Works Published in 2010
Displaying works 1 - 20 of 35 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2010 journal article
Modeling Liver-Related Adverse Effects of Drugs UsingkNearest Neighbor Quantitative Structure−Activity Relationship Method
Chemical Research in Toxicology, 23(4), 724–732.
MeSH headings : Algorithms; Chemical and Drug Induced Liver Injury / etiology; Databases, Factual; Drug-Related Side Effects and Adverse Reactions; Humans; Models, Biological; Models, Molecular; Quantitative Structure-Activity Relationship
TL;DR:
Validated QSAR models of liver AEDs based on the data from the FDA spontaneous reporting system can be employed as sensitive and specific predictors of Aeds in preclinical screening of drug candidates for potential hepatotoxicity in humans.
(via Semantic Scholar)
europepmc.org (repository)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: January 24, 2021
2010 journal article
Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in Heliconius erato
PLoS Genetics, 6(2), e1000796.
Ed(s): M. Nachman
MeSH headings : Adaptation, Physiological / genetics; Animals; Butterflies / genetics; Chromosomes, Artificial, Bacterial / genetics; Gene Expression Regulation; Genetic Loci / genetics; Genetic Variation; Genetics, Population; Genome / genetics; Genotype; Hybridization, Genetic; Linkage Disequilibrium / genetics; Open Reading Frames / genetics; Peru; Phenotype; Physical Chromosome Mapping; Pigmentation / genetics; Polymorphism, Single Nucleotide / genetics; Sequence Analysis, DNA
TL;DR:
Detailed characterize nucleotide variation, genotype-by-phenotype associations, linkage disequilibrium (LD), and candidate gene expression patterns across two unlinked genomic intervals that control yellow and red wing pattern variation among mimetic forms of Heliconius erato and provides convincing evidence for parallel changes in gene regulation across co-mimetic lineages.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Sources: Crossref, NC State University Libraries
Added: September 5, 2020
2010 journal article
Cheminformatics Analysis of Assertions Mined from Literature That Describe Drug-Induced Liver Injury in Different Species
Chemical Research in Toxicology, 23(1), 171–183.
MeSH headings : Animals; Chemical and Drug Induced Liver Injury; Cluster Analysis; Databases, Factual; Humans; MEDLINE; Mice; Models, Chemical; Molecular Conformation; Quantitative Structure-Activity Relationship
TL;DR:
This is the first study for chemical toxicity prediction that applied QSAR modeling and other cheminformatics techniques to observational data generated by the means of automated text mining with limited manual curation, opening up new opportunities for generating and modeling chemical toxicology data.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2010 journal article
Quantitative Nanostructure−Activity Relationship Modeling
ACS Nano, 4(10), 5703–5712.
author keywords: nanoparticles; QSAR; cheminformatics; nanotoxicity; modeling
MeSH headings : Animals; Cell Line, Tumor; Humans; Metal Nanoparticles / chemistry; Microscopy, Atomic Force / methods; Models, Statistical; Models, Theoretical; Nanotechnology / methods; Oxides / chemistry; Quantitative Structure-Activity Relationship; Rats; Regression Analysis; Surface Properties; U937 Cells
TL;DR:
The results suggest that QNAR models can be employed for: (i) predicting biological activity profiles of novel nanomaterials, and (ii) prioritizing the design and manufacturing of nanom material toward better and safer products.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2010 journal article
Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set
Journal of Chemical Information and Modeling, 50(12), 2094–2111.
MeSH headings : Benchmarking / methods; Classification / methods; Mutagenicity Tests / methods; Mutagenicity Tests / standards; Principal Component Analysis; Quantitative Structure-Activity Relationship
TL;DR:
This work demonstrates that the DMs based on an ensemble (consensus) model provide systematically better performance than other DMs and can be used to halve the cost of experimental measurements by providing a similar prediction accuracy.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2010 journal article
Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research
Journal of Chemical Information and Modeling, 50(7), 1189–1204.
MeSH headings : Animals; Models, Chemical; Molecular Structure; Organometallic Compounds / chemistry; Quantitative Structure-Activity Relationship
TL;DR:
The need for a standardized chemical data curation strategy that should be followed at the onset of any molecular modeling investigation is emphasized and it is demonstrated that in some cases rigorously developed QSAR models could be even used to correct erroneous biological data associated with chemical compounds.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2010 journal article
Interactome analysis of longitudinal pharyngeal infection of cynomolgus macaques by group A Streptococcus
Proceedings of the National Academy of Sciences, 107(10), 4693–4698.
author keywords: epithelial growth factor receptor; host pathogen; microarray; Streptococcus pyogenes; transcriptome
MeSH headings : Animals; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Clathrin-Coated Vesicles / metabolism; Cytokines / metabolism; GTP Phosphohydrolases / genetics; GTP Phosphohydrolases / metabolism; Gene Expression Profiling; Host-Pathogen Interactions; Hyaluronic Acid / metabolism; Macaca fascicularis / genetics; Macaca fascicularis / metabolism; Macaca fascicularis / microbiology; Neutrophils / metabolism; Neutrophils / microbiology; Neutrophils / pathology; Oligonucleotide Array Sequence Analysis; Pharyngitis / genetics; Pharyngitis / microbiology; Pharynx / metabolism; Pharynx / microbiology; Pharynx / pathology; Reverse Transcriptase Polymerase Chain Reaction; Streptococcus pyogenes / genetics; Streptococcus pyogenes / metabolism; Streptococcus pyogenes / physiology
TL;DR:
These results are unique in providing a comprehensive understanding of the host–pathogen interactome during mucosal infection by a bacterial pathogen.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2010 journal article
Use of Pharmaco-Metabonomics for Early Prediction of Acetaminophen-Induced Hepatotoxicity in Humans
Clinical Pharmacology & Therapeutics, 88(1), 45–51.
MeSH headings : Acetaminophen / adverse effects; Acetaminophen / metabolism; Acetaminophen / pharmacology; Adolescent; Adult; Alanine Transaminase / blood; Analgesics, Non-Narcotic / adverse effects; Analgesics, Non-Narcotic / metabolism; Analgesics, Non-Narcotic / pharmacology; Biotransformation; Chemical and Drug Induced Liver Injury / diagnosis; Chemical and Drug Induced Liver Injury / genetics; Chemical and Drug Induced Liver Injury / urine; Cohort Studies; Data Interpretation, Statistical; Female; Humans; Least-Squares Analysis; Liver Function Tests; Magnetic Resonance Spectroscopy; Male; Middle Aged; Multivariate Analysis; Predictive Value of Tests; Young Adult
TL;DR:
It is demonstrated that the pattern of endogenous metabolites in urine could predict susceptibility to acetaminophen‐induced liver injury in rats, and this “early‐intervention pharmaco‐metabonomics” approach should now be tested in clinical trials of other potentially hepatotoxic drugs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2010 journal article
An approximate Bayesian approach for quantitative trait loci estimation
Computational Statistics & Data Analysis, 54(2), 565–574.
TL;DR:
This paper presents a Bayesian linkage model that offers directly interpretable posterior densities or Bayes factors for linkage, and employs the Laplace approximation for integration over nuisance parameters in backcross (BC) and F2 intercross designs.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2010 chapter
Grammatical Evolution Decision Trees for Detecting Gene-Gene Interactions
In Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (pp. 98–109).
Source: Crossref
Added: February 24, 2020
2010 journal article
In vitro screening of environmental chemicals for targeted testing prioritization: The toxcast project
Environmental Health Perspectives, 118(4), 485–492.
Contributors: R. Judson *, K. Houck *, R. Kavlock*, T. Knudsen *, M. Martin*, H. Mortensen *, D. Reif* , D. Rotroff *
author keywords: in vitro screening; liver proliferative lesions; liver tumors; pathways; ToxCast
MeSH headings : Animals; Cell Line; Cells, Cultured; Computer Simulation; Environmental Pollutants / toxicity; Humans; Rats; Toxicity Tests / methods; United States; United States Environmental Protection Agency
TL;DR:
A statistically significant inverse association between the number of pathways perturbed by a chemical at low in vitro concentrations and the lowest in vivo dose at which a chemical causes toxicity is found.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2010 journal article
Xenobiotic-metabolizing enzyme and transporter gene expression in primary cultures of human hepatocytes modulated by ToxCast chemicals.
Journal of Toxicology and Environmental Health - Part B: Critical Reviews, 13(2-4), 329–346.
Contributors: D. Rotroff *, A. Beam, D. Dix*, A. Farmer, K. Freeman, K. Houck *, R. Judson *, E. Lecluyse
MeSH headings : Adult; Animals; Cell Shape / drug effects; Cells, Cultured; Cholesterol / biosynthesis; Environmental Pollutants / chemistry; Environmental Pollutants / metabolism; Environmental Pollutants / toxicity; Gene Expression Regulation / drug effects; Hepatocytes / cytology; Hepatocytes / drug effects; Hepatocytes / enzymology; Hepatocytes / metabolism; Humans; Male; Middle Aged; Models, Biological; Rats; Signal Transduction / drug effects; Xenobiotics / chemistry; Xenobiotics / metabolism; Xenobiotics / toxicity
TL;DR:
Gene expression results identified various ToxCast chemicals that were potent or efficacious inducers of one or more of the 14 genes, and by inference the 5 nuclear receptor signaling pathways, as well as the five major receptor pathways.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2010 journal article
Research needs for community-based risk assessment: findings from a multi-disciplinary workshop
J Expos Sci Environ Epidemiol, 20(2), 186â195.
Contributors: Y. Sanchez*, K. Deener*, E. Hubal*, C. Knowlton*, D. Reif* & D. Segal*
author keywords: population-based studies; epidemiology; exposure modeling; analytical methods; empirical/statistical modeling; PBPK modeling
MeSH headings : Humans; Needs Assessment; Research; Risk Assessment; United States; United States Environmental Protection Agency
TL;DR:
This paper summarizes an Environmental Protection Agency (EPA) sponsored workshop, “Research Needs for Community-Based Risk Assessment,” and presents identified research needs, and explores future research opportunities in this emerging field.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2010 journal article
Incorporating human dosimetry and exposure into high-throughput in vitro toxicity screening.
Toxicological Sciences, 117(2), 348–358.
Contributors: D. Rotroff *, B. Wetmore *, D. Dix*, S. Ferguson, H. Clewell*, K. Houck *, E. LeCluyse, M. Andersen *
author keywords: reverse dosimetry; human exposure; ToxCast; high-throughput screening
MeSH headings : Cells, Cultured; Dose-Response Relationship, Drug; Female; Gas Chromatography-Mass Spectrometry; Hepatocytes / drug effects; Hepatocytes / metabolism; High-Throughput Screening Assays / methods; Humans; Male; Metabolic Clearance Rate; Protein Binding / drug effects; Risk Assessment; Toxicity Tests; Xenobiotics / classification; Xenobiotics / metabolism; Xenobiotics / toxicity
Source: ORCID
Added: May 14, 2019
2010 journal article
Impact of environmental chemicals on key transcription regulators and correlation to toxicity end points within EPA's ToxCast program.
Chemical Research in Toxicology, 23(3), 578–590.
Contributors: M. Martin*, D. Dix*, R. Judson *, R. Kavlock*, D. Reif* , A. Richard *, D. Rotroff *, S. Romanov*
MeSH headings : Animals; Biosensing Techniques / economics; Biosensing Techniques / instrumentation; Biosensing Techniques / methods; Environmental Pollutants / adverse effects; Hep G2 Cells; Rabbits; Rats; Receptors, Cytoplasmic and Nuclear / genetics; Response Elements / drug effects; Transcription Factors / genetics; Transcription, Genetic / drug effects
TL;DR:
A novel cellular biosensor system that enables rapid, high-content assessment of a compound's impact on gene regulatory networks and it is demonstrated that Nrf2 activity, a marker of oxidative stress, is highly correlated to the overall promiscuity of a chemical.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2010 journal article
Endocrine Profiling and Prioritization of Environmental Chemicals Using ToxCast Data
Environ Health Perspect, 118(12), 1714â1720.
Contributors: D. Reif* , M. Martin*, S. Tan*, K. Houck *, R. Judson *, A. Richard *, T. Knudsen *, D. Dix*, R. Kavlock*
author keywords: androgen; chemical prioritization; data integration; endocrine disruption; estrogen; screening; ToxCast; toxicity profile; ToxPi
MeSH headings : Decision Support Techniques; Endocrine Disruptors / classification; Endocrine Disruptors / toxicity; Endocrine System / drug effects; Environmental Pollutants / classification; Environmental Pollutants / toxicity; Signal Transduction / drug effects; Toxicity Tests / methods
TL;DR:
A flexible method to facilitate the rational prioritization of chemicals for further evaluation is developed and its application as a candidate decision-support tool for EDSP is demonstrated.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2010 journal article
Analysis of eight oil spill dispersants using rapid, in vitro tests for endocrine and other biological activity.
Environmental Science and Technology, 44(15), 5979–5985.
Contributors: R. Judson *, M. Martin*, D. Reif* , K. Houck *, T. Knudsen *, D. Rotroff *, M. Xia *, S. Sakamuru *
MeSH headings : Chemical Hazard Release; Endocrine Disruptors / analysis; Environmental Restoration and Remediation; Lipids / toxicity; Receptors, Estrogen / metabolism; Surface-Active Agents / toxicity; Water Pollutants, Chemical / toxicity
TL;DR:
A series of in vitro high-throughput assays on eight commercial dispersants focused on the estrogen and androgen receptors (ER and AR), but also included a larger battery of assays probing other biological pathways.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2010 review
Auriculotherapy for Pain Management: A Systematic Review and Meta-Analysis of Randomized Controlled Trials
[Review of ]. JOURNAL OF ALTERNATIVE AND COMPLEMENTARY MEDICINE, 16(10), 1097–1108.
MeSH headings : Acupuncture, Ear; Analgesia; Humans; Pain Management; Pain Measurement; Perioperative Period; Randomized Controlled Trials as Topic
TL;DR:
Auriculotherapy may be effective for the treatment of a variety of types of pain, especially postoperative pain, however, a more accurate estimate of the effect will require further large, well-designed trials.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2010 review
Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology
[Review of ]. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, 74(4), 479–503.
Contributors: T. Torto-Alalibo*, C. Collmer*, M. Gwinn-Giglio*, M. Lindeberg*, S. Meng n, M. Chibucos *, T. Tseng*, J. Lomax *
MeSH headings : Animals; Bacteria / genetics; Bacteria / metabolism; Bacterial Physiological Phenomena; Cell Adhesion; Computational Biology / methods; Fungi / genetics; Fungi / metabolism; Fungi / physiology; Host-Pathogen Interactions / genetics; Host-Pathogen Interactions / immunology; Plants / immunology; Plants / microbiology; Protein Transport; Symbiosis / genetics; Symbiosis / immunology; Virulence Factors
TL;DR:
Some unifying themes common to diverse host-microbe associations are reviewed and areas where new terms need to be developed are highlighted, an ongoing process that should involve the whole community.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2010 journal article
Global generic richness and distribution: new maps of the world of ants with examples of their use in the context of Asia
Asian Myrmecology, 3, 21–28.
Source: NC State University Libraries
Added: August 6, 2018
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