PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

© 2015 The Authors. Published by OUP. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1093/nar/gkv1047The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data.The Wellcome Trust [88944, 104948]; UK Biotechnology and Biological Sciences Research Council [BB/J007471/1, BB/K016970/1, BB/M013146/1, BB/M011674/1]; National Institutes of Health [GM079429]; UK Medical Research Council [MR/L007835/1]; European Union [284209]; CCP4; European Molecular Biology Laboratory (EMBL). Funding for open access charge: The Wellcome Trust.Published versio

The Rural Household Multiple Indicator Survey, data from 13,310 farm households in 21 countries

The Rural Household Multiple Indicator Survey (RHoMIS) is a standardized farm household survey approach which collects information on 758 variables covering household demographics, farm area, crops grown and their production, livestock holdings and their production, agricultural product use and variables underlying standard socio-economic and food security indicators such as the Probability of Poverty Index, the Household Food Insecurity Access Scale, and household dietary diversity. These variables are used to quantify more than 40 different indicators on farm and household characteristics, welfare, productivity, and economic performance. Between 2015 and the beginning of 2018, the survey instrument was applied in 21 countries in Central America, sub-Saharan Africa and Asia. The data presented here include the raw survey response data, the indicator calculation code, and the resulting indicator values. These data can be used to quantify on- and off-farm pathways to food security, diverse diets, and changes in poverty for rural smallholder farm households

Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action

Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or “golden rules,” for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice

Elephant Morphometrics and Tusk Size

Each row represent an individual elephant (no repeated measurements) with a sigle measurement each of shoulder height, total tusk length, tusk circumference at lip, age in years, and sampling period lumped into 2 categories. The column titles are clear and a detailed description can be found in the methods section of the manuscrip

Data from: Illegal tusk harvest and the decline of tusk size in the African elephant

Harvesting of wild populations can cause the evolution of morphological, behavioral, and life history traits that may compromise natural or sexual selection. Despite the vulnerability of large mammals to rapid population decline from harvesting, the evolutionary effects of harvesting on mega-fauna have received limited attention. In elephants, illegal ivory harvesting disproportionately affects older age classes and males because they carry large tusks, but its' effects on tusk size for age or tusk size for stature are less understood. We tested whether severe historical elephant harvests eliminated large tuskers among survivors and whether elephants born thereafter had smaller tusks. Adjusting for the influence of shoulder height – a metric strongly correlated with body size and age and often used as a proxy for age – we compared tusk size for elephants sampled in 1966–1968, prior to severe ivory harvesting in the late 1970s and early 1980s, with tusk size of survivors and elephants born during population recovery in the mid-1990s. In a regional population, tusk length declined by ˜21% in male and by ˜27% in female elephants born during population recovery, while tusk length declined by 22% in males and 37% in females among survivors. Tusk circumference at lip declined by 5% in males but not in females born during population recovery, whereas tusk circumference reduced by 8% in male and by 11% in female survivors. In a single subpopulation, mean tusk length at mean basal tusk circumference declined by 12.4% in males and 21% in females. Tusk size varied between elephant social groups. Tusk homogeneity within social groups and the often high genetic similarity within social groups suggest that tusk size may be heritable. Our findings support a hypothesis of selection of large tuskers by poachers as a driver of the decline in tusk size for age proxy and contemporary tusk evolution in African elephants

Cooperative breeding alters physiological and behavioral responses to habitat fragmentation

Animals respond to habitat alteration with changes in their behavior and physiology. These changes determine individual performance and thus precede changes in population size. They are therefore hypothesized to provide important insights into how animals cope with environmental change. Here, we investigated physiological and behavioral responses of a cooperatively breeding bird, the placid greenbul (Phyllastrephus placidus), in a severely fragmented tropical biodiversity hotspot and combined these data with remotely sensed (LiDAR) environmental data. We found that individuals had increased glucocorticoid hormone levels when breeding in territories with low native canopy cover or located within small fragments. However, when breeding with the help of subordinates, breeders in low quality territories had similar glucocorticoid levels as those in higher quality territories. Our study shows that sociality may impact how well animals cope with environmental change and contributes to our understanding of the role of glucocorticoid physiology and behavior in response to anthropogenic change.Peer reviewe

Streptococcus agalactiae cadD alleviates metal stress and promotes intracellular survival in macrophages and ascending infection during pregnancy

Perinatal infection with Streptococcus agalactiae, or Group B Streptococcus (GBS), is associated with preterm birth, neonatal sepsis, and stillbirth. Here, we study the interactions of GBS with macrophages, essential sentinel immune cells that defend the gravid reproductive tract. Transcriptional analyses of GBS-macrophage co-cultures reveal enhanced expression of a gene encoding a putative metal resistance determinant, cadD. Deletion of cadD reduces GBS survival in macrophages, metal efflux, and resistance to metal toxicity. In a mouse model of ascending infection during pregnancy, the ΔcadD strain displays attenuated bacterial burden, inflammation, and cytokine production in gestational tissues. Furthermore, depletion of host macrophages alters cytokine expression and decreases GBS invasion in a cadD-dependent fashion. Our results indicate that GBS cadD plays an important role in metal detoxification, which promotes immune evasion and bacterial proliferation in the pregnant host

The Rural Household Multiple Indicator Survey (RHoMIS) data of 13,310 farm households in 21 countries

The Rural Household Multiple Indicator Survey (RHoMIS) is a standardized farm household survey approach which collects information on 753 variables covering household demographics, farm area, crops grown and their production, livestock holdings and their production, agricultural product use and variables underlying standard socio-economic and food security indicators like the Poverty Probability Index, the Household Food Insecurity Access Scale and dietary diversity. These variables are used to quantify more than 40 different aggregate indicators on farm household characteristics, welfare, productivity and economic performance. Between 2015 and the beginning of 2018, the survey instrument has been applied in 21 countries in Central America, sub-Saharan Africa and Asia. The data presented here cover the raw data, the indicator calculation code and the resulting indicator values, and can be used to quantify on- and off-farm pathways to food security, diverse diets and reduced poverty of rural smallholder farm households. (2019-10-31

The Rural Household Multiple Indicator Survey (RHoMIS) data of 13,310 farm households in 21 countries

The Rural Household Multiple Indicator Survey (RHoMIS) is a standardized farm household survey approach which collects information on 753 variables covering household demographics, farm area, crops grown and their production, livestock holdings and their production, agricultural product use and variables underlying standard socio-economic and food security indicators like the Poverty Probability Index, the Household Food Insecurity Access Scale and dietary diversity. These variables are used to quantify more than 40 different aggregate indicators on farm household characteristics, welfare, productivity and economic performance. Between 2015 and the beginning of 2018, the survey instrument has been applied in 21 countries in Central America, sub-Saharan Africa and Asia. The data presented here cover the raw data, the indicator calculation code and the resulting indicator values, and can be used to quantify on- and off-farm pathways to food security, diverse diets and reduced poverty of rural smallholder farm households