Seasonal changes in nutritional condition of shorebirds (charadrii) during the non-breeding seasons

The nutritional condition (fat and protein reserves)of shorebirds was studied, mainly at Teesmouth and Lindisfarne, north-east England, during the non-breeding season. Normal patterns of fat and protein storage are similar in most coastal shorebird species. Fat reserves rise to a peak in midwinter. Fat is stored rapidly before both spring and autumn migrations. Protein reserves (measured as pectoral muscle size) remain steady during winter. Protein reserves increase before spring migration, but not before autumn migration. Most shorebirds regulate both fat and protein reserves during winter. Plovers (Charadriidae) have larger fat and protein reserves than Sandpipers (Scolopacidae). However rocky-shore species carry smaller reserves than species feeding on soft sediments. Interspecific differences are related to morphology, foraging behaviour, habitat use and winter movements. First-year shorebirds carry similar sized or larger reserves than adult conspecifics. Catabolism of nutritional reserves was studied during two periods of severe winter weather in north-east England. Reserves were catabolised faster by species that normally carried the largest regulated reserves. In eastern Britain some Redshanks cannot regulate their fat and protein reserves even during mild winters. Possible reasons are discussed. The condition of shorebirds that had starved to death during severe weather is examined. Redshanks, first-year Oystercatchers, inland species)and shorebirds that return early to breeding grounds are most at risk. Recovery of nutritional condition after starvation is examined. In addition to seasonal variation, differences in the size of regulated fat reserves occur in different wintering grounds. Total lean weights in relation to wing-length as a measure of body size are used to examine whether similar seasonal and latitudinal differences in protein reserves of shorebirds exist. Plovers have larger pectoral muscles than Sandpipers but similar total lean weight (measured in relation to body size). During winter, lean weights are lower in several equatorial and southern hemisphere areas than in northern temperate regions. Seasonal and latitutinal changes in lean weight are discussed in relation to periods of environmental stress

Influence of Crohn’s disease related polymorphisms in innate immune function on ileal microbiome

We have previously identified NOD2 genotype and inflammatory bowel diseases (IBD) phenotype, as associated with shifts in the ileal microbiome (“dysbiosis”) in a patient cohort. Here we report an integrative analysis of an expanded number of Crohn's disease (CD) related genetic defects in innate immune function (NOD2, ATG16L1, IRGM, CARD9, XBP1, ORMDL3) and composition of the ileal microbiome by combining the initial patient cohort (Batch 1, 2005–2010, n = 165) with a second consecutive patient cohort (Batch 2, 2010–2012, n = 118). These combined patient cohorts were composed of three non-overlapping phenotypes: 1.) 106 ileal CD subjects undergoing initial ileocolic resection for diseased ileum, 2.) 88 IBD colitis subjects without ileal disease (predominantly ulcerative colitis but also Crohn’s colitis and indeterminate colitis, and 3.) 89 non-IBD subjects. Significant differences (FDR C. difficile infection, and NOD2 genotype on ileal dysbiosis in the expanded analysis. The relative abundance of the Proteobacteria phylum was positively associated with ileal CD and colitis phenotypes, but negatively associated with NOD2R genotype. Additional associations with ORMDL3 and XBP1 were detected at the phylum/subphylum level. IBD medications, such as immunomodulators and anti-TNFα agents, may have a beneficial effect on reversing dysbiosis associated with the IBD phenotype. Exploratory analysis comparing microbial composition of the disease unaffected region of the resected ileum between 27 ileal CD patients who subsequently developed endoscopic recurrence within 6–12 months versus 34 patients who did not, suggested that microbial biomarkers in the resected specimen helped stratify patients with respect to risk of post-surgical recurrence.</div

THE MAGNETIC FIELD MORPHOLOGY OF THE CLASS 0 PROTOSTAR L1157-mm

We present the first detection of polarization around the Class 0 low-mass protostar L1157-mm at two different wavelengths. We show polarimetric maps at large scales (10 '' resolution at 350 mu m) from the SHARC-II Polarimeter and at smaller scales (1.'' 2-4.'' 5 at 1.3 mm) from the Combined Array for Research in Millimeter-wave Astronomy (CARMA). The observations are consistent with each other and show inferred magnetic field lines aligned with the outflow. The CARMA observations suggest a full hourglass magnetic field morphology centered about the core; this is only the second well-defined hourglass detected around a low-mass protostar to date. We apply two different methods to CARMA polarimetric observations to estimate the plane-of-sky magnetic field magnitude, finding values of 1.4 and 3.4 mG.</p

Political opportunity structures, democracy, and civil war

Theories of mobilization suggest that groups are more likely to resort to violence in the presence of political opportunity structures that afford greater prospects for extracting concessions from the government or better opportunities to topple ruling governments. However, existing efforts to consider the possible influences of political opportunity structures on incentives for violence and civil war empirically have almost invariably relied upon measures of democracy to proxy for the hypothesized mechanisms, most notably the argument that the opposing effects of political accommodation and repression will give rise to an inverted U-shaped relationship between democracy and the risk of civil war. The authors detail a number of problems with measures of democracy as proxies for political opportunity structures and develop alternative measures based on the likely risks that political leaders will lose power in irregular challenges and their implications for the incentives for resort to violence. The authors evaluate empirically how the security with which leaders hold office influences the prospects of violent civil conflict. The findings indicate that recent irregular leader entry and transitions indeed increase the risk of conflict onset, while democratic institutions are found to decrease the risk of civil war, after controlling for the new measures of state weakness. </jats:p

Urban Airborne Lead: X-Ray Absorption Spectroscopy Establishes Soil as Dominant Source

BACKGROUND: Despite the dramatic decrease in airborne lead over the past three decades, there are calls for regulatory limits on this potent pediatric neurotoxin lower even than the new (2008) US Environmental Protection Agency standard. To achieve further decreases in airborne lead, what sources would need to be decreased and what costs would ensue? Our aim was to identify and, if possible, quantify the major species (compounds) of lead in recent ambient airborne particulate matter collected in El Paso, TX, USA. METHODOLOGY/PRINCIPAL FINDINGS: We used synchrotron-based XAFS (x-ray absorption fine structure) to identify and quantify the major Pb species. XAFS provides molecular-level structural information about a specific element in a bulk sample. Pb-humate is the dominant form of lead in contemporary El Paso air. Pb-humate is a stable, sorbed complex produced exclusively in the humus fraction of Pb-contaminated soils; it also is the major lead species in El Paso soils. Thus such soil must be the dominant source, and its resuspension into the air, the transfer process, providing lead particles to the local air. CONCLUSIONS/SIGNIFICANCE: Current industrial and commercial activity apparently is not a major source of airborne lead in El Paso, and presumably other locales that have eliminated such traditional sources as leaded gasoline. Instead, local contaminated soil, legacy of earlier anthropogenic Pb releases, serves as a long-term reservoir that gradually leaks particulate lead to the atmosphere. Given the difficulty and expense of large-scale soil remediation or removal, fugitive soil likely constrains a lower limit for airborne lead levels in many urban settings

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

Two Mechanistic Pathways for Thienopyridine-Associated Thrombotic Thrombocytopenic Purpura: A Report From the SERF-TTP Research Group and the RADAR Project

We sought to describe clinical and laboratory findings for a large cohort of patients with thienopyridine-associated thrombotic thrombocytopenic purpura (TTP)

Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management.

The COVID-19 pandemic has spread rapidly throughout the world. In the UK, the initial peak was in April 2020; in the county of Norfolk (UK) and surrounding areas, which has a stable, low-density population, over 3200 cases were reported between March and August 2020. As part of the activities of the national COVID-19 Genomics Consortium (COG-UK) we undertook whole genome sequencing of the SARS-CoV-2 genomes present in positive clinical samples from the Norfolk region. These samples were collected by four major hospitals, multiple minor hospitals, care facilities and community organizations within Norfolk and surrounding areas. We combined clinical metadata with the sequencing data from regional SARS-CoV-2 genomes to understand the origins, genetic variation, transmission and expansion (spread) of the virus within the region and provide context nationally. Data were fed back into the national effort for pandemic management, whilst simultaneously being used to assist local outbreak analyses. Overall, 1565 positive samples (172 per 100 000 population) from 1376 cases were evaluated; for 140 cases between two and six samples were available providing longitudinal data. This represented 42.6 % of all positive samples identified by hospital testing in the region and encompassed those with clinical need, and health and care workers and their families. In total, 1035 cases had genome sequences of sufficient quality to provide phylogenetic lineages. These genomes belonged to 26 distinct global lineages, indicating that there were multiple separate introductions into the region. Furthermore, 100 genetically distinct UK lineages were detected demonstrating local evolution, at a rate of ~2 SNPs per month, and multiple co-occurring lineages as the pandemic progressed. Our analysis: identified a discrete sublineage associated with six care facilities; found no evidence of reinfection in longitudinal samples; ruled out a nosocomial outbreak; identified 16 lineages in key workers which were not in patients, indicating infection control measures were effective; and found the D614G spike protein mutation which is linked to increased transmissibility dominates the samples and rapidly confirmed relatedness of cases in an outbreak at a food processing facility. The large-scale genome sequencing of SARS-CoV-2-positive samples has provided valuable additional data for public health epidemiology in the Norfolk region, and will continue to help identify and untangle hidden transmission chains as the pandemic evolves.The sequencing costs were funded by the COVID-19 Genomics UK (COG-UK) Consortium which is supported by funding from the Medical Research Council (MRC) part of UK Research and Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute

Protecting Important Sites for Biodiversity Contributes to Meeting Global Conservation Targets

Protected areas (PAs) are a cornerstone of conservation efforts and now cover nearly 13% of the world's land surface, with the world's governments committed to expand this to 17%. However, as biodiversity continues to decline, the effectiveness of PAs in reducing the extinction risk of species remains largely untested. We analyzed PA coverage and trends in species' extinction risk at globally significant sites for conserving birds (10,993 Important Bird Areas, IBAs) and highly threatened vertebrates and conifers (588 Alliance for Zero Extinction sites, AZEs) (referred to collectively hereafter as ‘important sites’). Species occurring in important sites with greater PA coverage experienced smaller increases in extinction risk over recent decades: the increase was half as large for bird species with>50% of the IBAs at which they occur completely covered by PAs, and a third lower for birds, mammals and amphibians restricted to protected AZEs (compared with unprotected or partially protected sites). Globally, half of the important sites for biodiversity conservation remain unprotected (49% of IBAs, 51% of AZEs). While PA coverage of important sites has increased over time, the proportion of PA area covering important sites, as opposed to less important land, has declined (by 0.45–1.14% annually since 1950 for IBAs and 0.79–1.49% annually for AZEs). Thus, while appropriately located PAs may slow the rate at which species are driven towards extinction, recent PA network expansion has under-represented important sites. We conclude that better targeted expansion of PA networks would help to improve biodiversity trends