Works (19)
Updated: July 5th, 2023 16:04
2001 journal article
A linear two-state model with complex dynamics
PHYSICS LETTERS A, 280(4), 204–208.
Source: Web Of Science
Added: August 6, 2018
2001 journal article
Improved inference of mutation rates - II. Generalization of the Luria-Delbruck distribution for realistic cell-cycle time distributions
THEORETICAL POPULATION BIOLOGY, 59(1), 49–59.
MeSH headings : Algorithms; Bias; Cell Cycle / genetics; Confidence Intervals; Data Interpretation, Statistical; Genetics, Population; Models, Genetic; Mutation / genetics; Phenotype; Phylogeny; Population Density; Statistical Distributions; Time Factors
TL;DR:
This paper introduces a two-parameter generalization of the continuum Luria-Delbrück distribution for two of the more commonly used cell-cycle time distributions: gamma and shifted exponential and obtains the generalized distribution by defining a map from the actual parameters to "effective" parameters.
(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
2001 journal article
Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations
BIOPHYSICAL JOURNAL, 81(6), 3116–3136.
MeSH headings : Feedback, Physiological; Gene Expression Regulation; Models, Theoretical; Monte Carlo Method; Promoter Regions, Genetic; Stochastic Processes; Time Factors; Transcription, Genetic
TL;DR:
Stochastic bistability where the deterministic equations predict monostability and vice-versa is found; among them, bifurcations driven solely by changing the rate of operator fluctuations even as the underlying deterministic system remains unchanged are found.
(via Semantic Scholar)
doi.org (publisher)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2001 journal article
Waiting times to appearance and dominance of advantageous mutants: estimation based on the likelihood
Mathematical Biosciences, 170(1), 59–77.
Source: NC State University Libraries
Added: August 6, 2018
2000 journal article
Quantitative evaluation of alternative mechanisms of blood disposition of di(n-butyl) phthalate and mono(n-butyl) phthalate in rats
TOXICOLOGICAL SCIENCES, 53(2), 173–184.
author keywords: phthalates; DBP; MBP; PBPK; model; flow-limited; diffusion-limited; pH trapping; enterohepatic circulation; log-likelihood ratio test
MeSH headings : Administration, Oral; Animals; Dibutyl Phthalate / analysis; Dibutyl Phthalate / pharmacokinetics; Environmental Pollutants / blood; Environmental Pollutants / pharmacokinetics; Injections, Intravenous; Male; Models, Biological; Phthalic Acids / blood; Phthalic Acids / pharmacokinetics; Rats; Rats, Sprague-Dawley; Rats, Wistar
TL;DR:
The application of the pH trapping model is a step toward developing a generic model structure for all phthalate esters, though more work is required before a generic structure can be identified with confidence.
(via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018
2000 journal article
The nucleotide-replacement spectrum under somatic hypermutation exhibits microsequence dependence that is strand-symmetric and distinct from that under germline mutation
JOURNAL OF IMMUNOLOGY, 164(4), 1971–1976.
MeSH headings : Adenine / immunology; Animals; Base Composition; Base Sequence; DNA Mutational Analysis / methods; DNA Mutational Analysis / statistics & numerical data; Gene Rearrangement; Germ-Line Mutation / immunology; Humans; Immunoglobulin Variable Region / genetics; Mice; Nucleotides / genetics; Nucleotides / immunology; Pseudogenes / immunology; Thymine / immunology
TL;DR:
The findings suggest that the mechanism of somatic hypermutation is complex, involving two or more stages: introduction of mis-pairs and their subsequent resolution, each with distinct sequence specificity and strand bias.
(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
1999 journal article
Enhanced evolvability in immunoglobulin V genes under somatic hypermutation
JOURNAL OF MOLECULAR EVOLUTION, 49(1), 23–26.
author keywords: genome evolution; adaptability; somatic hypermutation; affinity maturation
MeSH headings : Arthritis / genetics; Arthritis / immunology; Arthritis, Rheumatoid / genetics; Arthritis, Rheumatoid / immunology; DNA, Complementary / genetics; Evolution, Molecular; Gene Frequency; Genes, Immunoglobulin; Humans; Immunoglobulin Variable Region / genetics; Mutation; Selection, Genetic; Serine / genetics
TL;DR:
Using a χ2 test, it is shown that the number of mutations in the CDRs is significantly higher than the numberof mutations found in the FRs, providing direct evidence for the hypothesis that mutations are preferentially targeted into the CDR.
(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
1999 journal article
Genetic plasticity of V genes under somatic hypermutation: Statistical analyses using a new resampling-based methodology
GENOME RESEARCH, 9(12), 1294–1304.
MeSH headings : Base Sequence; Codon; Computational Biology; Genes, T-Cell Receptor / genetics; Humans; Immunoglobulin Variable Region / genetics; Molecular Sequence Data; Mutation; Phylogeny; Sequence Analysis, DNA
TL;DR:
The findings provide support to the hypothesis that somatic hypermutation appeared very early in the phylogeny of immune systems, that it is, to a large extent, shared between species, and that it makes an essential contribution to the generation of the antibody repertoire.
(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
1999 journal article
Human immunodeficiency virus type 1-specific cytotoxic T lymphocyte activity is inversely correlated with HIV type 1 viral load in HIV type 1-infected long-term survivors
AIDS RESEARCH AND HUMAN RETROVIRUSES, 15(13), 1219–1228.
MeSH headings : CD4 Lymphocyte Count; CD4-Positive T-Lymphocytes / immunology; Cross-Sectional Studies; Cytotoxicity Tests, Immunologic; Gene Products, pol / genetics; Gene Products, pol / metabolism; HIV Infections / immunology; HIV Infections / virology; HIV Long-Term Survivors; HIV-1 / immunology; HIV-1 / physiology; Histocompatibility Antigens Class I / classification; Histocompatibility Antigens Class I / genetics; Histocompatibility Antigens Class I / immunology; Humans; Longitudinal Studies; Male; Receptors, CCR5 / genetics; T-Lymphocytes, Cytotoxic / immunology; Viral Load
TL;DR:
The data suggest that the presence of HIV- 1-specific CTL activity in HIV-1-infected long-term survivors is an important component in the effective control of HIV -1 replication.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018
1999 journal article
Nucleotide pool imbalance and adenosine deaminase deficiency induce alterations of N-region insertions during V(D)J recombination
JOURNAL OF CLINICAL INVESTIGATION, 103(6), 833–841.
MeSH headings : Adenosine Deaminase / deficiency; Adenosine Deaminase Inhibitors; Adenosine Triphosphate / metabolism; Cells, Cultured; DNA Nucleotidylexotransferase / metabolism; Deoxyadenosines / pharmacology; Deoxyguanine Nucleotides / metabolism; Deoxyribonucleotides / metabolism; Gene Rearrangement, B-Lymphocyte; Humans; Immunoglobulin M / genetics; Purine-Pyrimidine Metabolism, Inborn Errors / enzymology; Recombination, Genetic; Sequence Analysis, DNA
TL;DR:
It is concluded that the frequency of V(D)J recombination and the composition of N-insertions are influenced by increases in dATP levels, potentially leading to alterations in antigen receptors and aberrant lymphoid development.
(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
1999 journal article
Quantitative evaluation of alternative mechanisms of blood and testes disposition of di(2-ethylhexyl) phthalate and mono(2-ethylhexyl) phthalate in rats
TOXICOLOGICAL SCIENCES, 49(2), 172–185.
author keywords: phthalates; DEHP; MEHP; PBPK; model; flow-limited; diffusion-limited; pH trapping; enterohepatic circulation; log-likelihood ratio test
MeSH headings : Animals; Diffusion; Enterohepatic Circulation / physiology; Hydrogen-Ion Concentration; Male; Models, Biological; Phthalic Acids / blood; Phthalic Acids / pharmacokinetics; Plasticizers / metabolism; Rats; Rats, Sprague-Dawley; Solubility; Testis / metabolism
TL;DR:
To quantify the testes dose of MEHP with various routes of exposure and dose levels, a physiologically based pharmacokinetic (PBPK) model was developed and the pH-trapping model gave the best predictions with the largest value of the log likelihood function.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
1998 journal article
Density-dependent prenatal androgen exposure as an endogenous mechanism for the generation of cycles in small mammal populations
JOURNAL OF THEORETICAL BIOLOGY, 190(1), 93–106.
TL;DR:
A mathematical model is developed and analysed to investigate the possible role of prenatal androgen exposure in the generation of limit cycles and shows that limit cycles depend on three parameters: the delay between birth and sexual maturation, the slope of the function that relates average prenatal androgens exposure to total population density, and the difference between the maximum birth rates of the low- and high-androgen exposed females.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
5. Gender Equality
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
1998 journal article
Drug concentration heterogeneity facilitates the evolution of drug resistance
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 95(20), 11514–11519.
author keywords: sanctuary sites; HIV
MeSH headings : Anti-HIV Agents / administration & dosage; Anti-HIV Agents / pharmacokinetics; Anti-HIV Agents / pharmacology; Biological Evolution; Drug Resistance, Microbial / genetics; HIV Infections / drug therapy; HIV Infections / metabolism; HIV Infections / virology; HIV-1 / drug effects; HIV-1 / genetics; HIV-1 / physiology; Humans; Mathematics; Models, Biological; Mutation; Virus Replication
TL;DR:
It is argued that a quantitative understanding of the role played by heterogeneity in drug levels and pathogen transport is crucial for attempts to control re-emergent infectious disease.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018
1998 chapter
Plasticity under somatic mutation in antigen receptors
In G. Kelsoe & M. F. Flajnik (Eds.), Somatic diversification of immune responses (Current topics in microbiology and immunology ; 229) (Vol. 229, pp. 149–162). Berlin; New York: Springer.
Ed(s): . G. Kelsoe & M. Flajnik
Source: NC State University Libraries
Added: August 6, 2018
1998 journal article
Predicted and inferred waiting times for key mutations in the germinal centre reaction: Evidence for stochasticity in selection
IMMUNOLOGY AND CELL BIOLOGY, 76(4), 373–381.
author keywords: b-lymphocytes; germinal centre; immunoglobulins; maximum likelihood estimates; statistical models
MeSH headings : Animals; Cell Differentiation; Germinal Center; Humans; Mutation; Stochastic Processes; Time Factors
TL;DR:
It is proposed that the remaining disparity is attributable to some further stochastic process in the GCR: many early key mutations arise but fail to ‘take root’ within the GC, either due to emigration or failure of cognate T cell/B cell interaction.
(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
1998 journal article
The distribution of variation in regulatory gene segments, as present in MHC class II promoters
GENOME RESEARCH, 8(2), 124–134.
MeSH headings : Animals; Binding Sites / genetics; Binding Sites / immunology; Chickens; Genes, MHC Class II; Genetic Variation / genetics; Genetic Variation / immunology; Humans; Mice; Mole Rats; Promoter Regions, Genetic / immunology; Regulatory Sequences, Nucleic Acid / immunology; Selection, Genetic; Sequence Analysis, DNA; Species Specificity; Zebrafish
TL;DR:
A high level of intraspecies variability in MHC class II gene promoters in man and mouse is observed, which in mouse but not in man is localized to a significant extent near the binding sites of transcription factors-sites that are conserved over longer evolutionary distances.
(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
1997 journal article
Codon bias and plasticity in immunoglobulins
MOLECULAR BIOLOGY AND EVOLUTION, 14(6), 637–643.
author keywords: codon bias; immunoglobulin; somatic mutation; hypermutation; immunity
MeSH headings : Amino Acids / genetics; Binding Sites; Codon; Genetic Variation; Humans; Immunoglobulin Variable Region / genetics; Immunoglobulins / physiology; Linear Models; Models, Genetic; Molecular Sequence Data; Mutation; Selection, Genetic; Sequence Alignment
TL;DR:
Two statistical tests strongly suggest that evolution has acted to enhance the plasticity of immunoglobulin genes under somatic hypermutation.
(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
1996 journal article
Interdependence of N nucleotide addition and recombination site choice in V(D)J rearrangement
Journal of Immunology, 157(10), 4451.
Source: NC State University Libraries
Added: August 6, 2018
1995 journal article
Cellular interaction in germinal-centers - roles of cd40 ligand and b7-2 in established germinal-centers
Journal of Immunology, 155(2), 556–567.
Source: NC State University Libraries
Added: August 6, 2018
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