute of Technology14, Tsinghua University15, Pacific Northwest National Laboratory16, McGill University17
TL;DR: This paper reviews and synthesizes the current state of knowledge on the acidity of atmospheric condensed phases, specifically particles and cloud droplets, including recommendations for estimating acidity and pH, standard nomenclature, a synthesis of current pH estimates based on observations, and new model calculations on the local and global scale.
Abstract: . Acidity, defined as pH, is a central component of aqueous
chemistry. In the atmosphere, the acidity of condensed phases (aerosol
particles, cloud water, and fog droplets) governs the phase partitioning of
semivolatile gases such as HNO3 , NH3 , HCl, and organic acids and
bases as well as chemical reaction rates. It has implications for the
atmospheric lifetime of pollutants, deposition, and human health. Despite
its fundamental role in atmospheric processes, only recently has this field
seen a growth in the number of studies on particle acidity. Even with this
growth, many fine-particle pH estimates must be based on thermodynamic model
calculations since no operational techniques exist for direct measurements.
Current information indicates acidic fine particles are ubiquitous, but
observationally constrained pH estimates are limited in spatial and temporal
coverage. Clouds and fogs are also generally acidic, but to a lesser degree
than particles, and have a range of pH that is quite sensitive to
anthropogenic emissions of sulfur and nitrogen oxides, as well as ambient
ammonia. Historical measurements indicate that cloud and fog droplet pH has
changed in recent decades in response to controls on anthropogenic
emissions, while the limited trend data for aerosol particles indicate
acidity may be relatively constant due to the semivolatile nature of the
key acids and bases and buffering in particles. This paper reviews and
synthesizes the current state of knowledge on the acidity of atmospheric
condensed phases, specifically particles and cloud droplets. It includes
recommendations for estimating acidity and pH, standard nomenclature, a
synthesis of current pH estimates based on observations, and new model
calculations on the local and global scale.
TL;DR: The results suggest that the potential contagion prevention from school closures needs to be carefully weighted with the potential loss of health-care workers from the standpoint of reducing cumulative mortality due to COVID-19, in the absence of mitigating measures.
Abstract: Summary Background The coronavirus disease 2019 (COVID-19) pandemic is leading to social (physical) distancing policies worldwide, including in the USA. Some of the first actions taken by governments are the closing of schools. The evidence that mandatory school closures reduce the number of cases and, ultimately, mortality comes from experience with influenza or from models that do not include the effect of school closure on the health-care labour force. The potential benefits from school closures need to be weighed against costs of health-care worker absenteeism associated with additional child-care obligations. In this study, we aimed to measure child-care obligations for US health-care workers arising from school closures when these are used as a social distancing measure. We then assessed how important the contribution of health-care workers would have to be in reducing mortality for their absenteeism due to child-care obligations to undo the benefits of school closures in reducing the number of cases. Methods For this modelling analysis, we used data from the monthly releases of the US Current Population Survey to characterise the family structure and probable within-household child-care options of US health-care workers. We accounted for the occupation within the health-care sector, state, and household structure to identify the segments of the health-care workforce that are most exposed to child-care obligations from school closures. We used these estimates to identify the critical level at which the importance of health-care labour supply in increasing the survival probability of a patient with COVID-19 would undo the benefits of school closures and ultimately increase cumulative mortality. Findings Between January, 2018, and January, 2020, the US Current Population Survey included information on more than 3·1 million individuals across 1·3 million households. We found that the US health-care sector has some of the highest child-care obligations in the USA, with 28·8% (95% CI 28·5–29·1) of the health-care workforce needing to provide care for children aged 3–12 years. Assuming non-working adults or a sibling aged 13 years or older can provide child care, 15·0% (14·8–15·2) of the health-care workforce would still be in need of child care during a school closure. We observed substantial variation within the health-care system. We estimated that, combined with reasonable parameters for COVID-19 such as a 15·0% case reduction from school closings and 2·0% baseline mortality rate, a 15·0% decrease in the health-care labour force would need to decrease the survival probability per percent health-care worker lost by 17·6% for a school closure to increase cumulative mortality. Our model estimates that if the infection mortality rate of COVID-19 increases from 2·00% to 2·35% when the health-care workforce declines by 15·0%, school closures could lead to a greater number of deaths than they prevent. Interpretation School closures come with many trade-offs, and can create unintended child-care obligations. Our results suggest that the potential contagion prevention from school closures needs to be carefully weighted with the potential loss of health-care workers from the standpoint of reducing cumulative mortality due to COVID-19, in the absence of mitigating measures. Funding None.
University of California, Berkeley1, Technical University of Denmark2, Japan Atomic Energy Agency3, Stanford University4, Colorado State University5, University of Toronto6, Joint Genome Institute7, Sun Yat-sen University8, University of Cape Town9, University of Pittsburgh10, University of Auvergne11, University College London12
TL;DR: Genomic analyses of major clades of huge phages sampled from across Earth’s ecosystems show that they have diverse genetic inventories, including a variety of CRISPR–Cas systems and translation-relevant genes.
Abstract: Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.
TL;DR: DRAM (Distilled and Refined Annotation of Metabolism) is presented, a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits and provides critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.
Abstract: Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.
University of Colorado Boulder1, United States Forest Service2, Colorado State University3, University of Montana4, University of New Mexico5, Natural Resources Canada6, Kent State University7, University of California, Berkeley8, University of Arizona9, Northern Arizona University10, University of Washington11, University of Vermont12, United States Geological Survey13, University of Wisconsin-Madison14
TL;DR: This article synthesizes a growing body of evidence of fire-driven conversion and understanding of its causes across western North America and proposes key themes for applied research coproduced by scientists and managers to support decision-making in an era when the prefire forest may not return.
Abstract: Changing disturbance regimes and climate can overcome forest ecosystem resilience. Following high-severity fire, forest recovery may be compromised by lack of tree seed sources, warmer and drier postfire climate, or short-interval reburning. A potential outcome of the loss of resilience is the conversion of the prefire forest to a different forest type or nonforest vegetation. Conversion implies major, extensive, and enduring changes in dominant species, life forms, or functions, with impacts on ecosystem services. In the present article, we synthesize a growing body of evidence of fire-driven conversion and our understanding of its causes across western North America. We assess our capacity to predict conversion and highlight important uncertainties. Increasing forest vulnerability to changing fire activity and climate compels shifts in management approaches, and we propose key themes for applied research coproduced by scientists and managers to support decision-making in an era when the prefire forest may not return.
TL;DR: It is confirmed that cats are susceptible to productive SARS-CoV-2 infection, but are unlikely to develop clinical disease, and that cats developed a robust neutralizing antibody response that prevented reinfection following a second viral challenge.
Abstract: The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reached nearly every country in the world with extraordinary person-to-person transmission. The most likely original source of the virus was spillover from an animal reservoir and subsequent adaptation to humans sometime during the winter of 2019 in Wuhan Province, China. Because of its genetic similarity to SARS-CoV-1, it is probable that this novel virus has a similar host range and receptor specificity. Due to concern for human-pet transmission, we investigated the susceptibility of domestic cats and dogs to infection and potential for infected cats to transmit to naive cats. We report that cats are highly susceptible to infection, with a prolonged period of oral and nasal viral shedding that is not accompanied by clinical signs, and are capable of direct contact transmission to other cats. These studies confirm that cats are susceptible to productive SARS-CoV-2 infection, but are unlikely to develop clinical disease. Further, we document that cats developed a robust neutralizing antibody response that prevented reinfection following a second viral challenge. Conversely, we found that dogs do not shed virus following infection but do seroconvert and mount an antiviral neutralizing antibody response. There is currently no evidence that cats or dogs play a significant role in human infection; however, reverse zoonosis is possible if infected owners expose their domestic pets to the virus during acute infection. Resistance to reinfection holds promise that a vaccine strategy may protect cats and, by extension, humans.
TL;DR: A promising NA candidate is mapped to the nucleoside active site of SARS-CoV RdRp and ExoN proteins, identifying the residues important for nucleotide recognition, discrimination, and excision, and Interestingly, GS-441524 addresses both enzyme active sites in a manner consistent with significant incorporation, delayed chain termination, and altered excision due to the ribose 1'-CN group, which may account for the increased antiviral effect.
TL;DR: Space-borne observations of vegetation greenness show a large increase with time over this study period, supporting the timing and increase in the land carbon sink over these afforestation regions.
Abstract: Limiting the rise in global mean temperatures relies on reducing carbon dioxide (CO2) emissions and on the removal of CO2 by land carbon sinks. China is currently the single largest emitter of CO2, responsible for approximately 27 per cent (2.67 petagrams of carbon per year) of global fossil fuel emissions in 20171. Understanding of Chinese land biosphere fluxes has been hampered by sparse data coverage2–4, which has resulted in a wide range of a posteriori estimates of flux. Here we present recently available data on the atmospheric mole fraction of CO2, measured from six sites across China during 2009 to 2016. Using these data, we estimate a mean Chinese land biosphere sink of −1.11 ± 0.38 petagrams of carbon per year during 2010 to 2016, equivalent to about 45 per cent of our estimate of annual Chinese anthropogenic emissions over that period. Our estimate reflects a previously underestimated land carbon sink over southwest China (Yunnan, Guizhou and Guangxi provinces) throughout the year, and over northeast China (especially Heilongjiang and Jilin provinces) during summer months. These provinces have established a pattern of rapid afforestation of progressively larger regions5,6, with provincial forest areas increasing by between 0.04 million and 0.44 million hectares per year over the past 10 to 15 years. These large-scale changes reflect the expansion of fast-growing plantation forests that contribute to timber exports and the domestic production of paper7. Space-borne observations of vegetation greenness show a large increase with time over this study period, supporting the timing and increase in the land carbon sink over these afforestation regions. Newly available atmospheric carbon dioxide measurements from six sites across China during 2009 to 2016 indicate a larger land carbon sink than previously thought, reflecting increased afforestation.
TL;DR: The vast array of herbicide-resistance mechanisms for generalist (NTSR) and specialist (TSR and some NTSR) adaptations that have evolved over a few decades illustrate the evolutionary resilience of weed populations to extreme selection pressures.
TL;DR: In this paper, the authors summarized the causes and effects of grassland degradation, restoration practices used on degraded grasslands, impacts of climate change and nitrogen deposition on plants and soils, adaptation strategies to climate changes and sustainable grazing management on the Qinghai-Tibetan Plateau (QTP).
28 Sep 2020
TL;DR: In this paper, the authors investigated the influence of feedstock selection and pyrolysis temperature on biochar physicochemical properties, including C and specific surface area (SSA).
Abstract: Various studies have established that feedstock choice, pyrolysis temperature, and pyrolysis type influence final biochar physicochemical characteristics. However, overarching analyses of pre-biochar creation choices and correlations to biochar characteristics are severely lacking. Thus, the objective of this work was to help researchers, biochar-stakeholders, and practitioners make more well-informed choices in terms of how these three major parameters influence the final biochar product. Utilizing approximately 5400 peer-reviewed journal articles and over 50,800 individual data points, herein we elucidate the selections that influence final biochar physical and chemical properties, total nutrient content, and perhaps more importantly tools one can use to predict biochar’s nutrient availability. Based on the large dataset collected, it appears that pyrolysis type (fast or slow) plays a minor role in biochar physico- (inorganic) chemical characteristics; few differences were evident between production styles. Pyrolysis temperature, however, affects biochar’s longevity, with pyrolysis temperatures > 500 °C generally leading to longer-term (i.e., > 1000 years) half-lives. Greater pyrolysis temperatures also led to biochars containing greater overall C and specific surface area (SSA), which could promote soil physico-chemical improvements. However, based on the collected data, it appears that feedstock selection has the largest influence on biochar properties. Specific surface area is greatest in wood-based biochars, which in combination with pyrolysis temperature could likely promote greater changes in soil physical characteristics over other feedstock-based biochars. Crop- and other grass-based biochars appear to have cation exchange capacities greater than other biochars, which in combination with pyrolysis temperature could potentially lead to longer-term changes in soil nutrient retention. The collected data also suggest that one can reasonably predict the availability of various biochar nutrients (e.g., N, P, K, Ca, Mg, Fe, and Cu) based on feedstock choice and total nutrient content. Results can be used to create designer biochars to help solve environmental issues and supply a variety of plant-available nutrients for crop growth.
University of Bonn1, Forschungszentrum Jülich2, The Nature Conservancy3, Wageningen University and Research Centre4, Technische Universität München5, Cornell University6, University of California, Berkeley7, University of Reading8, Ohio State University9, University of Sydney10, Nanjing Agricultural University11, Colorado State University12, Centre national de la recherche scientifique13, Indiana University14, Université catholique de Louvain15, University of Illinois at Urbana–Champaign16
TL;DR: This work proposes the establishment of a soil information system containing localised information on soil group, degradation status, crop yield gap, and the associated carbon-sequestration potentials, as well as the provision of incentives and policies to translate management options into region- and soil-specific practices.
Abstract: Sustainable soil carbon sequestration practices need to be rapidly scaled up and implemented to contribute to climate change mitigation. We highlight that the major potential for carbon sequestration is in cropland soils, especially those with large yield gaps and/or large historic soil organic carbon losses. The implementation of soil carbon sequestration measures requires a diverse set of options, each adapted to local soil conditions and management opportunities, and accounting for site-specific trade-offs. We propose the establishment of a soil information system containing localised information on soil group, degradation status, crop yield gap, and the associated carbon-sequestration potentials, as well as the provision of incentives and policies to translate management options into region- and soil-specific practices.
Morton Arboretum1, Cardiff University2, University of Idaho3, University of Toulouse4, Environmental Protection Agency5, University of Freiburg6, University of British Columbia7, City College of New York8, University of Pretoria9, Flinders University10, National Autonomous University of Mexico11, Colorado State University12, University of Sydney13, United States Geological Survey14, University of São Paulo15, Massey University16, Research Institute for Nature and Forest17, Katholieke Universiteit Leuven18, Natural History Museum19, Tarbiat Modares University20, Scottish Natural Heritage21, University of Edinburgh22, State University of Campinas23, National Centre for Biological Sciences24, University of Yaoundé I25, Stockholm University26
TL;DR: The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development and benefit sharing.
Kansas State University1, University of Montana2, Michigan State University3, Woods Hole Research Center4, University of Tennessee5, National Center for Atmospheric Research6, Tall Timbers Research Station and Land Conservancy7, University of Colorado Boulder8, Washington University in St. Louis9, University of Melbourne10, University of Nevada, Reno11, University of California, Irvine12, Boise State University13, Syracuse University14, University of Florida15, University of British Columbia16, Murdoch University17, University of Washington18, Oregon State University19, Auburn University20, Northern Arizona University21, University of Idaho22, Colgate University23, University of Amsterdam24, University of California, Santa Barbara25, Spanish National Research Council26, Stanford University27, Louisiana State University28, United States Forest Service29, University of California, Merced30, North Carolina State University31, Humboldt State University32, Davidson College33, Colorado State University34, Desert Research Institute35
TL;DR: In this paper, the diversity of ways in which fire operates as a fundamental ecological and evolutionary process on Earth is described, and the need to study fire across temporal scales, to assess the mechanisms underlying a variety of ecological feedbacks involving fire and to improve representation of fire in a range of modelling contexts.
Abstract: 1. Fire is a powerful ecological and evolutionary force that regulates organismal traits, population sizes, species interactions, community composition, carbon and nutrient cycling and ecosystem function. It also presents a rapidly growing societal challenge, due to both increasingly destructive wildfires and fire exclusion in fire-dependent ecosystems. As an ecological process, fire integrates complex feedbacks among biological, social and geophysical processes, requiring coordination across several fields and scales of study. 2. Here, we describe the diversity of ways in which fire operates as a fundamental ecological and evolutionary process on Earth. We explore research priorities in six categories of fire ecology: (a) characteristics of fire regimes, (b) changing fire regimes, (c) fire effects on above-ground ecology, (d) fire effects on below-ground ecology, (e) fire behaviour and (f) fire ecology modelling. 3. We identify three emergent themes: the need to study fire across temporal scales, to assess the mechanisms underlying a variety of ecological feedbacks involving fire and to improve representation of fire in a range of modelling contexts. 4. Synthesis: As fire regimes and our relationships with fire continue to change, prioritizing these research areas will facilitate understanding of the ecological causes and consequences of future fires and rethinking fire management alternatives.