ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute ...of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.
We report initial observations and analysis on the Type IIb SN 2016gkg in the nearby galaxy NGC 613. SN 2016gkg exhibited a clear double-peaked light curve during its early evolution, as evidenced by ...our intensive photometric follow-up campaign. SN 2016gkg shows strong similarities with other Type IIb SNe, in particular, with respect to the He i emission features observed in both the optical and near-infrared. SN 2016gkg evolved faster than the prototypical Type IIb SN 1993J, with a decline similar to that of SN 2011dh after the first peak. The analysis of archival Hubble Space Telescope images indicate a pre-explosion source at SN 2016gkg's position, suggesting a progenitor star with a ∼mid-F spectral type and initial mass M , depending on the distance modulus adopted for NGC 613. Modeling the temperature evolution within of explosion, we obtain a progenitor radius of R , smaller than that obtained from the analysis of the pre-explosion images ( R ).
Anthropogenic modification of habitats may reduce the resources available for native species, leading to population declines and extinction. These same habitats often have the highest richness of ...non-native species. This pattern may be explained if recently human-modified habitats provide novel resources that are more accessible to non-native species than native species. Using non-native birds in the Iberian Peninsula as a case study, we conduct a large-scale study to investigate whether non-native species are positively associated with human modified habitats, and to investigate whether this positive association may be driven by the presence of resources that are not fully exploited by native species. We do this by comparing the functional diversity and resource use of native and non-native bird communities in a recently human-modified habitat (rice fields) and in more traditional habitats in the Iberian Peninsula. The functional diversity of native bird communities was lower in rice fields, but non-native birds were positively associated with rice fields and plugged this gap. Differences in resource use between native and non-native species allowed non-native species to exploit resources that were plentiful in rice fields, supporting the role of underexploited resources in driving the positive association of non-native birds with rice fields. Our results provide a potential mechanism explaining the positive association of non-native species with anthropogenic habitats, and further work is needed to test if this applies more generally.
Although copy number variants (CNVs) are important in genomic medicine, CNVs have not been systematically assessed for many complex traits. Several large rare CNVs increase risk for schizophrenia ...(SCZ) and autism and often demonstrate pleiotropic effects; however, their frequencies in the general population and other complex traits are unknown. Genotyping large numbers of samples is essential for progress. Large cohorts from many different diseases are being genotyped using exome-focused arrays designed to detect uncommon or rare protein-altering sequence variation. Although these arrays were not designed for CNV detection, the hybridization intensity data generated in each experiment could, in principle, be used for gene-focused CNV analysis. Our goal was to evaluate the extent to which CNVs can be detected using data from one particular exome array (the Illumina Human Exome Bead Chip). We genotyped 9100 Swedish subjects (3962 cases with SCZ and 5138 controls) using both standard genome-wide association study (GWAS) and exome arrays. In comparison with CNVs detected using GWAS arrays, we observed high sensitivity and specificity for detecting genic CNVs 400 kb including known pathogenic CNVs along with replicating the literature finding that cases with SCZ had greater enrichment for genic CNVs. Our data confirm the association of SCZ with 16p11.2 duplications and 22q11.2 deletions, and suggest a novel association with deletions at 11q12.2. Our results suggest the utility of exome-focused arrays in surveying large genic CNVs in very large samples; and thereby open the door for new opportunities such as conducting well-powered CNV assessment and comparisons between different diseases. The use of a single platform also minimizes potential confounding factors that could impact accurate detection.
We report the discovery of a microlensing planet-MOA-2016-BLG-227Lb-with a large planet/host mass ratio of q 9 × 10−3. This event was located near the K2 Campaign 9 field that was observed by a large ...number of telescopes. As a result, the event was in the microlensing survey area of a number of these telescopes, and this enabled good coverage of the planetary light-curve signal. High angular resolution adaptive optics images from the Keck telescope reveal excess flux at the position of the source above the flux of the source star, as indicated by the light-curve model. This excess flux could be due to the lens star, but it could also be due to a companion to the source or lens star, or even an unrelated star. We consider all these possibilities in a Bayesian analysis in the context of a standard Galactic model. Our analysis indicates that it is unlikely that a large fraction of the excess flux comes from the lens, unless solar-type stars are much more likely to host planets of this mass ratio than lower mass stars. We recommend that a method similar to the one developed in this paper be used for other events with high angular resolution follow-up observations when the follow-up observations are insufficient to measure the lens-source relative proper motion.
The American Thoracic Society/European Respiratory Society jointly created a Task Force on "Outcomes for COPD pharmacological trials: from lung function to biomarkers" to inform the chronic ...obstructive pulmonary disease research community about the possible use and limitations of current outcomes and markers when evaluating the impact of a pharmacological therapy. Based on their review of the published literature, the following document has been prepared with individual sections that address specific outcomes and markers, and a final section that summarises their recommendations.
The outstanding tropical land climate characteristic over the past decades is rapid warming, with no significant large-scale precipitation trends. This warming is expected to continue but the effects ...on tropical vegetation are unknown. El Niño-related heat peaks may provide a test bed for a future hotter world. Here we analyse tropical land carbon cycle responses to the 2015/16 El Niño heat and drought anomalies using an atmospheric transport inversion. Based on the global atmospheric CO2 and fossil fuel emission records, we find no obvious signs of anomalously large carbon release compared with earlier El Niño events, suggesting resilience of tropical vegetation. We find roughly equal net carbon release anomalies from Amazonia and tropical Africa, approximately 0.5 PgC each, and smaller carbon release anomalies from tropical East Asia and southern Africa. Atmospheric CO anomalies reveal substantial fire carbon release from tropical East Asia peaking in October 2015 while fires contribute only a minor amount to the Amazonian carbon flux anomaly. Anomalously large Amazonian carbon flux release is consistent with downregulation of primary productivity during peak negative near-surface water anomaly (October 2015 to March 2016) as diagnosed by solar-induced fluorescence. Finally, we find an unexpected anomalous positive flux to the atmosphere from tropical Africa early in 2016, coincident with substantial CO release.
This article is part of a discussion meeting issue ‘The impact of the 2015/2016 El Niño on the terrestrial tropical carbon cycle: patterns, mechanisms and implications’.
Since 1995, more than 500 exoplanets have been detected using different techniques, of which 12 were detected with gravitational microlensing. Most of these are gravitationally bound to their host ...stars. There is some evidence of free-floating planetary-mass objects in young star-forming regions, but these objects are limited to massive objects of 3 to 15 Jupiter masses with large uncertainties in photometric mass estimates and their abundance. Here, we report the discovery of a population of unbound or distant Jupiter-mass objects, which are almost twice (1.8(+1.7)(-0.8)) as common as main-sequence stars, based on two years of gravitational microlensing survey observations towards the Galactic Bulge. These planetary-mass objects have no host stars that can be detected within about ten astronomical units by gravitational microlensing. However, a comparison with constraints from direct imaging suggests that most of these planetary-mass objects are not bound to any host star. An abrupt change in the mass function at about one Jupiter mass favours the idea that their formation process is different from that of stars and brown dwarfs. They may have formed in proto-planetary disks and subsequently scattered into unbound or very distant orbits.
Spatial heterogeneity of species (beta diversity) is an important attribute of ecological communities, but is less frequently considered when assessing restoration success than other aspects of ...diversity (gamma and alpha). Differences in beta diversity between restored and natural sites may arise due to differences in environmental heterogeneity.
We used a nested sampling design to survey plant communities and environmental conditions (elevation, redox potential and metrics of topography) on four pairs of restored and natural saltmarshes. We assessed whether there were differences in both alpha and beta diversity between natural and restored sites and analysed their environmental drivers.
Topography was an important driver of plant alpha diversity and beta diversity on saltmarshes. The effects of topography were partly indirect, mediated though changes in redox potential, but topography also influenced plant communities independently of both elevation and redox.
Restored saltmarshes were less heterogeneous in topography than natural marshes. This reduced topography was reflected in lower beta diversity; plant communities 1 m apart in natural marshes were as dissimilar as those found 20 m apart in restored marshes.
Large‐scale topographic manipulation carried out at one site a decade after initial restoration successfully increased topographic heterogeneity and increased beta diversity when surveyed 3 years after manipulation. These changes were still evident when resurveyed after a further 2 years.
Synthesis and applications. Increasing environmental heterogeneity can improve restoration outcomes by increasing beta diversity on restored sites. The effect of environmental heterogeneity is likely to be particularly strong within intertidal habitats such as saltmarshes, where small changes in topography can determine whether a species can occur at a given location. Topographic manipulation is a feasible post‐restoration technique that can be applied to ensure restored saltmarshes better meet policy targets of biological, physical and functional equivalence with natural marshes.
Increasing environmental heterogeneity can improve restoration outcomes by increasing beta diversity on restored sites. The effect of environmental heterogeneity is likely to be particularly strong within intertidal habitats such as saltmarshes, where small changes in topography can determine whether a species can occur at a given location. Topographic manipulation is a feasible post‐restoration technique that can be applied to ensure restored saltmarshes better meet policy targets of biological, physical and functional equivalence with natural marshes.
Ischaemic heart disease evokes a complex immune response. However, tools to track the systemic behaviour and dynamics of leukocytes non-invasively in vivo are lacking. Here, we present a multimodal ...hot-spot imaging approach using an innovative high-density lipoprotein-derived nanotracer with a perfluoro-crown ether payload (
F-HDL) to allow myeloid cell tracking by
F magnetic resonance imaging. The
F-HDL nanotracer can additionally be labelled with zirconium-89 and fluorophores to detect myeloid cells by in vivo positron emission tomography imaging and optical modalities, respectively. Using our nanotracer in atherosclerotic mice with myocardial infarction, we observed rapid myeloid cell egress from the spleen and bone marrow by in vivo
F-HDL magnetic resonance imaging. Concurrently, using ex vivo techniques, we showed that circulating pro-inflammatory myeloid cells accumulated in atherosclerotic plaques and at the myocardial infarct site. Our multimodality imaging approach is a valuable addition to the immunology toolbox, enabling the study of complex myeloid cell behaviour dynamically.
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