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  • Articles  (23)
  • 2015-2019  (23)
  • 2019  (12)
  • 2016  (11)
  • International Journal of Environmental Research and Public Health  (8)
  • Nucleic Acids Research  (7)
  • 52459
  • 60967
  • 1
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    WormBase 2016: expanding to enable helminth genomic research (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: WormBase ( www.wormbase.org ) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite ( parasite.wormbase.org ) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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    Ensembl Genomes 2016: more genomes, more complexity (2016)
    Oxford University Press
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    Publication Date: 2016-01-07
    Description: Ensembl Genomes ( http://www.ensemblgenomes.org ) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project ( http://www.ensembl.org ). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    IJERPH, Vol. 13, Pages 563: Hand- and Object-Mouthing of Rural Bangladeshi Children 3–18 Months Old (2016)
    MDPI Publishing
    Details
    Publication Date: 2016-06-05
    Description: Children are exposed to environmental contaminants by placing contaminated hands or objects in their mouths. We quantified hand- and object-mouthing frequencies of Bangladeshi children and determined if they differ from those of U.S. children to evaluate the appropriateness of applying U.S. exposure models in other socio-cultural contexts. We conducted a five-hour structured observation of the mouthing behaviors of 148 rural Bangladeshi children aged 3–18 months. We modeled mouthing frequencies using 2-parameter Weibull distributions to compare the modeled medians with those of U.S. children. In Bangladesh the median frequency of hand-mouthing was 37.3 contacts/h for children 3–6 months old, 34.4 contacts/h for children 6–12 months old, and 29.7 contacts/h for children 12–18 months old. The median frequency of object-mouthing was 23.1 contacts/h for children 3–6 months old, 29.6 contacts/h for children 6–12 months old, and 15.2 contacts/h for children 12–18 months old. At all ages both hand- and object-mouthing frequencies were higher than those of U.S. children. Mouthing frequencies were not associated with child location (indoor/outdoor). Using hand- and object-mouthing exposure models from U.S. and other high-income countries might not accurately estimate children’s exposure to environmental contaminants via mouthing in low- and middle-income countries.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Published by MDPI Publishing
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    IJERPH, Vol. 13, Pages 920: DengueME: A Tool for the Modeling and Simulation of Dengue Spatiotemporal Dynamics (2016)
    MDPI Publishing
    Details
    Publication Date: 2016-09-16
    Description: The prevention and control of dengue are great public health challenges for many countries, particularly since 2015, as other arboviruses have been observed to interact significantly with dengue virus. Different approaches and methodologies have been proposed and discussed by the research community. An important tool widely used is modeling and simulation, which help us to understand epidemic dynamics and create scenarios to support planning and decision making processes. With this aim, we proposed and developed DengueME, a collaborative open source platform to simulate dengue disease and its vector’s dynamics. It supports compartmental and individual-based models, implemented over a GIS database, that represent Aedes aegypti population dynamics, human demography, human mobility, urban landscape and dengue transmission mediated by human and mosquito encounters. A user-friendly graphical interface was developed to facilitate model configuration and data input, and a library of models was developed to support teaching-learning activities. DengueME was applied in study cases and evaluated by specialists. Other improvements will be made in future work, to enhance its extensibility and usability.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Published by MDPI Publishing
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  • 5
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    Beegle: from literature mining to disease-gene discovery (2016)
    Oxford University Press
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    Publication Date: 2016-01-30
    Description: Disease-gene identification is a challenging process that has multiple applications within functional genomics and personalized medicine. Typically, this process involves both finding genes known to be associated with the disease (through literature search) and carrying out preliminary experiments or screens (e.g. linkage or association studies, copy number analyses, expression profiling) to determine a set of promising candidates for experimental validation. This requires extensive time and monetary resources. We describe Beegle , an online search and discovery engine that attempts to simplify this process by automating the typical approaches. It starts by mining the literature to quickly extract a set of genes known to be linked with a given query, then it integrates the learning methodology of Endeavour (a gene prioritization tool) to train a genomic model and rank a set of candidate genes to generate novel hypotheses. In a realistic evaluation setup, Beegle has an average recall of 84% in the top 100 returned genes as a search engine, which improves the discovery engine by 12.6% in the top 5% prioritized genes. Beegle is publicly available at http://beegle.esat.kuleuven.be/ .
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Phosphorylation of Ku dictates DNA double-strand break (DSB) repair pathway choice in S phase (2016)
    Oxford University Press
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    Publication Date: 2016-03-01
    Description: Multiple DNA double-strand break (DSB) repair pathways are active in S phase of the cell cycle; however, DSBs are primarily repaired by homologous recombination (HR) in this cell cycle phase. As the non-homologous end-joining (NHEJ) factor, Ku70/80 (Ku), is quickly recruited to DSBs in S phase, we hypothesized that an orchestrated mechanism modulates pathway choice between HR and NHEJ via displacement of the Ku heterodimer from DSBs to allow HR. Here, we provide evidence that phosphorylation at a cluster of sites in the junction of the pillar and bridge regions of Ku70 mediates the dissociation of Ku from DSBs. Mimicking phosphorylation at these sites reduces Ku's affinity for DSB ends, suggesting that phosphorylation of Ku70 induces a conformational change responsible for the dissociation of the Ku heterodimer from DNA ends. Ablating phosphorylation of Ku70 leads to the sustained retention of Ku at DSBs, resulting in a significant decrease in DNA end resection and HR, specifically in S phase. This decrease in HR is specific as these phosphorylation sites are not required for NHEJ. Our results demonstrate that the phosphorylation-mediated dissociation of Ku70/80 from DSBs frees DNA ends, allowing the initiation of HR in S phase and providing a mechanism of DSB repair pathway choice in mammalian cells.
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    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    IJERPH, Vol. 16, Pages 960: Meta-Analysis of Heterogeneity in the Effects of Wildfire Smoke Exposure on Respiratory Health in North America (2019)
    MDPI
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    Publication Date: 2019
    Description: Epidemiological studies consistently show an association between wildfire-related smoke exposure and adverse respiratory health. We conducted a systematic review of evidence in published literature pertaining to heterogeneity of respiratory effects from this exposure in North America. We calculated the within-study ratio of relative risks (RRR) and 95% confidence intervals (CI) to examine heterogeneity of effect by population subgroup, and then summarized the RRRs using meta-analysis. We found evidence of a greater effect of wildfire smoke on respiratory health among females relative to males for asthma (RRR: 1.035, 95% CI: 1.013, 1.057) and chronic obstructive pulmonary disease (RRR: 1.018, 95% CI: 1.003, 1.032). There was evidence of a lower relative risk for all respiratory outcomes among youth compared to adults (RRR: 0.976, 95% CI: 0.963, 0.989). We also found wildfire smoke effects stratified by income, race, education, health behaviors, access to care, housing occupancy, geographic region, and urban/rural status. However, data were insufficient to quantitatively evaluate effect modification by these characteristics. While we found evidence that certain demographic subgroups of the population are more susceptible to respiratory health outcomes from wildfire smoke, it is unclear whether this information can be used to inform policy aimed to reduce health impact of wildfires.
    Print ISSN: 1661-7827
    Electronic ISSN: 1660-4601
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
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  • 8
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    IJERPH, Vol. 16, Pages 433: Association between Occupational Injury and Subsequent Employment Termination among Newly Hired Manufacturing Workers (2019)
    MDPI
    Details
    Publication Date: 2019
    Description: Few longitudinal studies have examined occupational injury as a predictor of employment termination, particularly during the earliest stages of employment when the risk of occupational injury may be greatest. Human resources (HR) records were used to establish a cohort of 3752 hourly employees newly hired by a large manufacturing facility from 2 January 2012, through 25 November 2016. The HR records were linked with records of employee visits to an on-site occupational health center (OHC) for reasons consistent with occupational injury. Cox regression methods were then used to estimate the risk of employment termination following a first-time visit to the OHC, with time to termination as the dependent variable. Analyses were restricted to the time period ending 60 calendar days from the date of hire. Of the 3752 employees, 1172 (31.2%) terminated employment prior to 60 days from date of hire. Of these, 345 terminated voluntarily and 793 were terminated involuntarily. The risk of termination for any reason was greater among those who visited the OHC during the first 60 days of employment than among those who did not visit the OHC during the first 60 days of employment (adjusted hazard ratio = 2.58, 95% CI = 2.12–3.15). The magnitude of effect was similar regardless of the nature of the injury or the body area affected, and the risk of involuntary termination was generally greater than the risk of voluntary termination. The results support activities to manage workplace safety and health hazards in an effort to reduce employee turnover rates.
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
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  • 9
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    IJERPH, Vol. 16, Pages 3603: Illuminating Stakeholder Perspectives at the Intersection of Air Quality Health Risk Communication and Cardiac Rehabilitation (2019)
    MDPI
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    Publication Date: 2019
    Description: There is ample evidence of adverse cardiovascular health outcomes associated with exposure to air pollution and cardiac rehabilitation patients are at increased risk for future adverse health events related to air quality. Risk communication and health messaging about recommended behaviors to reduce exposure to air pollution can be integrated into existing care routines and structures. How this can be achieved most appropriately and effectively is not well understood. A focus group design is used to investigate cardiovascular patient and provider experiences, attitudes and beliefs about the risks of air pollution, related health risk messaging and factors that may influence integrating that topic into patient care and communication. Three discussions were hosted, one with cardiac patients, a second with non-physician cardiac rehabilitation providers and a third with physicians who treat cardiac patients. A within-case thematic inductive analysis of each discussion is used to understand the nature of communication, logistics, guidance and overall substance of the cardiac rehabilitation educational experience. Results suggest that air pollution may be an unrecognized risk factor for cardiac patients and cardiac rehabilitation is a prime setting for communicating air pollution health risk messaging. However, to effectively integrate air quality health risk messaging into cardiac rehabilitation, it is critical to account for the existing knowledge-base and behaviors of both providers and patients.
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
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  • 10
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    IJERPH, Vol. 16, Pages 3712: UK Postal Delivery Workers’ Occupational Sun Safety: Using Behavior Change Theories to Identify Intervention Pathways (2019)
    MDPI
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    Publication Date: 2019
    Description: Postal delivery workers have substantial sun exposure. In the United Kingdom (UK) a high proportion of workers possesses a sun sensitive skin type. This population is at elevated risk for skin cancer, yet uptake of sun safety practices is low. Studies are needed to identify the underlying factors that contribute to the uptake of occupational sun safety practices that may be targeted during behavior change interventions. This study integrated the Theory of Planned Behavior (TPB) and the Transtheoretical Model’s stages of change (SoC) as guiding frameworks to identify underlying beliefs that influence UK postal delivery workers’ uptake of occupational sun safety practices. Thirty-four workers participated in semi-structured interviews that used the SoC to establish current receptiveness to and adoption of two sun safety practices (using sunscreen of at least sun protection factor (SPF) 30 on exposed skin and wearing a wide-brimmed hat when working outdoors in the summer). Beliefs underlying current practices were elicited in accordance with the TPB and stratified by the SoC. For sunscreen use and wearing a wide-brimmed hat, 64% and 3% of participants were in the action or maintenance SoC, respectively. Behavioral and control beliefs differed by SoC, with those in the earlier stages more likely than those in the latter stages to report negative attitudes to, and difficulty enacting, sun safety practices. Normative beliefs concerning the views of colleagues and employers towards sunscreen were relatively consistent across the SoC. This study highlights the need for tailored and targeted behavior change interventions. The SoC-stratified accounts of the influence of TPB components on behavior provide a basis for bespoke interventions that reflect inter-individual and inter-practice differences in their working mechanisms.
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Published by MDPI
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