LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics

<p>Abstract</p> <p>Background</p> <p>A key abstraction in representing proteomics knowledge is the notion of unique identifiers for individual entities (e.g. proteins) and the massive graph of relationships among them. These relationships are sometimes simple (e.g. synonyms) but are often more complex (e.g. one-to-many relationships in protein family membership).</p> <p>Results</p> <p>We have built a software system called LinkHub using Semantic Web RDF that manages the graph of identifier relationships and allows exploration with a variety of interfaces. For efficiency, we also provide relational-database access and translation between the relational and RDF versions. LinkHub is practically useful in creating small, local hubs on common topics and then connecting these to major portals in a federated architecture; we have used LinkHub to establish such a relationship between UniProt and the North East Structural Genomics Consortium. LinkHub also facilitates queries and access to information and documents related to identifiers spread across multiple databases, acting as "connecting glue" between different identifier spaces. We demonstrate this with example queries discovering "interologs" of yeast protein interactions in the worm and exploring the relationship between gene essentiality and pseudogene content. We also show how "protein family based" retrieval of documents can be achieved. LinkHub is available at hub.gersteinlab.org and hub.nesg.org with supplement, database models and full-source code.</p> <p>Conclusion</p> <p>LinkHub leverages Semantic Web standards-based integrated data to provide novel information retrieval to identifier-related documents through relational graph queries, simplifies and manages connections to major hubs such as UniProt, and provides useful interactive and query interfaces for exploring the integrated data.</p

Dataset of EEG power integral, spontaneous recurrent seizure and behavioral responses following combination drug therapy in soman-exposed rats.

This article investigated the efficacy of the combination of antiepileptic drug therapy in protecting against soman-induced seizure severity, epileptogenesis and performance deficits. Adult male rats with implanted telemetry transmitters for continuous recording of electroencephalographic (EEG) activity were exposed to soman and treated with atropine sulfate and the oxime HI-6 one minute after soman exposure and with midazolam, ketamine and/or valproic acid 40 min after seizure onset. Rats exposed to soman and treated with medical countermeasures were evaluated for survival, seizure severity, the development of spontaneous recurrent seizure and performance deficits; combination anti-epileptic drug therapy was compared with midazolam monotherapy. Telemetry transmitters were used to record EEG activity, and a customized MATLAB algorithm was used to analyze the telemetry data. Survival data, EEG power integral data, spontaneous recurrent seizure data and behavioral data are illustrated in figures and included as raw data. In addition, edf files of one month telemetry recordings from soman-exposed rats treated with delayed midazolam are provided as supplementary materials. Data presented in this article are related to research articles "Rational Polytherapy in the Treatment of Cholinergic Seizures" [1] and "Early polytherapy for benzodiazepine-refractory status epilepticus [4]

Patterns and predictors of engagement in peer support among homeless veterans with mental health conditions and substance use histories

OBJECTIVES: Patterns and predictors of engagement in peer support services were examined among 50 previously homeless veterans with co-occurring mental health conditions and substance use histories receiving services from the Veterans Health Administration supported housing program. METHOD: Veteran peer specialists were trained to deliver sessions focusing on mental health and substance use recovery to veterans for an intended 1-hr weekly contact over 9 months. Trajectories of peer engagement over the study\u27s duration are summarized. A mixed-effects log-linear model of the rate of peer engagement is tested with three sets of covariates representing characteristics of the veterans. These sets were demographics, mental health and substance use status, and indicators of community participation and support. RESULTS: Data indicate that veterans engaged with peers about once per month rather than the intended once per week. However, frequency of contacts varied greatly. The best predictor of engagement was time, with most contacts occurring within the first 6 months. No other veteran characteristic was a statistically significant predictor of engagement. Older veterans tended to have higher rates of engagement with peer supporters. CONCLUSIONS AND IMPLICATIONS FOR PRACTICE: Planners of peer support services could consider yardsticks of monthly services up to 6 months. Peer support services need a flexible strategy with varying levels of intensity according to need. Peer support services will need to be tailored to better engage younger veterans. Future research should consider other sources of variation in engagement with peer support such as characteristics of the peer supporters and service content and setting

Feed System Innovation for Gasification of Locally Economical Alternative Fuels (FIGLEAF)

The Feed System Innovation for Gasification of Locally Economical Alternative Fuels (FIGLEAF) project was conducted by the Energy & Environmental Research Center and Gasification Engineering Corporation of Houston, Texas (a subsidiary of Global Energy Inc., Cincinnati, Ohio), with 80% cofunding from the U.S. Department of Energy (DOE). The goal of the project was to identify and evaluate low-value fuels that could serve as alternative feedstocks and to develop a feed system to facilitate their use in integrated gasification combined-cycle and gasification coproduction facilities. The long-term goal, to be accomplished in a subsequent project, is to install a feed system for the selected fuel(s) at Global Energy's commercial-scale 262-MW Wabash River Coal Gasification Facility in West Terre Haute, Indiana. The feasibility study undertaken for the project consisted of identifying and evaluating the economic feasibility of potential fuel sources, developing a feed system design capable of providing a fuel at 400 psig to the second stage of the E-Gas (Destec) gasifier to be cogasified with coal, performing bench- and pilot-scale testing to verify concepts and clarify decision-based options, reviewing information on high-pressure feed system designs, and determining the economics of cofeeding alternative feedstocks with the conceptual feed system design. A preliminary assessment of feedstock availability within Indiana and Illinois was conducted. Feedstocks evaluated included those with potential tipping fees to offset processing cost: sewage sludge, municipal solid waste, used railroad ties, urban wood waste (UWW), and used tires/tire-derived fuel. Agricultural residues and dedicated energy crop fuels were not considered since they would have a net positive cost to the plant. Based on the feedstock assessment, sewage sludge was selected as the primary feedstock for consideration at the Wabash River Plant. Because of the limited waste heat available for drying and the ability of the gasifier to operate with alternative feedstocks at up to 80% moisture, a decision was made to investigate a pumping system for delivering the as-received fuel across the pressure boundary into the second stage of the gasifier. A high-pressure feed pump and fuel dispersion nozzles were tested for their ability to cross the pressure boundary and adequately disperse the sludge into the second stage of the gasifier. These results suggest that it is technically feasible to get the sludge dispersed to an appropriate size into the second stage of the gasifier although the recycle syngas pressure needed to disperse the sludge would be higher than originally desired. A preliminary design was prepared for a sludge-receiving, storage, and high-pressure feeding system at the Wabash River Plant. The installed capital costs were estimated at approximately $9.7 million, within an accuracy of {+-}10$12.40 per wet ton of municipal sludge delivered. This is based on operation with petroleum coke as the primary fuel. Similarly, with coal as the primary fuel, a minimum tipping of $16.70 would be required. The availability of delivered sludge from Indianapolis, Indiana, in this tipping-fee range is unlikely; however, given the higher treatment costs associated with sludge treatment in Chicago, Illinois, delivery of sludge from Chicago, given adequate rail access, might be economically viable

Aligning Practice to Policies: Changing the Culture to Recognize and Reward Teaching at Research Universities

Recent calls for improvement in undergraduate education within STEM (science, technology, engineering, and mathematics) disciplines are hampered by the methods used to evaluate teaching effectiveness. Faculty members at research universities are commonly assessed and promoted mainly on the basis of research success. To improve the quality of undergraduate teaching across all disciplines, not only STEM fields, requires creating an environment wherein continuous improvement of teaching is valued, assessed, and rewarded at various stages of a faculty member’s career. This requires consistent application of policies that reflect well-established best practices for evaluating teaching at the department, college, and university levels. Evidence shows most teaching evaluation practices do not reflect stated policies, even when the policies specifically espouse teaching as a value. Thus, alignment of practice to policy is a major barrier to establishing a culture in which teaching is valued. Situated in the context of current national efforts to improve undergraduate STEM education, including the Association of American Universities Undergraduate STEM Education Initiative, this essay discusses four guiding principles for aligning practice with stated priorities in formal policies: 1) enhancing the role of deans and chairs; 2) effectively using the hiring process; 3) improving communication; and 4) improving the understanding of teaching as a scholarly activity. In addition, three specific examples of efforts to improve the practice of evaluating teaching are presented as examples: 1) Three Bucket Model of merit review at the University of California, Irvine; (2) Evaluation of Teaching Rubric, University of Kansas; and (3) Teaching Quality Framework, University of Colorado, Boulder. These examples provide flexible criteria to holistically evaluate and improve the quality of teaching across the diverse institutions comprising modern higher education

Data quality in the human and environmental health sciences: Using statistical confidence scoring to improve QSAR/QSPR modeling

A greater number of toxicity data are becoming publicly available allowing for in silico modeling. However, questions often arise as how to incorporate data quality and how to deal with contradicting data if more than a single datum point is available for the same compound. In this study, two well-known and studied QSAR/QSPR models for skin permeability and aquatic toxicology have been investigated in the context of statistical data quality. In particular, the potential benefits of the incorporation of the statistical Confidence Scoring (CS) approach within modelling and validation. As a result, robust QSAR/QSPR models for the skin permeability coefficient and the toxicity of nonpolar narcotics to Aliivibrio fischeri assay were created. CSweighted linear regression for training and CS-weighted root mean square error (RMSE) for validation were statistically superior compared to standard linear regression and standard RMSE. Strategies are proposed as to how to interpret data with high and low CS, as well as how to deal with large datasets containing multiple entries

Rudimentary G-Quadruplex-Based Telomere Capping In Saccharomyces Cerevisiae

Telomere capping conceals chromosome ends from exonucleases and checkpoints, but the full range of capping mechanisms is not well defined. Telomeres have the potential to form G-quadruplex (G4) DNA, although evidence for telomere G4 DNA function in vivo is limited. In budding yeast, capping requires the Cdc13 protein and is lost at nonpermissive temperatures in cdc13-1 mutants. Here, we use several independent G4 DNA-stabilizing treatments to suppress cdc13-1 capping defects. These include overexpression of three different G4 DNA binding proteins, loss of the G4 DNA unwinding helicase Sgs1, or treatment with small molecule G4 DNA ligands. In vitro, we show that protein-bound G4 DNA at a 3\u27 overhang inhibits 5\u27-\u3e 3\u27 resection of a paired strand by exonuclease I. These findings demonstrate that, at least in the absence of full natural capping, G4 DNA can play a positive role at telomeres in vivo

Increased Extra-axial Cerebrospinal Fluid in High-Risk Infants Who Later Develop Autism

Background We previously reported that infants who developed autism spectrum disorder (ASD) had increased cerebrospinal fluid (CSF) in the subarachnoid space (i.e., extra-axial CSF) from 6 to 24 months of age. We attempted to confirm and extend this finding in a larger independent sample. Methods A longitudinal magnetic resonance imaging study of infants at risk for ASD was carried out on 343 infants, who underwent neuroimaging at 6, 12, and 24 months. Of these infants, 221 were at high risk for ASD because of an older sibling with ASD, and 122 were at low risk with no family history of ASD. A total of 47 infants were diagnosed with ASD at 24 months and were compared with 174 high-risk and 122 low-risk infants without ASD. Results Infants who developed ASD had significantly greater extra-axial CSF volume at 6 months compared with both comparison groups without ASD (18% greater than high-risk infants without ASD; Cohen's d = 0.54). Extra-axial CSF volume remained elevated through 24 months (d = 0.46). Infants with more severe autism symptoms had an even greater volume of extra-axial CSF from 6 to 24 months (24% greater at 6 months, d = 0.70; 15% greater at 24 months, d = 0.70). Extra-axial CSF volume at 6 months predicted which high-risk infants would be diagnosed with ASD at 24 months with an overall accuracy of 69% and corresponding 66% sensitivity and 68% specificity, which was fully cross-validated in a separate sample. Conclusions This study confirms and extends previous findings that increased extra-axial CSF is detectable at 6 months in high-risk infants who develop ASD. Future studies will address whether this anomaly is a contributing factor to the etiology of ASD or an early risk marker for ASD

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin