Gene3D: expanding the utility of domain assignments

Gene3D http://gene3d.biochem.ucl.ac.uk is a database of domain annotations of Ensembl and UniProtKB protein sequences. Domains are predicted using a library of profile HMMs representing 2737 CATH superfamilies. Gene3D has previously featured in the Database issue of NAR and here we report updates to the website and database. The current Gene3D (v14) release has expanded its domain assignments to ∼20 000 cellular genomes and over 43 million unique protein sequences, more than doubling the number of protein sequences since our last publication. Amongst other updates, we have improved our Functional Family annotation method. We have also improved the quality and coverage of our 3D homology modelling pipeline of predicted CATH domains. Additionally, the structural models have been expanded to include an extra model organism (Drosophila melanogaster). We also document a number of additional visualization tools in the Gene3D website

A complete transition to clean household energy can save one–quarter of the healthy life lost to particulate matter pollution exposure in India

Exposure to fine particulate matter (PM _2.5 ) is a leading contributor to the disease burden in India, largely due to widespread household solid fuel use. The transition from solid to clean fuels in households has the potential to substantially improve public health. India has implemented large initiatives to promote clean fuel access, but how these initiatives will reduce PM _2.5 exposure and the associated health benefits have not yet been established. We quantified the impacts of a transition of household energy from solid fuel use to liquefied petroleum gas (LPG) on public health in India from ambient and household PM _2.5 exposure. We estimate that the transition to LPG would reduce ambient PM _2.5 concentrations by 25%. Reduced exposure to total PM _2.5 results in a 29% reduction in the loss of healthy life, preventing 348 000 (95% uncertainty interval, UI: 284 000–373 000) premature mortalities every year. Achieving these benefits requires a complete transition to LPG. If access to LPG is restricted to within 15 km of urban centres, then the health benefits of the clean fuel transition are reduced by 50%. If half of original solid fuel users continue to use solid fuels in addition to LPG, then the health benefits of the clean fuel transition are reduced by 75%. As the exposure–outcome associations are non–linear, it is critical for air pollution studies to consider the disease burden attributed to total PM _2.5 exposure, and not only the portion attributed to either ambient or household PM _2.5 exposure. Our work shows that a transition to clean household energy can substantially improve public health in India, however, these large public health benefits are dependent on the complete transition to clean fuels for all

Impacts of household sources on air pollution at village and regional scales in India

Approximately 3 billion people worldwide cook with solid fuels, such as wood, charcoal, and agricultural residues. These fuels, also used for residential heating, are often combusted in inefficient devices, producing carbonaceous emissions. Between 2.6 and 3.8 million premature deaths occur as a result of exposure to fine particulate matter from the resulting household air pollution (Health Effects Institute, 2018a; World Health Organization, 2018). Household air pollution also contributes to ambient air pollution; the magnitude of this contribution is uncertain. Here, we simulate the distribution of the two major health-damaging outdoor air pollutants (PM2:5 and O3) using state-of-thescience emissions databases and atmospheric chemical transport models to estimate the impact of household combustion on ambient air quality in India. The present study focuses on New Delhi and the SOMAARTH Demographic, Development, and Environmental Surveillance Site (DDESS) in the Palwal District of Haryana, located about 80 km south of New Delhi. The DDESS covers an approximate population of 200 000 within 52 villages. The emissions inventory used in the present study was prepared based on a national inventory in India (Sharma et al., 2015, 2016), an updated residential sector inventory prepared at the University of Illinois, updated cookstove emissions factors from Fleming et al. (2018b), and PM2:5 speciation from cooking fires from Jayarathne et al. (2018). Simulation of regional air quality was carried out using the US Environmental Protection Agency Community Multiscale Air Quality modeling system (CMAQ) in conjunction with the Weather Research and Forecasting modeling system (WRF) to simulate the meteorological inputs for CMAQ, and the global chemical transport model GEOS-Chem to generate concentrations on the boundary of the computational domain. Comparisons between observed and simulated O3 and PM2:5 levels are carried out to assess overall airborne levels and to estimate the contribution of household cooking emissions

Microwave-assisted pyrolysis with chemical activation, an innovative method to convert orange peel into activated carbon with improved properties as dye adsorbent

Microwave-assisted pyrolysis with chemical activation was developed and optimized to transform orange peel into activated carbon (AC) desirable for use as a dye adsorbent. The orange peel was first carbonized via microwave-assisted pyrolysis to produce a biochar, which was then activated and converted into AC via chemical impregnation coupled with microwave-assisted pyrolysis. The process parameters involved was optimized to maximize the yield of AC and its adsorption efficiency on malachite green dye using response surface methodology adopting central composite design. The use of microwave-assisted pyrolysis provided a fast heating rate and short process time in converting orange peel into AC, recording a heating rate of up to 112 °C/min in a process taking about 25 min, representing a method that is potentially faster and more energy efficient compared to that shown by the method commonly performed using conventional heating source (≥1 h). The results showed that AC with the highest yield (87 wt% of biochar) and optimal adsorption efficiency (28.5 mg of dye/g of AC) can be obtained by performing chemical impregnation at an impregnation ratio of 1:1 coupled with microwave-assisted pyrolysis under microwave irradiation (heating) for 5 min using 550 W of microwave power. The addition of chemical activation with alkali metal hydroxides resulted in the production of AC with improved properties. The AC showed a highly porous structure containing high content of fixed carbon (83 wt%) and high BET surface area (1350 m 2 /g). The adsorption–desorption isotherm showed a combination of Type I and Type II isotherms, which indicates the presence of microporous-mesoporous structure, thus exhibiting a characteristic of improved pores accessibility and high adsorption capacity. Combined with the detection of low ash (3.2 wt%) and moisture content (5 wt%), the AC shows great promise as a high-grade dye adsorbent with high adsorption capacity and potentially increased durability since a low moisture content could increase the rate of adsorption of dye contaminants and a high ash content could promote undesirable catalytic reactions and reduce the adsorption capacity and reactivation efficiency of AC. The recovery of AC with improved properties and the desirable process features (fast heating rate, short process time) suggest the great potential of this method as an alternative for the treatment and recovery of fruit peel

Infrequent Detection of KI, WU and MC Polyomaviruses in Immunosuppressed Individuals with or without Progressive Multifocal Leukoencephalopathy

Conflicting prevalence of newly identified KI(KIPyV), WU(WUPyV) and Merkel Cell Carcinoma(MCPyV) polyomaviruses have been reported in progressive multifocal leukoencephalopathy(PML) patient samples, ranging from 0 to 14.3%. We analyzed the prevalence of these polyomaviruses in cerebrospinal fluid(CSF), peripheral blood mononuclear cells(PBMC), and bone marrow samples from PML patients, immunosuppressed individuals with or without HIV, and multiple sclerosis(MS) patients. Distinct PCR tests for KIPyV, WUPyV and MCPyV DNA performed in two independent laboratories detected low levels of MCPyV DNA only in 1/269 samples. The infrequent detections of these viruses in multiple samples from immunosuppressed individuals including those with PML suggest that their reactivation mechanisms may be different from that of JC polyomavirus (JCPyV) and that they do not play a role in the pathogenesis of PML

The Cassava Genome: Current Progress, Future Directions

The starchy swollen roots of cassava provide an essential food source for nearly a billion people, as well as possibilities for bioenergy, yet improvements to nutritional content and resistance to threatening diseases are currently impeded. A 454-based whole genome shotgun sequence has been assembled, which covers 69% of the predicted genome size and 96% of protein-coding gene space, with genome finishing underway. The predicted 30,666 genes and 3,485 alternate splice forms are supported by 1.4 M expressed sequence tags (ESTs). Maps based on simple sequence repeat (SSR)-, and EST-derived single nucleotide polymorphisms (SNPs) already exist. Thanks to the genome sequence, a high-density linkage map is currently being developed from a cross between two diverse cassava cultivars: one susceptible to cassava brown streak disease; the other resistant. An efficient genotyping-by-sequencing (GBS) approach is being developed to catalog SNPs both within the mapping population and among diverse African farmer-preferred varieties of cassava. These resources will accelerate marker-assisted breeding programs, allowing improvements in disease-resistance and nutrition, and will help us understand the genetic basis for disease resistance

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

<p>Abstract</p> <p>Background</p> <p>Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations. Protein databases compiled from high quality empirical protein identifications that are in turn based on correct gene models increase the correctness, sensitivity, and quantitative accuracy of systems biology genome-scale experiments.</p> <p>Results</p> <p>In this manuscript, we present the <it>Drosophila melanogaster </it>PeptideAtlas, a fly proteomics and genomics resource of unsurpassed depth. Based on peptide mass spectrometry data collected in our laboratory the portal <url>http://www.drosophila-peptideatlas.org</url> allows querying fly protein data observed with respect to gene model confirmation and splice site verification as well as for the identification of proteotypic peptides suited for targeted proteomics studies. Additionally, the database provides consensus mass spectra for observed peptides along with qualitative and quantitative information about the number of observations of a particular peptide and the sample(s) in which it was observed.</p> <p>Conclusion</p> <p>PeptideAtlas is an open access database for the <it>Drosophila </it>community that has several features and applications that support (1) reduction of the complexity inherently associated with performing targeted proteomic studies, (2) designing and accelerating shotgun proteomics experiments, (3) confirming or questioning gene models, and (4) adjusting gene models such that they are in line with observed <it>Drosophila </it>peptides. While the database consists of proteomic data it is not required that the user is a proteomics expert.</p

Chinese and white Canadian satisfaction and compliance with physicians

BACKGROUND: Patient satisfaction has become an important indicator of primary care and healthcare system performance. Ethnic disparities in patient satisfaction and compliance with physician care have been studied in several countries. However, this issue has not received significant attention in Canada. The unique characteristics of the Canadian healthcare system and ethnic population make it worthwhile to examine this issue in this population. Therefore, we conducted a survey among Chinese and Whites in a Canadian city to determine their reported satisfaction, and perceptions of physicians. METHODS: The survey was conducted in English, Mandarin and Cantonese in 2005 among Chinese and White Canadians, 18 years of age or older, who had visited at least one physician in Canada. RESULTS: We analyzed 746 Chinese and 711 Whites in the general practitioner (GP) visit group and 485 Chinese and 637 Whites in the specialist visit group. A lower proportion of Chinese compared to Whites reported that they were very satisfied or satisfied with GP (73.7% vs. 92.8%) and specialist care (75.5% vs. 85.6%) and the differences between the two groups remained after adjustment for demographic variables and chronic conditions (risk adjusted OR: 0.70, 95%CI: 0.42–1.18 for the GP visit group and OR: 0.77, 95%CI: 0.48–1.23 for the specialist visit group). A similar proportion of Chinese and Whites reported that they always followed a physician's advice (59.4% vs. 59.6% for the GP visit group and 67.2% vs. 62.8% for the specialist visit group). Non-English speaking Chinese and recent arrivals in Canada were less likely to be satisfied with GPs than Chinese born in Canada [risk adjusted OR: 0.5, 95%CI: 0.3–0.9, 0.2 and 0.1–0.7, respectively]. CONCLUSION: Chinese Canadians reported lower satisfaction with physicians and perceived physicians slightly more negatively than White Canadians. Particularly, Chinese with limited English and short length of stay in Canada were less satisfied than Canadian born Chinese

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

Mass Spectrometry-Based (GeLC-MS/MS) Comparative Proteomic Analysis of Endoscopically (ePFT) Collected Pancreatic and Gastroduodenal Fluids

Objectives: The secretin-stimulated endoscopic pancreatic function test (ePFT) allows for the safe collection of gastroduodenal and pancreatic fluid from the duodenum. We test the hypothesis that these endoscopically collected fluids have different proteomes. As such, we aim to show that the ePFT method can be used to collect fluid enriched in pancreatic proteins to test for pancreatic function. Methods: Gastroduodenal and pancreatic fluid were collected sequentially from chronic pancreatitis patients undergoing an ePFT. Proteins from each fluid type were extracted using previously published optimized methods and subjected to GeLC-MS/MS analysis for protein identification and bioinformatics analysis. Results: Mass spectrometry analysis identified proteins that were exclusive in either gastroduodenal (46) or pancreatic fluid (234). Subsequent quantitative analysis revealed proteins that were differentially abundant with statistical significance. As expected, proteolytic enzymes and protease inhibitors were among the differentially detected proteins. The proteases pepsinogens and gastrin were enriched in gastroduodenal fluid, while common pancreatic enzymes (e.g., aminopeptidase N, chymotrypsin C, elastase-3A, trypsin, and carboxypeptidase A1, and elastase 2B) were found in greater abundance in pancreatic fluid. Similarly for protease inhibitors, members of the cystatin family were exclusive to gastroduodenal fluid, while serpins A11, B4, and D1 were exclusive to pancreatic fluid. Conclusions: We have shown that ePFT collection coupled with mass spectrometry can be used to identify differentially detected proteins in gastroduodenal and pancreatic fluids. The data obtained using GeLC-MS/MS techniques provide further evidence supporting the feasibility of using ePFT-collected fluid to study specific diseases of the upper gastrointestinal tract, such as chronic pancreatitis