Showing papers by "Michigan State University published in 2012"
TL;DR: The Global Burden of Diseases, Injuries, and Risk Factors Study 2010 aimed to estimate annual deaths for the world and 21 regions between 1980 and 2010 for 235 causes, with uncertainty intervals (UIs), separately by age and sex, using the Cause of Death Ensemble model.
11,809 citations
TL;DR: In this article, a search for the Standard Model Higgs boson in proton-proton collisions with the ATLAS detector at the LHC is presented, which has a significance of 5.9 standard deviations, corresponding to a background fluctuation probability of 1.7×10−9.
9,282 citations
TL;DR: The Human Microbiome Project Consortium reported the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome as discussed by the authors.
Abstract: The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.
8,410 citations
TL;DR: Prevalence and severity of health loss were weakly correlated and age-specific prevalence of YLDs increased with age in all regions and has decreased slightly from 1990 to 2010, but population growth and ageing have increased YLD numbers and crude rates over the past two decades.
7,021 citations
TL;DR: The results for 1990 and 2010 supersede all previously published Global Burden of Disease results and highlight the importance of understanding local burden of disease and setting goals and targets for the post-2015 agenda taking such patterns into account.
6,861 citations
TL;DR: It is shown that heat-carrying phonons with long mean free paths can be scattered by controlling and fine-tuning the mesoscale architecture of nanostructured thermoelectric materials, and an increase in ZT beyond the threshold of 2 highlights the role of, and need for, multiscale hierarchical architecture in controlling phonon scattering in bulk thermoeLECTrics.
Abstract: Controlling the structure of thermoelectric materials on all length scales (atomic, nanoscale and mesoscale) relevant for phonon scattering makes it possible to increase the dimensionless figure of merit to more than two, which could allow for the recovery of a significant fraction of waste heat with which to produce electricity.
3,670 citations
TL;DR: The results indicate that the revised CHARMM 36 parameters represent an improved model for the modeling and simulation studies of proteins, including studies of protein folding, assembly and functionally relevant conformational changes.
Abstract: While the quality of the current CHARMM22/CMAP additive force field for proteins has been demonstrated in a large number of applications, limitations in the model with respect to the equilibrium between the sampling of helical and extended conformations in folding simulations have been noted. To overcome this, as well as make other improvements in the model, we present a combination of refinements that should result in enhanced accuracy in simulations of proteins. The common (non Gly, Pro) backbone CMAP potential has been refined against experimental solution NMR data for weakly structured peptides, resulting in a rebalancing of the energies of the α-helix and extended regions of the Ramachandran map, correcting the α-helical bias of CHARMM22/CMAP. The Gly and Pro CMAPs have been refitted to more accurate quantum-mechanical energy surfaces. Side-chain torsion parameters have been optimized by fitting to backbone-dependent quantum-mechanical energy surfaces, followed by additional empirical optimization targeting NMR scalar couplings for unfolded proteins. A comprehensive validation of the revised force field was then performed against data not used to guide parametrization: (i) comparison of simulations of eight proteins in their crystal environments with crystal structures; (ii) comparison with backbone scalar couplings for weakly structured peptides; (iii) comparison with NMR residual dipolar couplings and scalar couplings for both backbone and side-chains in folded proteins; (iv) equilibrium folding of mini-proteins. The results indicate that the revised CHARMM 36 parameters represent an improved model for the modeling and simulation studies of proteins, including studies of protein folding, assembly and functionally relevant conformational changes.
3,421 citations
TL;DR: The Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomics data available to the scientific community as mentioned in this paper.
Abstract: A variety of microbial communities and their genes (microbiome) exist throughout the human body, playing fundamental roles in human health and disease. The NIH funded Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 to 18 body sites up to three times, which to date, have generated 5,177 microbial taxonomic profiles from 16S rRNA genes and over 3.5 Tb of metagenomic sequence. In parallel, approximately 800 human-associated reference genomes have been sequenced. Collectively, these data represent the largest resource to date describing the abundance and variety of the human microbiome, while providing a platform for current and future studies.
2,172 citations
TL;DR: The notion of culturally sustaining pedagogy was introduced by as discussed by the authors, who argued that teaching and learning relevant and responsive to the languages, literacies, and cultural practices of students across categories of difference and (in)equality.
Abstract: Seventeen years ago Gloria Ladson-Billings (1995) published the landmark article “Toward a Theory of Culturally Relevant Pedagogy,” giving a coherent theoretical statement for resource pedagogies that had been building throughout the 1970s and 1980s. I, like countless teachers and university-based researchers, have been inspired by what it means to make teaching and learning relevant and responsive to the languages, literacies, and cultural practices of students across categories of difference and (in)equality. Recently, however, I have begun to question if the terms “relevant” and “responsive” are really descriptive of much of the teaching and research founded upon them and, more importantly, if they go far enough in their orientation to the languages and literacies and other cultural practices of communities marginalized by systemic inequalities to ensure the valuing and maintenance of our multiethnic and multilingual society. In this essay, I offer the term and stance of culturally sustaining pedagogy ...
1,921 citations
Lawrence Berkeley National Laboratory1, University of California, Berkeley2, Australian Astronomical Observatory3, Pontifical Catholic University of Chile4, Harvard University5, Hamilton College6, University of Utah7, University of Tokyo8, Michigan State University9, Space Telescope Science Institute10, California Institute of Technology11, University of Colorado Boulder12, University of California, Santa Cruz13, University of Waterloo14, University of Chicago15, University of Florida16, Stockholm University17, University of Minnesota18, National Institutes of Natural Sciences, Japan19, Leiden University20, Northwestern University21, University of Bonn22, University of California, Davis23, University of Washington24, Kyoto University25, Pennsylvania State University26, European Southern Observatory27, Lawrence Livermore National Laboratory28, University of Lisbon29, Texas A&M University30, University of Toronto31
TL;DR: In this article, Advanced Camera for Surveys, NICMOS and Keck adaptive-optics-assisted photometry of 20 Type Ia supernovae (SNe Ia) from the Hubble Space Telescope (HST) Cluster Supernova Survey was presented.
Abstract: We present Advanced Camera for Surveys, NICMOS, and Keck adaptive-optics-assisted photometry of 20 Type Ia supernovae (SNe Ia) from the Hubble Space Telescope (HST) Cluster Supernova Survey. The SNe Ia were discovered over the redshift interval 0.623 1 SNe Ia. We describe how such a sample could be efficiently obtained by targeting cluster fields with WFC3 on board HST. The updated supernova Union2.1 compilation of 580 SNe is available at http://supernova.lbl.gov/Union.
1,784 citations
Christopher P. Ahn1, Rachael Alexandroff2, Carlos Allende Prieto3, Scott F. Anderson4 +256 more•Institutions (65)
TL;DR: In this paper, the authors presented the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS) for the Sloan Digital Sky Survey III (SDSS-III) dataset.
Abstract: The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z ~ 0.52), 102,100 new quasar spectra (median z ~ 2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T eff -0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SEGUE-2. The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the APOGEE along with another year of data from BOSS, followed by the final SDSS-III data release in 2014 December.
TL;DR: In this article, a comprehensive empirical examination of LMX antecedents and consequences has been conducted, which included 247 studies, containing 290 samples, and 21 antecedent and 16 consequences of leader-member exchange quality.
La Trobe University1, Harvard University2, German Cancer Research Center3, Yale University4, Morehouse School of Medicine5, Autonomous University of Barcelona6, University of Massachusetts Medical School7, Semmelweis University8, Cardiff University9, Ikerbasque10, Karolinska Institutet11, Pohang University of Science and Technology12, Allahabad University13, Ghent University14, University of Melbourne15, London Metropolitan University16, Erasmus University Rotterdam17, University of Mainz18, National University of Singapore19, University of Oslo20, University of Gothenburg21, University of Valencia22, Umeå University23, University of Freiburg24, University of Amsterdam25, Utrecht University26, Johns Hopkins University27, Mayo Clinic28, Ohio State University29, University of Cambridge30, University of Zurich31, Curie Institute32, Michigan State University33, Autonomous University of Madrid34, University of Helsinki35, Aalborg University36, University of Louisville37, Carlos III Health Institute38, Centre national de la recherche scientifique39, Heidelberg University40
TL;DR: Vesiclepedia is a community-annotated compendium of molecular data on extracellular vesicles that aims to provide a single authoritative source for information on vesicle structure and function.
Abstract: Extracellular vesicles (EVs) are membraneous vesicles released by a variety of cells into their microenvironment. Recent studies have elucidated the role of EVs in intercellular communication, pathogenesis, drug, vaccine and gene-vector delivery, and as possible reservoirs of biomarkers. These findings have generated immense interest, along with an exponential increase in molecular data pertaining to EVs. Here, we describe Vesiclepedia, a manually curated compendium of molecular data (lipid, RNA, and protein) identified in different classes of EVs from more than 300 independent studies published over the past several years. Even though databases are indispensable resources for the scientific community, recent studies have shown that more than 50% of the databases are not regularly updated. In addition, more than 20% of the database links are inactive. To prevent such database and link decay, we have initiated a continuous community annotation project with the active involvement of EV researchers. The EV research community can set a gold standard in data sharing with Vesiclepedia, which could evolve as a primary resource for the field.
TL;DR: An overview of the concepts of stability that are relevant for microbial communities is provided, and thoughts about the unique insights that systems perspectives – informed by meta-omics data – may provide about microbial community stability are concluded.
Abstract: Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure and predict. Understanding the drivers of microbial community stability, including resistance (insensitivity to disturbance) and resilience (the rate of recovery after disturbance) is important for predicting community response to disturbance. Here, we provide an overview of the concepts of stability that are relevant for microbial communities. First, we highlight insights from ecology that are useful for defining and measuring stability. To determine whether general disturbance responses exist for microbial communities, we next examine representative studies from the literature that investigated community responses to press (long-term) and pulse (short-term) disturbances in a variety of habitats. Then we discuss the biological features of individual microorganisms, of microbial populations, and of microbial communities that may govern overall community stability. We conclude with thoughts about the unique insights that systems perspectives - informed by meta-omics data - may provide about microbial community stability.
TL;DR: A 2001 systematic review of the effects of these training interventions for healthcare providers that aim to promote patient-centred care in clinical consultations was updated by as discussed by the authors, who found 29 new randomized trials (up to June 2010), bringing the total of studies included in the review to 43.
Abstract: Problems may arise when healthcare providers focus on managing diseases rather than on people and their health problems. Patient-centred approaches to care delivery in the patient encounter are increasingly advocated by consumers and clinicians and incorporated into training for healthcare providers. The authors updated a 2001 systematic review of the effects of these training interventions for healthcare providers that aim to promote patient-centred care in clinical consultations.
They found 29 new randomized trials (up to June 2010), bringing the total of studies included in the review to 43. In most of the studies, training interventions were directed at primary care physicians (general practitioners, internists, paediatricians or family doctors) or nurses practising in community or hospital outpatient settings. Some studies trained specialists. Patients were predominantly adults with general medical problems, though two studies included children with asthma.
These studies showed that training providers to improve their ability to share control with patients about topics and decisions addressed in consultations are largely successful in teaching providers new skills. Short-term training (less than 10 hours) is as successful in this regard as longer training. Results are mixed about whether patients are more satisfied when providers practice these skills. The impact on general health is also mixed, although the limited data that could be pooled showed small positive effects on health status. Patients' specific health behaviours show improvement in the small number of studies where interventions use provider training combined with condition-specific educational materials and/or training for patients, such as teaching question-asking during the consultation or medication-taking after the consultation. However, the number of studies is too small to determine which elements of these multi-faceted studies are essential in helping patients change their healthcare behaviours.
National Institutes of Health1, University of Pittsburgh2, Bayer Corporation3, CHDI Foundation4, Cornell University5, Rockefeller University6, Alzheimer's Drug Discovery Foundation7, University of Massachusetts Medical School8, University of Nebraska Medical Center9, American Medical Association10, Michigan State University11, University of Rochester12, University of Melbourne13, Stanford University14, American Association for the Advancement of Science15, Harvard University16, Hoffmann-La Roche17, University of California, Los Angeles18, University of Edinburgh19, University of California, San Francisco20, Amyotrophic Lateral Sclerosis Therapy Development Institute21, University of California, Irvine22, Food and Drug Administration23
TL;DR: The main workshop recommendation is that at a minimum studies should report on sample-size estimation, whether and how animals were randomized, whether investigators were blind to the treatment, and the handling of data.
Abstract: The US National Institute of Neurological Disorders and Stroke convened major stakeholders in June 2012 to discuss how to improve the methodological reporting of animal studies in grant applications and publications. The main workshop recommendation is that at a minimum studies should report on sample-size estimation, whether and how animals were randomized, whether investigators were blind to the treatment, and the handling of data. We recognize that achieving a meaningful improvement in the quality of reporting will require a concerted effort by investigators, reviewers, funding agencies and journal editors. Requiring better reporting of animal studies will raise awareness of the importance of rigorous study design to accelerate scientific progress.
TL;DR: The findings show that life events have very different effects on affective and cognitive well-being and that for most events the effects of life events on cognitive well -being are stronger and more consistent across samples.
Abstract: Previous research has shown that major life events can have short- and long-term effects on subjective well-being (SWB). The present meta-analysis examines (a) whether life events have different effects on affective and cognitive well-being and (b) how the rate of adaptation varies across different life events. Longitudinal data from 188 publications (313 samples, N = 65,911) were integrated to describe the reaction and adaptation to 4 family events (marriage, divorce, bereavement, childbirth) and 4 work events (unemployment, reemployment, retirement, relocation/migration). The findings show that life events have very different effects on affective and cognitive well-being and that for most events the effects of life events on cognitive well-being are stronger and more consistent across samples. Different life events differ in their effects on SWB, but these effects are not a function of the alleged desirability of events. The results are discussed with respect to their theoretical implications, and recommendations for future studies on adaptation are given.
Space Telescope Science Institute1, Spanish National Research Council2, University of the Basque Country3, Michigan State University4, Johns Hopkins University5, Tel Aviv University6, University of California, Berkeley7, California Institute of Technology8, European Southern Observatory9, Academia Sinica10, Leiden University11, University College London12, Pontifical Catholic University of Chile13, Rutgers University14, Carnegie Institution for Science15, Ohio State University16, INAF17, University of California, San Diego18, CERN19, Max Planck Society20
TL;DR: The Cluster Lensing And Supernova Survey with Hubble (CLASH) as mentioned in this paper is a 524-orbit Multi-Cycle Treasury Program to use the gravitational lensing properties of 25 galaxy clusters to accurately constrain their mass distributions.
Abstract: The Cluster Lensing And Supernova survey with Hubble (CLASH) is a 524-orbit Multi-Cycle Treasury Program to use the gravitational lensing properties of 25 galaxy clusters to accurately constrain their mass distributions. The survey, described in detail in this paper, will definitively establish the degree of concentration of dark matter in the cluster cores, a key prediction of structure formation models. The CLASH cluster sample is larger and less biased than current samples of space-based imaging studies of clusters to similar depth, as we have minimized lensing-based selection that favors systems with overly dense cores. Specifically, 20 CLASH clusters are solely X-ray selected. The X-ray-selected clusters are massive (kT > 5 keV) and, in most cases, dynamically relaxed. Five additional clusters are included for their lensing strength (θ_Ein > 35" at z_s = 2) to optimize the likelihood of finding highly magnified high-z (z > 7) galaxies. A total of 16 broadband filters, spanning the near-UV to near-IR, are employed for each 20-orbit campaign on each cluster. These data are used to measure precise (σ_z ~ 0.02(1 + z)) photometric redshifts for newly discovered arcs. Observations of each cluster are spread over eight epochs to enable a search for Type Ia supernovae at z > 1 to improve constraints on the time dependence of the dark energy equation of state and the evolution of supernovae. We present newly re-derived X-ray luminosities, temperatures, and Fe abundances for the CLASH clusters as well as a representative source list for MACS1149.6+2223 (z = 0.544).
TL;DR: The Black Queen Hypothesis as mentioned in this paper predicts that the loss of a costly, leaky function is selectively favored at the individual level and will proceed until the production of public goods is just sufficient to support the equilibrium community; at that point, the benefit of any further loss would be offset by the cost.
Abstract: Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococ- cus and "Candidatus Pelagibacter," and in these cases the reduction appears to be driven by natural selection rather than drift. Gene loss in free-living organisms may leave them dependent on cooccurring microbes for lost metabolic functions. We present the Black Queen Hypothesis (BQH), a novel theory of reductive evolution that explains how selection leads to such dependen- cies; its name refers to the queen of spades in the game Hearts, where the usual strategy is to avoid taking this card. Gene loss can provide a selective advantage by conserving an organism's limiting resources, provided the gene's function is dispensable. Many vital genetic functions are leaky, thereby unavoidably producing public goods that are available to the entire community. Such leaky functions are thus dispensable for individuals, provided they are not lost entirely from the community. The BQH predicts that the loss of a costly, leaky function is selectively favored at the individual level and will proceed until the production of public goods is just sufficient to support the equilibrium community; at that point, the benefit of any further loss would be offset by the cost. Evolution in accordance with the BQH thus generates "beneficiaries" of reduced genomic content that are dependent on leaky "helpers," and it may explain the observed nonuniversality of prototrophy, stress resistance, and other cellular functions in the microbial world.
TL;DR: A large body of empirical research has shown that social relationships and the networks these relationships constitute are influential in explaining the processes of knowledge creation, diffusion, absorption, and use.
TL;DR: The utility of impedance spectroscopy in investigations of hematite electrodes is demonstrated to provide key parameters of photoelectrodes with a relatively simple measurement, and new evidence of the accumulation of holes in surface states at the semiconductor/electrolyte interface, which are responsible for water oxidation.
Abstract: Hematite (α-Fe2O3) constitutes one of the most promising semiconductor materials for the conversion of sunlight into chemical fuels by water splitting. Its inherent drawbacks related to the long penetration depth of light and poor charge carrier conductivity are being progressively overcome by employing nanostructuring strategies and improved catalysts. However, the physical–chemical mechanisms responsible for the photoelectrochemical performance of this material (J(V) response) are still poorly understood. In the present study we prepared thin film hematite electrodes by atomic layer deposition to study the photoelectrochemical properties of this material under water-splitting conditions. We employed impedance spectroscopy to determine the main steps involved in photocurrent production at different conditions of voltage, light intensity, and electrolyte pH. A general physical model is proposed, which includes the existence of a surface state at the semiconductor/liquid interface where holes accumulate. T...
University of British Columbia1, Grand Valley State University2, University of Gothenburg3, University of Sheffield4, Royal Swedish Academy of Sciences5, St. John's University6, University of Tromsø7, VU University Amsterdam8, Arizona State University9, American Museum of Natural History10, United States Forest Service11, Agricultural University of Iceland12, University of California, Berkeley13, University of Alberta14, University of Melbourne15, University of Iceland16, Norwegian University of Life Sciences17, Colorado State University18, Hokkaido University19, University of Copenhagen20, Florida International University21, University of Saskatchewan22, Pennsylvania State University23, University of Manchester24, Aarhus University25, Marine Biological Laboratory26, Finnish Forest Research Institute27, La Trobe University28, Michigan State University29, University of Alaska Anchorage30, University of Stirling31
TL;DR: In this article, a synthesis of 61 experimental warming studies, of up to 20 years duration, in tundra sites worldwide, was used to understand the sensitivity of tundras vegetation to climate warming and to forecast future biodiversity and vegetation feedbacks to climate.
Abstract: 35 Abstract Understanding the sensitivity of tundra vegetation to climate warming is critical to forecasting future biodiversity and vegetation feedbacks to climate. In situ warming experiments accelerate climate change on a small scale to forecast responses of local plant communities. Limitations of this approach include the apparent site-specificity of results and uncertainty about the power of short-term studies to anticipate longer term change. We address these issues with a synthesis of 61 experimental warming studies, of up to 20 years duration, in tundra sites worldwide. The response of plant groups to warming often differed with ambient summer temperature, soil moisture and experimental duration. Shrubs increased with warming only where ambient temperature was high, whereas graminoids increased primarily in the coldest study sites. Linear increases in effect size over time were frequently observed. There was little indication of saturating or accelerating effects, as would be predicted if negative or positive vegetation feedbacks were common. These results indicate that tundra vegetation exhibits strong regional variation in response to warming, and that in vulnerable regions, cumulative effects of long-term warming on tundra vegetation - and associated ecosystem consequences - have the potential to be much greater than we have observed to date.
10 Feb 2012
TL;DR: Analysis of the metagenomes showed that microbial functional genes relating to energy production and conversion were increased in the antibiotic-fed pigs and that antibiotic resistance genes increased in abundance and diversity in the medicated swine microbiome despite a high background of resistance genes in nonmedication swine.
Abstract: Antibiotics have been administered to agricultural animals for disease treatment, disease prevention, and growth promotion for over 50 y. The impact of such antibiotic use on the treatment of human diseases is hotly debated. We raised pigs in a highly controlled environment, with one portion of the littermates receiving a diet containing performance-enhancing antibiotics [chlortetracycline, sulfamethazine, and penicillin (known as ASP250)] and the other portion receiving the same diet but without the antibiotics. We used phylogenetic, metagenomic, and quantitative PCR-based approaches to address the impact of antibiotics on the swine gut microbiota. Bacterial phylotypes shifted after 14 d of antibiotic treatment, with the medicated pigs showing an increase in Proteobacteria (1–11%) compared with nonmedicated pigs at the same time point. This shift was driven by an increase in Escherichia coli populations. Analysis of the metagenomes showed that microbial functional genes relating to energy production and conversion were increased in the antibiotic-fed pigs. The results also indicate that antibiotic resistance genes increased in abundance and diversity in the medicated swine microbiome despite a high background of resistance genes in nonmedicated swine. Some enriched genes, such as aminoglycoside O-phosphotransferases, confer resistance to antibiotics that were not administered in this study, demonstrating the potential for indirect selection of resistance to classes of antibiotics not fed. The collateral effects of feeding subtherapeutic doses of antibiotics to agricultural animals are apparent and must be considered in cost-benefit analyses.
TL;DR: The use of plastic mulch in agriculture has increased dramatically in the last 10 years throughout the world as mentioned in this paper, due to benefits such as increase in soil temperature, reduced weed pressure, moisture conservation, reduction of certain insect pests, higher crop yields, and more efficient use of soil nutrients.
Abstract: The use of plastic mulch in agriculture has increased dramatically in the last 10 years throughout the world. This increase is due to benefits such as increase in soil temperature, reduced weed pressure, moisture conservation, reduction of certain insect pests, higher crop yields, and more efficient use of soil nutrients. However, disposing of used plastic films, which cause pollution, has led to development of photodegradable and biodegradable mulches. Here we review the use of plastic mulches in agriculture, with special reference to biodegradable mulches. Major topics discussed are (1) history of plastic mulch and impact on crop yield and pest management, (2) limitations of polyethylene mulches and potential alternatives, (3) biodegradable and photodegradable plastic mulches, (4) field performance of biodegradable mulches, and (5) use of biodegradable plastic mulches in organic production. We found that (1) despite multiple benefits, removal and disposal of conventional polyethylene mulches remains a major agronomic, economic, and environmental constraint; (2) early use of photodegradable plastic mulch during the 1970s and 1980s, wrongly named biodegradable mulch films, discouraged adoption of new biodegradable mulch films because they were too expensive and their breakdown was unpredictable; (3) biodegradable plastic films are converted through microbial activity in the soil to carbon dioxide, water, and natural substances; (4) polymers such as poly(lactic acid), poly(butylene adipate-coterephthalate), poly(e-caprolactone), and starch-based polymer blends or copolymers can degrade when exposed to bioactive environments such as soil and compost; (5) with truly biodegradable materials obtained from petroleum and natural resources, opportunity for using biodegradable polymers as agricultural mulch films has become more viable; and (6) the source of polymer and additives may limit use of some biodegradable mulches in organic production. More knowledge is needed on the effect of biodegradable mulches on crop growth, microclimate modifications, soil biota, soil fertility, and yields.
TL;DR: The second phase of the NLDAS-2 research partnership is presented in this article, where four land surface models (Noah, Variable Infiltration Capacity, Sacramento Soil Moisture Accounting, and Mosaic) are executed over the conterminous U.S. (CONUS) in real-time and retrospective modes.
Abstract: [1] Results are presented from the second phase of the multiinstitution North American Land Data Assimilation System (NLDAS-2) research partnership. In NLDAS, the Noah, Variable Infiltration Capacity, Sacramento Soil Moisture Accounting, and Mosaic land surface models (LSMs) are executed over the conterminous U.S. (CONUS) in realtime and retrospective modes. These runs support the drought analysis, monitoring and forecasting activities of the National Integrated Drought Information System, as well as efforts to monitor large-scale floods. NLDAS-2 builds upon the framework of the first phase of NLDAS (NLDAS-1) by increasing the accuracy and consistency of the surface forcing data, upgrading the land surface model code and parameters, and extending the study from a 3-year (1997–1999) to a 30-year (1979–2008) time window. As the first of two parts, this paper details the configuration of NLDAS-2, describes the upgrades to the forcing, parameters, and code of the four LSMs, and explores overall model-to-model comparisons of land surface water and energy flux and state variables over the CONUS. Focusing on model output rather than on observations, this study seeks to highlight the similarities and differences between models, and to assess changes in output from that seen in NLDAS-1. The second part of the two-part article focuses on the validation of model-simulated streamflow and evaporation against observations. The results depict a higher level of agreement among the four models over much of the CONUS than was found in the first phase of NLDAS. This is due, in part, to recent improvements in the parameters, code, and forcing of the NLDAS-2 LSMs that were initiated following NLDAS-1. However, large inter-model differences still exist in the northeast, Lake Superior, and western mountainous regions of the CONUS, which are associated with cold season processes. In addition, variations in the representation of sub-surface hydrology in the four LSMs lead to large differences in modeled evaporation and subsurface runoff. These issues are important targets for future research by the land surface modeling community. Finally, improvement from NLDAS-1 to NLDAS-2 is summarized by comparing the streamflow measured from U.S. Geological Survey stream gauges with that simulated by four NLDAS models over 961 small basins.
University of British Columbia1, Grand Valley State University2, University of Gothenburg3, Université du Québec à Trois-Rivières4, VU University Amsterdam5, Arizona State University6, Umeå University7, Moscow State University8, Environment Canada9, United States Department of Agriculture10, University of California, Berkeley11, University of Alberta12, University of Texas at El Paso13, University of Saskatchewan14, University of Iceland15, United States Fish and Wildlife Service16, Norwegian University of Life Sciences17, Colorado State University18, Hokkaido University19, University of Copenhagen20, Florida International University21, Swiss Federal Institute for Forest, Snow and Landscape Research22, Aarhus University23, Marine Biological Laboratory24, University of California, Davis25, University of Oulu26, La Trobe University27, Michigan State University28, University of Alaska Anchorage29
TL;DR: In this paper, remote sensing data indicate that contemporary climate warming has already resulted in increased productivity and increased productivity in the tundra biome (Tundra Tundra Bi biome).
Abstract: Temperature is increasing at unprecedented rates across most of the tundra biome(1). Remote-sensing data indicate that contemporary climate warming has already resulted in increased productivity ov ...
Max Planck Society1, University of Salamanca2, University of Kentucky3, Centraalbureau voor Schimmelcultures4, University of California, Davis5, Agricultural Research Organization, Volcani Center6, University of Cologne7, Broad Institute8, GATC Biotech9, Seoul National University10, United States Department of Agriculture11, University of Massachusetts Amherst12, DuPont Pioneer13, Centre national de la recherche scientifique14, Texas A&M University15, University of Erlangen-Nuremberg16, Kyoto Prefectural University17, Institut national de la recherche agronomique18, West Virginia University19, RWTH Aachen University20, University of Wisconsin-Madison21, National Center for Agricultural Utilization Research22, University of Florida23, Michigan State University24, Kyoto University25
TL;DR: Findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.
Abstract: Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize. Comparative genomics showed that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters and peptidases are expanded in C. higginsianum. Genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions: effectors and secondary metabolism enzymes are induced before penetration and during biotrophy, whereas most hydrolases and transporters are upregulated later, at the switch to necrotrophy. Our findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.
TL;DR: In this article, the authors summarize existing approaches to detect insufficient effort responding (IER) to low-stakes surveys and comprehensively evaluate these approaches and provide convergent validity evidence regarding various indices for IER.
Abstract: Responses provided by unmotivated survey participants in a careless, haphazard, or random fashion can threaten the quality of data in psychological and organizational research. The purpose of this study was to summarize existing approaches to detect insufficient effort responding (IER) to low-stakes surveys and to comprehensively evaluate these approaches. In an experiment (Study 1) and a nonexperimental survey (Study 2), 725 undergraduates responded to a personality survey online. Study 1 examined the presentation of warnings to respondents as a means of deterrence and showed the relative effectiveness of four indices for detecting IE responses: response time, long string, psychometric antonyms, and individual reliability coefficients. Study 2 demonstrated that the detection indices measured the same underlying construct and showed the improvement of psychometric properties (item interrelatedness, facet dimensionality, and factor structure) after removing IE respondents identified by each index. Three approaches (response time, psychometric antonyms, and individual reliability) with high specificity and moderate sensitivity were recommended as candidates for future application in survey research. The identification of effective IER indices may help researchers ensure the quality of their low-stake survey data. This study is a first attempt to comprehensively evaluate IER detection methods using both experimental and nonexperimental designs. Results from both studies corroborated each other in suggesting the three more effective approaches. This study also provided convergent validity evidence regarding various indices for IER.
TL;DR: A molecular cascade involving the COI1–JAZ–DELLA–PIF signaling module, by which angiosperm plants prioritize JA-mediated defense over growth, has been elucidated.
Abstract: Plants must effectively defend against biotic and abiotic stresses to survive in nature. However, this defense is costly and is often accompanied by significant growth inhibition. How plants coordinate the fluctuating growth-defense dynamics is not well understood and remains a fundamental question. Jasmonate (JA) and gibberellic acid (GA) are important plant hormones that mediate defense and growth, respectively. Binding of bioactive JA or GA ligands to cognate receptors leads to proteasome-dependent degradation of specific transcriptional repressors (the JAZ or DELLA family of proteins), which, at the resting state, represses cognate transcription factors involved in defense (e.g., MYCs) or growth [e.g. phytochrome interacting factors (PIFs)]. In this study, we found that the coi1 JA receptor mutants of rice (a domesticated monocot crop) and Arabidopsis (a model dicot plant) both exhibit hallmark phenotypes of GA-hypersensitive mutants. JA delays GA-mediated DELLA protein degradation, and the della mutant is less sensitive to JA for growth inhibition. Overexpression of a selected group of JAZ repressors in Arabidopsis plants partially phenocopies GA-associated phenotypes of the coi1 mutant, and JAZ9 inhibits RGA (a DELLA protein) interaction with transcription factor PIF3. Importantly, the pif quadruple (pifq) mutant no longer responds to JA-induced growth inhibition, and overexpression of PIF3 could partially overcome JA-induced growth inhibition. Thus, a molecular cascade involving the COI1–JAZ–DELLA–PIF signaling module, by which angiosperm plants prioritize JA-mediated defense over growth, has been elucidated.