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1.
Cell Genom ; 4(7): 100591, 2024 Jul 10.
Article in English | MEDLINE | ID: mdl-38925123

ABSTRACT

Understanding the complex interplay of genetic and environmental factors in disease etiology and the role of gene-environment interactions (GEIs) across human development stages is important. We review the state of GEI research, including challenges in measuring environmental factors and advantages of GEI analysis in understanding disease mechanisms. We discuss the evolution of GEI studies from candidate gene-environment studies to genome-wide interaction studies (GWISs) and the role of multi-omics in mediating GEI effects. We review advancements in GEI analysis methods and the importance of large-scale datasets. We also address the translation of GEI findings into precision environmental health (PEH), showcasing real-world applications in healthcare and disease prevention. Additionally, we highlight societal considerations in GEI research, including environmental justice, the return of results to participants, and data privacy. Overall, we underscore the significance of GEI for disease prediction and prevention and advocate for integrating the exposome into PEH omics studies.


Subject(s)
Environmental Health , Gene-Environment Interaction , Precision Medicine , Humans , Precision Medicine/methods , Genome-Wide Association Study , Environmental Exposure/adverse effects
2.
Exposome ; 4(1): osae003, 2024.
Article in English | MEDLINE | ID: mdl-38425336

ABSTRACT

The correlations among individual exposures in the exposome, which refers to all exposures an individual encounters throughout life, are important for understanding the landscape of how exposures co-occur, and how this impacts health and disease. Exposome-wide association studies (ExWAS), which are analogous to genome-wide association studies (GWAS), are increasingly being used to elucidate links between the exposome and disease. Despite increased interest in the exposome, tools and publications that characterize exposure correlations and their relationships with human disease are limited, and there is a lack of data and results sharing in resources like the GWAS catalog. To address these gaps, we developed the PEGS Explorer web application to explore exposure correlations in data from the diverse North Carolina-based Personalized Environment and Genes Study (PEGS) that were rigorously calculated to account for differing data types and previously published results from ExWAS. Through globe visualizations, PEGS Explorer allows users to explore correlations between exposures found to be associated with complex diseases. The exposome data used for analysis includes not only standard environmental exposures such as point source pollution and ozone levels but also exposures from diet, medication, lifestyle factors, stress, and occupation. The web application addresses the lack of accessible data and results sharing, a major challenge in the field, and enables users to put results in context, generate hypotheses, and, importantly, replicate findings in other cohorts. PEGS Explorer will be updated with additional results as they become available, ensuring it is an up-to-date resource in exposome science.

3.
Exposome ; 4(1): osae002, 2024.
Article in English | MEDLINE | ID: mdl-38450326

ABSTRACT

The exposome collectively refers to all exposures, beginning in utero and continuing throughout life, and comprises not only standard environmental exposures such as point source pollution and ozone levels but also exposures from diet, medication, lifestyle factors, stress, and occupation. The exposome interacts with individual genetic and epigenetic characteristics to affect human health and disease, but large-scale studies that characterize the exposome and its relationships with human disease are limited. To address this gap, we used extensive questionnaire data from the diverse North Carolina-based Personalized Environment and Genes Study (PEGS, n = 9, 429) to evaluate exposure associations in relation to common diseases. We performed an exposome-wide association study (ExWAS) to examine single exposure models and their associations with 11 common complex diseases, namely allergic rhinitis, asthma, bone loss, fibroids, high cholesterol, hypertension, iron-deficient anemia, ovarian cysts, lower GI polyps, migraines, and type 2 diabetes. Across diseases, we found associations with lifestyle factors and socioeconomic status as well as asbestos, various dust types, biohazardous material, and textile-related exposures. We also found disease-specific associations such as fishing with lead weights and migraines. To differentiate between a replicated result and a novel finding, we used an AI-based literature search and database tool that allowed us to examine the current literature. We found both replicated findings, especially for lifestyle factors such as sleep and smoking across diseases, and novel findings, especially for occupational exposures and multiple diseases.

4.
Toxics ; 11(5)2023 04 25.
Article in English | MEDLINE | ID: mdl-37235222

ABSTRACT

The embryonic zebrafish is a useful vertebrate model for assessing the effects of substances on growth and development. However, cross-laboratory developmental toxicity outcomes can vary and reported developmental defects in zebrafish may not be directly comparable between laboratories. To address these limitations for gaining broader adoption of the zebrafish model for toxicological screening, we established the Systematic Evaluation of the Application of Zebrafish in Toxicology (SEAZIT) program to investigate how experimental protocol differences can influence chemical-mediated effects on developmental toxicity (i.e., mortality and the incidence of altered phenotypes). As part of SEAZIT, three laboratories were provided a common and blinded dataset (42 substances) to evaluate substance-mediated effects on developmental toxicity in the embryonic zebrafish model. To facilitate cross-laboratory comparisons, all the raw experimental data were collected, stored in a relational database, and analyzed with a uniform data analysis pipeline. Due to variances in laboratory-specific terminology for altered phenotypes, we utilized ontology terms available from the Ontology Lookup Service (OLS) for Zebrafish Phenotype to enable additional cross-laboratory comparisons. In this manuscript, we utilized data from the first phase of screening (dose range finding, DRF) to highlight the methodology associated with the development of the database and data analysis pipeline, as well as zebrafish phenotype ontology mapping.

5.
Nucleic Acids Res ; 51(W1): W78-W82, 2023 07 05.
Article in English | MEDLINE | ID: mdl-37194699

ABSTRACT

Access to computationally based visualization tools to navigate chemical space has become more important due to the increasing size and diversity of publicly accessible databases, associated compendiums of high-throughput screening (HTS) results, and other descriptor and effects data. However, application of these techniques requires advanced programming skills that are beyond the capabilities of many stakeholders. Here we report the development of the second version of the ChemMaps.com webserver (https://sandbox.ntp.niehs.nih.gov/chemmaps/) focused on environmental chemical space. The chemical space of ChemMaps.com v2.0, released in 2022, now includes approximately one million environmental chemicals from the EPA Distributed Structure-Searchable Toxicity (DSSTox) inventory. ChemMaps.com v2.0 incorporates mapping of HTS assay data from the U.S. federal Tox21 research collaboration program, which includes results from around 2000 assays tested on up to 10 000 chemicals. As a case example, we showcased chemical space navigation for Perfluorooctanoic Acid (PFOA), part of the Per- and polyfluoroalkyl substances (PFAS) chemical family, which are of significant concern for their potential effects on human health and the environment.


Subject(s)
Databases, Chemical , High-Throughput Screening Assays , Software , Environment
6.
Diabetes Care ; 46(5): 929-937, 2023 05 01.
Article in English | MEDLINE | ID: mdl-36383734

ABSTRACT

OBJECTIVE: Environmental exposures may have greater predictive power for type 2 diabetes than polygenic scores (PGS). Studies examining environmental risk factors, however, have included only individuals with European ancestry, limiting the applicability of results. We conducted an exposome-wide association study in the multiancestry Personalized Environment and Genes Study to assess the effects of environmental factors on type 2 diabetes. RESEARCH DESIGN AND METHODS: Using logistic regression for single-exposure analysis, we identified exposures associated with type 2 diabetes, adjusting for age, BMI, household income, and self-reported sex and race. To compare cumulative genetic and environmental effects, we computed an overall clinical score (OCS) as a weighted sum of BMI and prediabetes, hypertension, and high cholesterol status and a polyexposure score (PXS) as a weighted sum of 13 environmental variables. Using UK Biobank data, we developed a multiancestry PGS and calculated it for participants. RESULTS: We found 76 significant associations with type 2 diabetes, including novel associations of asbestos and coal dust exposure. OCS, PXS, and PGS were significantly associated with type 2 diabetes. PXS had moderate power to determine associations, with larger effect size and greater power and reclassification improvement than PGS. For all scores, the results differed by race. CONCLUSIONS: Our findings in a multiancestry cohort elucidate how type 2 diabetes odds can be attributed to clinical, genetic, and environmental factors and emphasize the need for exposome data in disease-risk association studies. Race-based differences in predictive scores highlight the need for genetic and exposome-wide studies in diverse populations.


Subject(s)
Diabetes Mellitus, Type 2 , Hypertension , Humans , Diabetes Mellitus, Type 2/epidemiology , Diabetes Mellitus, Type 2/genetics , Hypertension/complications , Environmental Exposure , Multifactorial Inheritance/genetics , Surveys and Questionnaires , Genome-Wide Association Study , Risk Factors
7.
Environ Int ; 171: 107687, 2023 01.
Article in English | MEDLINE | ID: mdl-36527873

ABSTRACT

BACKGROUND: Concentrated animal feeding operations (CAFOs) are a source of environmental pollution and have been associated with a variety of health outcomes. Immune-mediated diseases (IMD) are characterized by dysregulation of the normal immune response and, while they may be affected by gene and environmental factors, their association with living in proximity to a CAFO is unknown. OBJECTIVES: We explored gene, environment, and gene-environment (GxE) relationships between IMD, CAFOs, and single nucleotide polymorphisms (SNPs) of prototypical xenobiotic response genes AHR, ARNT, and AHRR and prototypical immune response gene PTPN22. METHODS: The exposure analysis cohort consisted of 6,464 participants who completed the Personalized Environment and Genes Study Health and Exposure Survey and a subset of 1,541 participants who were genotyped. We assessed the association between participants' residential proximity to a CAFO in gene, environment, and GxE models. We recombined individual associations in a transethnic model using METAL meta-analysis. RESULTS: In White participants, ARNT SNP rs11204735 was associated with autoimmune diseases and rheumatoid arthritis (RA), and ARNT SNP rs1889740 was associated with RA. In a transethnic genetic analysis, ARNT SNPs rs11204735 and rs1889740 and PTPN22 SNP rs2476601 were associated with autoimmune diseases and RA. In participants living closer than one mile to a CAFO, the log-distance to a CAFO was associated with autoimmune diseases and RA. In a GxE interaction model, White participants with ARNT SNPs rs11204735 and rs1889740 living closer than eight miles to a CAFO had increased odds of RA and autoimmune diseases, respectively. The transethnic model revealed similar GxE interactions. CONCLUSIONS: Our results suggest increased risk of autoimmune diseases and RA in those living in proximity to a CAFO and a potential role of the AHR-ARNT pathway in conferring risk. We also report the first association of ARNT SNPs rs11204735 and rs1889740 with RA. Our findings, if confirmed, could allow for novel genetically-targeted or other preventive approaches for certain IMD.


Subject(s)
Arthritis, Rheumatoid , Autoimmune Diseases , Animals , Swine , Autoimmune Diseases/genetics , Genotype , Polymorphism, Single Nucleotide , Genetic Predisposition to Disease
8.
J Expo Sci Environ Epidemiol ; 33(3): 474-481, 2023 05.
Article in English | MEDLINE | ID: mdl-36460922

ABSTRACT

BACKGROUND: Autoimmune (AI) diseases appear to be a product of genetic predisposition and environmental triggers. Disruption of the skin barrier causes exacerbation of psoriasis/eczema. Oxidative stress is a mechanistic pathway for pathogenesis of the disease and is also a primary mechanism for the detrimental effects of air pollution. METHODS: We evaluated the association between autoimmune skin diseases (psoriasis or eczema) and air pollutant mixtures in 9060 subjects from the Personalized Environment and Genes Study (PEGS) cohort. Pollutant exposure data on six criteria air pollutants are publicly available from the Center for Air, Climate, and Energy Solutions and the Atmospheric Composition Analysis Group. For increased spatial resolution, we included spatially cumulative exposure to volatile organic compounds from sites in the United States Environmental Protection Agency Toxic Release Inventory and the density of major roads within a 5 km radius of a participant's address from the United States Geological Survey. We applied logistic regression with quantile g-computation, adjusting for age, sex, diagnosis with an autoimmune disease in family or self, and smoking history to evaluate the relationship between self-reported diagnosis of an AI skin condition and air pollution mixtures. RESULTS: Only one air pollution variable, sulfate, was significant individually (OR = 1.06, p = 3.99E-2); however, the conditional odds ratio for the combined mixture components of PM2.5 (black carbon, sulfate, sea salt, and soil), CO, SO2, benzene, toluene, and ethylbenzene is 1.10 (p-value = 5.4E-3). SIGNIFICANCE: While the etiology of autoimmune skin disorders is not clear, this study provides evidence that air pollutants are associated with an increased prevalence of these disorders. The results provide further evidence of potential health impacts of air pollution exposures on life-altering diseases. SIGNIFICANCE AND IMPACT STATEMENT: The impact of air pollution on non-pulmonary and cardiovascular diseases is understudied and under-reported. We find that air pollution significantly increased the odds of psoriasis or eczema in our cohort and the magnitude is comparable to the risk associated with smoking exposure. Autoimmune diseases like psoriasis and eczema are likely impacted by air pollution, particularly complex mixtures and our study underscores the importance of quantifying air pollution-associated risks in autoimmune disease.


Subject(s)
Air Pollutants , Air Pollution , Eczema , Psoriasis , Humans , United States/epidemiology , Air Pollutants/adverse effects , Air Pollutants/analysis , Particulate Matter/adverse effects , Particulate Matter/analysis , Environmental Exposure/adverse effects , Environmental Exposure/analysis , Air Pollution/adverse effects , Air Pollution/analysis , Eczema/chemically induced , Eczema/epidemiology , Psoriasis/chemically induced , Psoriasis/epidemiology , Psoriasis/genetics
9.
Environ Res ; 212(Pt D): 113463, 2022 09.
Article in English | MEDLINE | ID: mdl-35605674

ABSTRACT

While multiple factors are associated with cardiovascular disease (CVD), many environmental exposures that may contribute to CVD have not been examined. To understand environmental effects on cardiovascular health, we performed an exposome-wide association study (ExWAS), a hypothesis-free approach, using survey data on endogenous and exogenous exposures at home and work and data from health and medical histories from the North Carolina-based Personalized Environment and Genes Study (PEGS) (n = 5015). We performed ExWAS analyses separately on six cardiovascular outcomes (cardiac arrhythmia, congestive heart failure, coronary artery disease, heart attack, stroke, and a combined atherogenic-related outcome comprising angina, angioplasty, atherosclerosis, coronary artery disease, heart attack, and stroke) using logistic regression and a false discovery rate of 5%. For each CVD outcome, we tested 502 single exposures and built multi-exposure models using the deletion-substitution-addition (DSA) algorithm. To evaluate complex nonlinear relationships, we employed the knockoff boosted tree (KOBT) algorithm. We adjusted all analyses for age, sex, race, BMI, and annual household income. ExWAS analyses revealed novel associations that include blood type A (Rh-) with heart attack (OR[95%CI] = 8.2[2.2:29.7]); paint exposures with stroke (paint related chemicals: 6.1[2.2:16.0], acrylic paint: 8.1[2.6:22.9], primer: 6.7[2.2:18.6]); biohazardous materials exposure with arrhythmia (1.8[1.5:2.3]); and higher paternal education level with reduced risk of multiple CVD outcomes (stroke, heart attack, coronary artery disease, and combined atherogenic outcome). In multi-exposure models, trouble sleeping and smoking remained important risk factors. KOBT identified significant nonlinear effects of sleep disorder, regular intake of grapefruit, and a family history of blood clotting problems for multiple CVD outcomes (combined atherogenic outcome, congestive heart failure, and coronary artery disease). In conclusion, using statistics and machine learning, these findings identify novel potential risk factors for CVD, enable hypothesis generation, provide insights into the complex relationships between risk factors and CVD, and highlight the importance of considering multiple exposures when examining CVD outcomes.


Subject(s)
Cardiovascular Diseases , Coronary Artery Disease , Exposome , Heart Failure , Myocardial Infarction , Stroke , Cardiovascular Diseases/epidemiology , Cardiovascular Diseases/etiology , Humans , Risk Factors , Stroke/epidemiology , Surveys and Questionnaires
10.
Environ Int ; 159: 107025, 2022 01 15.
Article in English | MEDLINE | ID: mdl-34920276

ABSTRACT

INTRODUCTION: There has been limited development and uptake of machine-learning methods to automate data extraction for literature-based assessments. Although advanced extraction approaches have been applied to some clinical research reviews, existing methods are not well suited for addressing toxicology or environmental health questions due to unique data needs to support reviews in these fields. OBJECTIVES: To develop and evaluate a flexible, web-based tool for semi-automated data extraction that: 1) makes data extraction predictions with user verification, 2) integrates token-level annotations, and 3) connects extracted entities to support hierarchical data extraction. METHODS: Dextr was developed with Agile software methodology using a two-team approach. The development team outlined proposed features and coded the software. The advisory team guided developers and evaluated Dextr's performance on precision, recall, and extraction time by comparing a manual extraction workflow to a semi-automated extraction workflow using a dataset of 51 environmental health animal studies. RESULTS: The semi-automated workflow did not appear to affect precision rate (96.0% vs. 95.4% manual, p = 0.38), resulted in a small reduction in recall rate (91.8% vs. 97.0% manual, p < 0.01), and substantially reduced the median extraction time (436 s vs. 933 s per study manual, p < 0.01) compared to a manual workflow. DISCUSSION: Dextr provides similar performance to manual extraction in terms of recall and precision and greatly reduces data extraction time. Unlike other tools, Dextr provides the ability to extract complex concepts (e.g., multiple experiments with various exposures and doses within a single study), properly connect the extracted elements within a study, and effectively limit the work required by researchers to generate machine-readable, annotated exports. The Dextr tool addresses data-extraction challenges associated with environmental health sciences literature with a simple user interface, incorporates the key capabilities of user verification and entity connecting, provides a platform for further automation developments, and has the potential to improve data extraction for literature reviews in this and other fields.


Subject(s)
Machine Learning , Public Health , Animals , Review Literature as Topic , Software
11.
Article in English | MEDLINE | ID: mdl-34501574

ABSTRACT

Harmonized language is critical for helping researchers to find data, collecting scientific data to facilitate comparison, and performing pooled and meta-analyses. Using standard terms to link data to knowledge systems facilitates knowledge-driven analysis, allows for the use of biomedical knowledge bases for scientific interpretation and hypothesis generation, and increasingly supports artificial intelligence (AI) and machine learning. Due to the breadth of environmental health sciences (EHS) research and the continuous evolution in scientific methods, the gaps in standard terminologies, vocabularies, ontologies, and related tools hamper the capabilities to address large-scale, complex EHS research questions that require the integration of disparate data and knowledge sources. The results of prior workshops to advance a harmonized environmental health language demonstrate that future efforts should be sustained and grounded in scientific need. We describe a community initiative whose mission was to advance integrative environmental health sciences research via the development and adoption of a harmonized language. The products, outcomes, and recommendations developed and endorsed by this community are expected to enhance data collection and management efforts for NIEHS and the EHS community, making data more findable and interoperable. This initiative will provide a community of practice space to exchange information and expertise, be a coordination hub for identifying and prioritizing activities, and a collaboration platform for the development and adoption of semantic solutions. We encourage anyone interested in advancing this mission to engage in this community.


Subject(s)
Artificial Intelligence , Language , Environmental Health , Knowledge Bases , National Institute of Environmental Health Sciences (U.S.) , United States
12.
Article in English | MEDLINE | ID: mdl-32708093

ABSTRACT

Environmental exposures have profound effects on health and disease. While public repositories exist for a variety of exposures data, these are generally difficult to access, navigate, and interpret. We describe the research, development, and application of three open application programming interfaces (APIs) that support access to usable, nationwide, exposures data from three public repositories: airborne pollutant estimates from the US Environmental Protection Agency; roadway data from the US Department of Transportation; and socio-environmental exposures from the US Census Bureau's American Community Survey. Three open APIs were successfully developed, deployed, and tested using random latitude/longitude values and time periods as input parameters. After confirming the accuracy of the data, we used the APIs to extract exposures data on 2550 participants from a cohort within the Environmental Polymorphisms Registry (EPR) at the National Institute of Environmental Health Sciences, and we successfully linked the exposure estimates with participant-level data derived from the EPR. We then conducted an exploratory, proof-of-concept analysis of the integrated data for a subset of participants with self-reported asthma and largely replicated our prior findings on the impact of select exposures and demographic factors on asthma exacerbations. Together, the three open exposures APIs provide a valuable resource, with application across environmental and public health fields.


Subject(s)
Air Pollutants/adverse effects , Environmental Exposure/adverse effects , Environmental Pollutants , Social Environment , Access to Information , Air Pollutants/analysis , Environmental Exposure/analysis , Female , Humans , Male , Socioeconomic Factors , United States , United States Environmental Protection Agency
13.
EGEMS (Wash DC) ; 4(1): 1198, 2016.
Article in English | MEDLINE | ID: mdl-27195307

ABSTRACT

INTRODUCTION: In genomics and other fields, it is now possible to capture and store large amounts of data in electronic medical records (EMRs). However, it is not clear if the routine accumulation of massive amounts of (largely uninterpretable) data will yield any health benefits to patients. Nevertheless, the use of large-scale medical data is likely to grow. To meet emerging challenges and facilitate optimal use of genomic data, our institution initiated a comprehensive planning process that addresses the needs of all stakeholders (e.g., patients, families, healthcare providers, researchers, technical staff, administrators). Our experience with this process and a key genomics research project contributed to the proposed framework. FRAMEWORK: We propose a two-pronged Genomic Clinical Decision Support System (CDSS) that encompasses the concept of the "Clinical Mendeliome" as a patient-centric list of genomic variants that are clinically actionable and introduces the concept of the "Archival Value Criterion" as a decision-making formalism that approximates the cost-effectiveness of capturing, storing, and curating genome-scale sequencing data. We describe a prototype Genomic CDSS that we developed as a first step toward implementation of the framework. CONCLUSION: The proposed framework and prototype solution are designed to address the perspectives of stakeholders, stimulate effective clinical use of genomic data, drive genomic research, and meet current and future needs. The framework also can be broadly applied to additional fields, including other '-omics' fields. We advocate for the creation of a Task Force on the Clinical Mendeliome, charged with defining Clinical Mendeliomes and drafting clinical guidelines for their use.

14.
Clin Transl Sci ; 6(3): 222-5, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23751029

ABSTRACT

Clinical data have tremendous value for translational research, but only if security and privacy concerns can be addressed satisfactorily. A collaboration of clinical and informatics teams, including RENCI, NC TraCS, UNC's School of Information and Library Science, Information Technology Service's Research Computing and other partners at the University of North Carolina at Chapel Hill have developed a system called the Secure Medical Research Workspace (SMRW) that enables researchers to use clinical data securely for research. SMRW significantly minimizes the risk presented when using identified clinical data, thereby protecting patients, researchers, and institutions associated with the data. The SMRW is built on a novel combination of virtualization and data leakage protection and can be combined with other protection methodologies and scaled to production levels.


Subject(s)
Biomedical Research , Computer Security , Databases as Topic , Medical Informatics , Confidentiality , Humans
15.
Genet Med ; 15(1): 36-44, 2013 Jan.
Article in English | MEDLINE | ID: mdl-22995991

ABSTRACT

PURPOSE: Next-generation sequencing has transformed genetic research and is poised to revolutionize clinical diagnosis. However, the vast amount of data and inevitable discovery of incidental findings require novel analytic approaches. We therefore implemented for the first time a strategy that utilizes an a priori structured framework and a conservative threshold for selecting clinically relevant incidental findings. METHODS: We categorized 2,016 genes linked with Mendelian diseases into "bins" based on clinical utility and validity, and used a computational algorithm to analyze 80 whole-genome sequences in order to explore the use of such an approach in a simulated real-world setting. RESULTS: The algorithm effectively reduced the number of variants requiring human review and identified incidental variants with likely clinical relevance. Incorporation of the Human Gene Mutation Database improved the yield for missense mutations but also revealed that a substantial proportion of purported disease-causing mutations were misleading. CONCLUSION: This approach is adaptable to any clinically relevant bin structure, scalable to the demands of a clinical laboratory workflow, and flexible with respect to advances in genomics. We anticipate that application of this strategy will facilitate pretest informed consent, laboratory analysis, and posttest return of results in a clinical context.


Subject(s)
Genome-Wide Association Study/methods , Genomics/methods , Algorithms , Alleles , Databases, Genetic , Gene Frequency , Humans , Mutation
16.
Front Psychiatry ; 2: 47, 2011.
Article in English | MEDLINE | ID: mdl-21811476

ABSTRACT

The success of research in the field of maternal-infant health, or in any scientific field, relies on the adoption of best practices for data and knowledge management. Prior work by our group and others has identified evidence-based solutions to many of the data management challenges that exist, including cost-effective practices for ensuring high-quality data entry and proper construction and maintenance of data standards and ontologies. Quality assurance practices for data entry and processing are necessary to ensure that data are not denigrated during processing, but the use of these practices has not been widely adopted in the fields of psychology and biology. Furthermore, collaborative research is becoming more common. Collaborative research often involves multiple laboratories, different scientific disciplines, numerous data sources, large data sets, and data sets from public and commercial sources. These factors present new challenges for data and knowledge management. Data security and privacy concerns are increased as data may be accessed by investigators affiliated with different institutions. Collaborative groups must address the challenges associated with federating data access between the data-collecting sites and a centralized data management site. The merging of ontologies between different data sets can become formidable, especially in fields with evolving ontologies. The increased use of automated data acquisition can yield more data, but it can also increase the risk of introducing error or systematic biases into data. In addition, the integration of data collected from different assay types often requires the development of new tools to analyze the data. All of these challenges act to increase the costs and time spent on data management for a given project, and they increase the likelihood of decreasing the quality of the data. In this paper, we review these issues and discuss theoretical and practical approaches for addressing these issues.

17.
Cell Biochem Biophys ; 53(2): 101-14, 2009.
Article in English | MEDLINE | ID: mdl-19156361

ABSTRACT

To obtain a systems-level perspective on the topological and functional relationships among proteins contributing to nucleotide excision repair (NER) in Saccharomyces cerevisiae, we built two models to analyze protein-protein physical interactions. A recursive computational model based on set theory systematically computed overlaps among protein interaction neighborhoods. A statistical model scored computation results to detect significant overlaps which exposed protein modules and hubs concurrently. We used these protein entities to guide the construction of a multi-resolution landscape which showed relationships among NER, transcription, DNA replication, chromatin remodeling, and cell cycle regulation. Literature curation was used to support the biological significance of identified modules and hubs. The NER landscape revealed a hierarchical topology and a recurrent pattern of kernel modules coupling a variety of proteins in structures that provide diverse functions. Our analysis offers a computational framework that can be applied to construct landscapes for other biological processes.


Subject(s)
Computational Biology , DNA Repair , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Adenosine Triphosphatases/metabolism , Cell Cycle , Chromatin Assembly and Disassembly , Computer Simulation , DNA Damage , DNA Helicases/metabolism , DNA Repair Enzymes , DNA Replication , Databases, Genetic , Deoxyribonucleases/metabolism , Genome, Fungal , Humans , Models, Biological , Protein Binding , Transcription Factor TFIIH/metabolism , Transcription, Genetic
18.
Brain Behav Immun ; 21(1): 68-78, 2007 Jan.
Article in English | MEDLINE | ID: mdl-16603335

ABSTRACT

The present study used inbred, histocompatible Fischer 344 (FIS) and Lewis (LEW) rats to begin to explore the role of the hypothalamic-pituitary-adrenal (HPA) axis in the immune processes and pain behavior associated with the carrageenan model of acute hindpaw inflammation. Because the HPA axis contributes in part to morphine's analgesic and immunomodulatory properties, the present study also assessed the effects of morphine in carrageenan-inflamed LEW and FIS rats. The results showed that carrageenan-induced hindpaw swelling and pain behavior were greater in FIS than in LEW rats. The enhanced hindpaw swelling in FIS rats correlated with an increase in myeloperoxidase (MPO; a measure of neutrophils) in the inflamed hindpaw. FIS rats showed lower circulating levels of TNFalpha, higher IL-6 levels, and similar IL-1beta and nitric oxide levels, when compared to LEW rats. Morphine produced a significant decrease in carrageenan-induced hindpaw swelling and MPO in both strains, but morphine did not significantly alter circulating cytokine/mediator levels. Morphine's analgesic effects were greater in the inflamed than the noninflamed hindpaw, and they did not correlate with morphine's anti-inflammatory effects. In fact, low doses of morphine produced a mechanical allodynia and hyperalgesia in the noninflamed hindpaw of FIS, but not LEW, rats. These results suggest a positive relationship between HPA axis activity and acute inflammation and inflammatory pain. In contrast, little evidence is provided for HPA axis involvement in morphine's anti-inflammatory or analgesic effects.


Subject(s)
Hypothalamo-Hypophyseal System/immunology , Inflammation/immunology , Morphine/pharmacology , Pain/immunology , Pituitary-Adrenal System/immunology , Acute Disease , Analgesics, Opioid/immunology , Analgesics, Opioid/pharmacology , Analysis of Variance , Animals , Carrageenan , Inflammation/chemically induced , Inflammation/complications , Male , Morphine/immunology , Neuroimmunomodulation/drug effects , Neuroimmunomodulation/physiology , Pain/drug therapy , Pain Threshold/drug effects , Pain Threshold/physiology , Rats , Rats, Inbred F344 , Rats, Inbred Lew , Regression Analysis , Statistics, Nonparametric
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