Works Published in 2013
Displaying works 41 - 60 of 90 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2013 journal article
An ITAM in a Nonenveloped Virus Regulates Activation of NF- B, Induction of Beta Interferon, and Viral Spread
Journal of Virology, 88(5), 2572–2583.
MeSH headings : Amino Acid Sequence; Animals; Cell Line; Enzyme Activation; Humans; Immunoreceptor Tyrosine-Based Activation Motif; Interferon-beta / metabolism; Intracellular Signaling Peptides and Proteins / metabolism; Mice; Molecular Sequence Data; Myocytes, Cardiac / metabolism; Myocytes, Cardiac / virology; NF-kappa B / metabolism; Phosphorylation; Protein Binding; Protein-Tyrosine Kinases / metabolism; Reoviridae / pathogenicity; Reoviridae / physiology; Sequence Alignment; Syk Kinase; Tyrosine / metabolism; Viral Proteins / chemistry; Viral Proteins / metabolism; Viral Tropism
TL;DR:
It is demonstrated for the first time that μ2 is phosphorylated, contains a functional ITAM, and activates NF-κB, and the results suggest that the cell type-specific effect of the μ2 ITAM on viral spread reflects the celltype-specific effects of NF-β and IFN-β.
(via Semantic Scholar)
jvi.asm.org (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: NC State University Libraries, Crossref
Added: May 17, 2019
2013 journal article
Using in vitro high throughput screening assays to identify potential endocrine-disrupting chemicals.
Environmental Health Perspectives, 121(1), 7–14.
Contributors: D. Rotroff *, D. Dix, K. Houck, T. Knudsen, M. Martin, K. McLaurin, D. Reif* , K. Crofton*
author keywords: androgen; endocrine; estrogen; high throughput; in vitro; ToxCast
MeSH headings : Androgens / analysis; Endocrine Disruptors / analysis; Estrogens / analysis; High-Throughput Screening Assays / methods; United States; United States Environmental Protection Agency
TL;DR:
Overall, results suggest that current ToxCast assays can accurately identify chemicals with potential to interact with the estrogenic and androgenic pathways, and could help prioritize chemicals for EDSP T1S assays.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
ToxPi GUI: an interactive visualization tool for transparent integration of data from diverse sources of evidence.
Bioinformatics, 29(3), 402–403.
Contributors: D. Reif* , M. Sypa*, E. Lock *, F. Wright*, A. Wilson *, T. Cathey*, R. Judson *, I. Rusyn *
MeSH headings : Computer Graphics; Software; Toxicity Tests / methods; User-Computer Interface
TL;DR:
The Toxicological Prioritization Index (ToxPi) was developed to enable integration of multiple sources of evidence on exposure and/or safety, transformed into transparent visual rankings to facilitate decision making.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
Real-time growth kinetics measuring hormone mimicry for ToxCast chemicals in T-47D human ductal carcinoma cells.
Chemical Research in Toxicology, 26(7), 1097–1107.
Contributors: D. Rotroff *, D. Dix*, K. Houck *, R. Kavlock*, T. Knudsen *, M. Martin*, D. Reif* , A. Richard *
MeSH headings : Breast Neoplasms / metabolism; Breast Neoplasms / pathology; Carcinoma, Ductal, Breast / metabolism; Carcinoma, Ductal, Breast / pathology; Cell Line, Tumor; Cell Proliferation / drug effects; Environmental Pollutants / toxicity; Female; High-Throughput Screening Assays; Hormones / metabolism; Humans; Kinetics; Molecular Mimicry; Receptors, Estrogen / metabolism; Time Factors; Toxicity Tests
TL;DR:
This cell-based assay rapidly detects chemical effects on T-47D growth and shows potential, in combination with other HTS assays, to detect environmentally relevant chemicals with potential estrogenic activity.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
Perspectives on validation of high-throughput assays supporting 21st century toxicity testing.
Altex, 30(1), 51–66. http://europepmc.org/abstract/med/23338806
Contributors: R. Judson, R. Kavlock, M. Martin, D. Reif , K. Houck, T. Knudsen, A. Richard, R. Tice
Source: ORCID
Added: May 14, 2019
2013 journal article
In vitro perturbations of targets in cancer hallmark processes predict rodent chemical carcinogenesis.
Toxicological Sciences, 131(1), 40–55.
Contributors: N. Kleinstreuer *, D. Dix*, K. Houck *, R. Kavlock*, T. Knudsen *, M. Martin*, K. Paul*, D. Reif*
author keywords: cancer hallmarks; carcinogenesis; predictive toxicology; in vitro and alternatives; bioinformatics
MeSH headings : Animals; Biomarkers, Tumor / analysis; Biomarkers, Tumor / genetics; Carcinogenicity Tests; Carcinogens / chemistry; Carcinogens / toxicity; Databases, Factual; Endpoint Determination; High-Throughput Screening Assays; In Vitro Techniques; Mice; Neoplasms / chemically induced; Neoplasms / genetics; Predictive Value of Tests; Rats; Species Specificity; Thyroid Neoplasms / chemically induced; Thyroid Neoplasms / genetics
TL;DR:
A model was developed in which genes/pathways function as hypothetical enhancers or promoters of rat thyroid tumors, acting secondary to the key initiating event of thyroid hormone disruption, which represents a chemical carcinogenicity prioritization tool supporting targeted testing and functional validation of cancer pathways.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes.
BMC Systems Biology, 7, 119.
Contributors: C. Williams-DeVane *, D. Reif* , E. Cohen Hubal*, P. Bushel*, E. Hudgens*, J. Gallagher*, S. Edwards*
author keywords: Asthma; Endotypes; Gene Expression; Integrated analysis
MeSH headings : Adolescent; Asthma / blood; Asthma / genetics; Child; Cluster Analysis; Computational Biology / methods; Decision Trees; Demography; Gene Expression Profiling; Genome-Wide Association Study; Humans
TL;DR:
A multi-step decision tree-based method is described for defining endotypes based on gene expression, clinical covariates, and disease indicators using childhood asthma as a case study and it gives the best segregation of asthmatics and non-asthmatics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2013 journal article
Comparing metabolomic and pathologic biomarkers alone and in combination for discriminating Alzheimer’s disease from normal cognitive aging
Acta Neuropathologica Communications, 1(1), 28.
author keywords: Alzheimer's disease; Dementias; Metabolomics; Cerebrospinal fluid biomarkers; Stepwise logistic regression
MeSH headings : Aged; Aging / cerebrospinal fluid; Aging / drug effects; Aging / pathology; Alzheimer Disease / cerebrospinal fluid; Alzheimer Disease / diagnosis; Alzheimer Disease / drug therapy; Alzheimer Disease / pathology; Amyloid beta-Peptides / cerebrospinal fluid; Area Under Curve; Biomarkers / cerebrospinal fluid; Chromatography, Liquid; Cognition; Diagnosis, Differential; Female; Gas Chromatography-Mass Spectrometry; Humans; Logistic Models; Male; Metabolomics / methods; Neuropsychological Tests; tau Proteins / cerebrospinal fluid
TL;DR:
Several CSF small-molecule metabolites that discriminated especially well between clinically diagnosed AD and control groups appear to be suitable for further confirmatory and validation studies, and show the potential to provide predictive performance for AD.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
10. Reduced Inequalities
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2013 article
ToxCast: Predicting Toxicity Potential Through High-Throughput Bioactivity Profiling
Houck, K. A., Richard, A. M., Judson, R. S., Martin, M. T., Reif, D. M., & Shah, I. (2013, February). High-Throughput Screening Methods in Toxicity Testing, Vol. 2, p. 1â31.
Contributors: K. Houck *, A. Richard *, R. Judson *, M. Martin*, D. Reif* & I. Shah *
Source: ORCID
Added: May 14, 2019
2013 journal article
Profiling 976 ToxCast Chemicals across 331 Enzymatic and Receptor Signaling Assays
Chem. Res. Toxicol., 26(6), 878â895.
Contributors: N. Sipes *, M. Martin*, P. Kothiya *, D. Reif* , R. Judson *, A. Richard *, K. Houck *, D. Dix*, R. Kavlock*, T. Knudsen *
MeSH headings : Animals; Enzymes / metabolism; Guinea Pigs; High-Throughput Screening Assays; Humans; Membrane Transport Proteins / metabolism; Organic Chemicals / toxicity; Rats; Receptors, G-Protein-Coupled / antagonists & inhibitors; Receptors, G-Protein-Coupled / metabolism; Signal Transduction / drug effects
TL;DR:
Analyzes 976 chemicals in Phases I and II of the U.S. EPA’s ToxCast project across 331 cell-free enzymatic and ligand-binding high-throughput screening (HTS) assays to find novel findings for previously unreported chemical–target combinations clustered with known chemical– target interactions.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
Meta-analysis of toxicity and teratogenicity of 133 chemicals from zebrafish developmental toxicity studies.
Reproductive Toxicology, 41, 98–108.
Contributors: N. Ducharme*, L. Peterson*, E. Benfenati *, D. Reif* , C. McCollum*, J. Gustafsson *, M. Bondesson *
author keywords: Developmental toxicity; Zebrafish; ToxPi; Teratogen; Meta-analysis
MeSH headings : 1-Octanol / chemistry; Animals; Embryo, Nonmammalian / abnormalities; Embryo, Nonmammalian / drug effects; Teratogens / chemistry; Teratogens / toxicity; Toxicity Tests; Water / chemistry; Zebrafish
TL;DR:
It was found that the physical properties of chemicals did not fully predict lethality or developmental outcomes, and individual outcomes such as pericardial edema and yolk sac edema were more reliable indicators of developmental toxicity.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
High-throughput models for exposure-based chemical prioritization in the ExpoCast project.
Environmental Science and Technology, 47(15), 8479–8488.
Contributors: J. Wambaugh *, R. Setzer*, D. Reif* , S. Gangwal*, J. Mitchell-Blackwood*, J. Arnot *, O. Joliet*, A. Frame*
MeSH headings : Environmental Exposure; Environmental Pollutants / classification; Models, Theoretical
TL;DR:
An analysis was conducted that predicts human exposure potential for chemicals and estimates uncertainty in these predictions by comparison to biomonitoring data, and a framework for high-throughput exposure assessment is proposed.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
Dosimetric anchoring of in vivo and in vitro studies for perfluorooctanoate and perfluorooctanesulfonate.
Toxicological Sciences, 136(2), 308–327.
Contributors: J. Wambaugh *, R. Setzer*, A. Pitruzzello*, J. Liu *, D. Reif* , N. Kleinstreuer *, N. Wang*, N. Sipes *
author keywords: perfluorooctanoate; perfluorooctanoic acid; perfluorooctanesulfonate; perfluorooctanesulfonic acid; compartment model; saturable resorption model; pharmacokinetics; statistical analysis; Bayesian analysis; ToxCast; in vitro-in vivo extrapolation
MeSH headings : Alkanesulfonic Acids / pharmacokinetics; Alkanesulfonic Acids / toxicity; Animals; Caprylates / pharmacokinetics; Caprylates / toxicity; Dose-Response Relationship, Drug; Female; Fluorocarbons / pharmacokinetics; Fluorocarbons / toxicity; In Vitro Techniques; Macaca fascicularis; Male; Mice; Mice, Inbred C57BL; Rats; Rats, Sprague-Dawley
TL;DR:
In vitro assay results for PFOA and PFOS from EPA's ToxCast project were examined and it was found that most in vitro bioactivity occurs at concentrations lower than the predicted concentrations for the in vivo LOELs and higher than the expected concentrations forthe in vivo NOELs, for a variety of nonimmunological effects.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
A Computational Model Predicting Disruption of Blood Vessel Development
PLoS Comput Biol, 9(4), e1002996.
Contributors: N. Kleinstreuer *, D. Dix*, M. Rountree*, N. Baker *, N. Sipes *, D. Reif* , R. Spencer*, T. Knudsen *
Ed(s): S. Peirce
MeSH headings : Algorithms; Animals; Blood Vessels / embryology; Chemokines / metabolism; Chemotaxis; Computer Simulation; Endothelial Cells / cytology; Endothelium, Vascular / pathology; Humans; Inflammation; Models, Theoretical; Neovascularization, Physiologic; Phenotype; Signal Transduction; Software; Vascular Endothelial Growth Factor A / metabolism
TL;DR:
The model was shown to recapitulate stereotypical capillary plexus formation and structural emergence of non-coded cellular behaviors, such as a heterologous bridging phenomenon linking endothelial tip cells together during formation of polygonal endothelial cords, which support the utility of cell agent-based models for simulating a morphogenetic series of events and for the first time demonstrate the applicability of these models for predictive toxicology.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
Characterization of the Z lineage Major histocompatability complex class I genes in zebrafish
Immunogenetics, 66(3), 185–198.
author keywords: Teleost; MHC class I; Evolution; Polymorphism; Haplotype
MeSH headings : Alleles; Amino Acid Sequence; Animals; Chromosome Mapping; DNA, Complementary; Gene Expression; Gene Expression Regulation; Gene Order; Genes, MHC Class I; Genetic Linkage; Genetic Loci; Haplotypes; Molecular Sequence Data; Phylogeny; Polymorphism, Genetic; Sequence Alignment; Transcription, Genetic; Ubiquitination; Zebrafish / classification; Zebrafish / genetics; Zebrafish / immunology
TL;DR:
It is reported that neither of the Z transcripts previously described match the current genome assembly and these transcripts are classified as additional gene loci and a gene nomenclature system for the Z genes consistent with MHC nomenClature in other species and with the zebrafish gene nonymclature guidelines is presented.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Crossref
Added: February 13, 2019
2013 journal article
USE OF RECONSTITUTED WATERS TO EVALUATE EFFECTS OF ELEVATED MAJOR IONS ASSOCIATED WITH MOUNTAINTOP COAL MINING ON FRESHWATER INVERTEBRATES
ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY, 32(12), 2826–2835.
author keywords: Invertebrate toxicology; Mussels; Mayfly; Major ion toxicity
MeSH headings : Amphipoda / drug effects; Animals; Appalachian Region; Bicarbonates / toxicity; Chlorides / toxicity; Cladocera / drug effects; Coal Mining; Insecta / drug effects; Ions; Metals, Alkali / toxicity; Metals, Alkaline Earth / toxicity; Rivers; Sulfates / toxicity; Toxicity Tests, Chronic; Unionidae / drug effects; Water Pollutants, Chemical / toxicity
TL;DR:
Results indicate that, although elevated TDS can be correlated with toxicity, the specific major ion composition of the water is important and the choice of test organism is critical, particularly if a test species is to be used as a surrogate for a range of faunal groups.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2013 journal article
Immunohistochemical characterization of the hepatic progenitor cell compartment in medaka (oryzias latipes) following hepatic injury
Journal of Comparative Pathology, 149(4), 434–445.
MeSH headings : Animals; Animals, Genetically Modified; Cell Differentiation / physiology; Disease Models, Animal; Female; Hepatocytes / cytology; Hepatocytes / ultrastructure; Immunohistochemistry; Liver / injuries; Liver Regeneration / physiology; Male; Microscopy, Electron, Transmission; Oryzias; Stem Cells / cytology; Stem Cells / ultrastructure
TL;DR:
The present study defines the process of OC differentiation in fish liver using histopathology, immunohistochemistry and transmission electron microscopy and confirms the presence of, and support the putative bipotential lineage capabilities of, the fish OC.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: NC State University Libraries, NC State University Libraries
Added: August 6, 2018
2013 journal article
Understanding the Role of Proteolytic Digestion on Discovery and Targeted Proteomic Measurements Using Liquid Chromatography Tandem Mass Spectrometry and Design of Experiments
JOURNAL OF PROTEOME RESEARCH, 12(12), 5820–5829.
author keywords: design of experiments; proteolytic digestion; LC-MS/MS; Populus trichocarpa
MeSH headings : Amino Acid Sequence; Animals; Cattle; Chromatography, Liquid / standards; Factor Analysis, Statistical; Hydrogen-Ion Concentration; Isotope Labeling; Molecular Sequence Annotation; Molecular Sequence Data; Peptide Fragments / chemistry; Peptide Fragments / isolation & purification; Plant Proteins / chemistry; Plant Proteins / isolation & purification; Populus / chemistry; Protein Stability; Proteolysis; Proteomics / methods; Proteomics / standards; Research Design; Swine; Tandem Mass Spectrometry / standards; Trypsin / chemistry; Xylem / chemistry
TL;DR:
The tryptic digest optimization described here has eliminated this previously observed peptide decay as well as provided a greater understanding and standardization for a common but critical sample treatment used across the field of proteomics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2013 journal article
Comprehensive Assessment of Hormones, Phytoestrogens, and Estrogenic Activity in an Anaerobic Swine Waste Lagoon
ENVIRONMENTAL SCIENCE & TECHNOLOGY, 47(23), 13781–13790.
MeSH headings : Anaerobiosis; Animals; Chromatography, Liquid; Estrogens / analysis; Mass Spectrometry; Phytoestrogens / analysis; Sewage / chemistry; Swine; Wastewater / chemistry; Water Pollutants, Chemical / analysis
TL;DR:
Findings emphasize the importance of adsorption and transformation processes in governing the fate of these compounds in lagoon waste, which is ultimately used for broadcast application as a fertilizer.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2013 journal article
A generalized multistage optimization modeling framework for life cycle assessment-based integrated solid waste management
ENVIRONMENTAL MODELLING & SOFTWARE, 50, 51–65.
author keywords: Solid waste; Optimization; Multi-stage; Life cycle assessment; Decision support
TL;DR:
This paper presents the first life cycle-based framework to optimize-over multiple time stages-the collection and treatment of all waste materials from curb to final disposal by minimizing cost or environmental impacts while considering user-defined emissions and waste diversion constraints.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
11. Sustainable Cities and Communities
(Web of Science)
12. Responsible Consumption and Production
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
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