Showing papers by "Research Triangle Park published in 2000"
TL;DR: The expert panel reached a consensus that the optimal version of the Comet assay for identifying agents with genotoxic activity was the alkaline (pH > 13) versions of the assay developed by Singh et al.
Abstract: Atthe International Workshop on Genotoxicity Test Procedures (IWGTP) held in Washington, DC, March 25-26, 1999, an expert panel met to develop guidelines for the use of the single-cell gel (SCG)/Comet assay in genetic toxicology. The expert panel reached a consensus that the optimal version of the Comet assay for identifying agents with genotoxic activity was the alkaline (pH > 13) version of the assay developed by Singh et al. [1988]. The pH > 13 version is capable of detecting DNA single-strand breaks (SSB), alkali-labile sites (ALS), DNA-DNA/DNA-protein cross-linking, and SSB associated with incomplete excision repair sites. Relative to other genotoxicity tests, the advantages of the SCG assay include its demonstrated sensitivity for detecting low levels of DNA damage, the requirement for small numbers of cells per sample, its flexibility, its low costs, its ease of application, and the short time needed to complete a study. The expert panel decided that no single version of the alkaline (pH > 13) Comet assay was clearly superior. However, critical technical steps within the assay were discussed and guidelines developed for preparing slides with agarose gels, lysing cells to liberate DNA, exposing the liberated DNA to alkali to produce single-stranded DNA and to express ALS as SSB, electrophoresing the DNA using pH > 13 alkaline conditions, alkali neutralization, DNA staining, comet visualization, and data collection. Based on the current state of knowledge, the expert panel developed guidelines for conducting in vitro or in vivo Comet assays. The goal of the expert panel was to identify minimal standards for obtaining reproducible and reliable Comet data deemed suitable for regulatory submission. The expert panel used the current Organization for Economic Co-operation and Development (OECD) guidelines for in vitro and in vivo genetic toxicological studies as guides during the development of the corresponding in vitro and in vivo SCG assay guidelines. Guideline topics considered included initial considerations, principles of the test method, description of the test method, procedure, results, data analysis and reporting. Special consideration was given by the expert panel to the potential adverse effect of DNA degradation associated with cytotoxicity on the interpretation of Comet assay results. The expert panel also discussed related SCG methodologies that might be useful in the interpretation of positive Comet data. The related methodologies discussed included: (1) the use of different pH conditions during electrophoreses to discriminate between DNA strand breaks and ALS; (2) the use of repair enzymes or antibodies to detect specific classes of DNA damage; (3) the use of a neutral diffusion assay to identify apoptotic/necrotic cells; and (4) the use of the acellular SCG assay to evaluate the ability of a test substance to interact directly with DNA. The alkaline (pH > 13) Comet assay guidelines developed by the expert panel represent a work in progress. Additional information is needed before the assay can be critically evaluated for its utility in genetic toxicology. The information needed includes comprehensive data on the different sources of variability (e.g., cell to cell, gel to gel, run to run, culture to culture, animal to animal, experiment to experiment) intrinsic to the alkaline (pH > 3) SCG assay, the generation of a large database based on in vitro and in vivo testing using these guidelines, and the results of appropriately designed multilaboratory international validation studies.
4,583 citations
TL;DR: This brief note presents a general proof that the estimator is unbiased for cluster-correlated data regardless of the setting.
Abstract: There is a simple robust variance estimator for cluster-correlated data. While this estimator is well known, it is poorly documented, and its wide range of applicability is often not understood. The estimator is widely used in sample survey research, but the results in the sample survey literature are not easily applied because of complications due to unequal probability sampling. This brief note presents a general proof that the estimator is unbiased for cluster-correlated data regardless of the setting. The result is not new, but a simple and general reference is not readily available. The use of the method will benefit from a general explanation of its wide applicability.
2,506 citations
TL;DR: Recommendations for the “cancer‐related check‐up,” in which clinical encounters provide case‐finding and health counseling opportunities, and an update of the most recent data pertaining to participation rates in cancer screening by age, gender, and ethnicity from the Centers for Disease Control and Prevention's Behavioral Risk Factor Surveillance System and National Health Interview Survey.
Abstract: Each year the American Cancer Society publishes a summary of existing recommendations for early cancer detection, including updates, and/or emerging issues that are relevant to screening for cancer. In last year's article, the guidelines regarding screening for the early detection of prostate, colorectal, and endometrial cancers were updated, as was the narrative pertaining to testing for early lung cancer detection. Although none of the ACS's guidelines were updated in 2001, work is proceeding on an update of screening recommendations for breast and cervical cancer and an update of these guidelines will be announced in the January/February 2003 issue of CA. As in previous issues, we review recommendations for the "cancer-related check-up," in which clinical encounters provide case-finding and health counseling opportunities. Finally, we provide an update of the most recent data pertaining to participation rates in cancer screening by age, gender, and ethnicity from the Centers for Disease Control and Prevention's Behavioral Risk Factor Surveillance System (BRFSS) and National Health Interview Survey (NHIS).
1,783 citations
1,775 citations
TL;DR: A potent, nonsteroidal FXR ligand is used to show that FXR induces expression of small heterodimer partner 1 (SHP-1), an atypical member of the nuclear receptor family that lacks a DNA-binding domain that provides a molecular basis for the coordinate suppression of CYP7A1 and other genes involved in bile acid biosynthesis.
1,717 citations
TL;DR: A novel implementation of perfectly matched layer (PML) media is presented for the termination of FDTD lattices based on the stretched coordinate form of the PML, a recursive convolution, and the use of complex frequency, shifted (CFS) PML parameters.
Abstract: A novel implementation of perfectly matched layer (PML) media is presented for the termination of FDTD lattices. The implementation is based on the stretched coordinate form of the PML, a recursive convolution, and the use of complex frequency, shifted (CFS) PML parameters. The method, referred to here as the convolutional PML (CPML), offers a number of advantages over the traditional implementations of the PML. Specifically, the application of the CPML is completely independent of the host medium. Thus, no modifications are necessary when applying it to inhomogeneous, lossy, anisotropic, dispersive, or nonlinear media. Secondly, it is shown that the CFS–PML is highly absorptive of evanescent modes and can provide significant memory savings when computing the wave interaction of elongated structures, sharp corners, or low-frequency excitations. © 2000 John Wiley & Sons, Inc. Microwave Opt Technol Lett 27: 334–339, 2000.
1,176 citations
TL;DR: The peroxisome proliferator-activated receptors (PPARs) are nuclear receptors for fatty acids (FAs) that regulate glucose and lipid homeostasis as mentioned in this paper.
1,110 citations
TL;DR: This work monitored gene-expression changes in Arabidopsis thaliana under 14 different SAR-inducing or SAR-repressing conditions using a DNA microarray and derived groups of genes with common regulation patterns, or regulons.
Abstract: Infected plants undergo transcriptional reprogramming during initiation of both local defence and systemic acquired resistance (SAR). We monitored gene-expression changes in Arabidopsis thaliana under 14 different SAR-inducing or SAR-repressing conditions using a DNA microarray representing approximately 25-30% of all A. thaliana genes. We derived groups of genes with common regulation patterns, or regulons. The regulon containing PR-1, a reliable marker gene for SAR in A. thaliana, contains known PR genes and novel genes likely to function during SAR and disease resistance. We identified a common promoter element in genes of this regulon that binds members of a plant-specific transcription factor family. Our results extend expression profiling to definition of regulatory networks and gene discovery in plants.
1,020 citations
TL;DR: It is hypothesized that the phthalate esters that altered testis function in the pubertal male rat would also alter testisfunction in the fetal male and produce malformations of androgen-dependent tissues and, in summary, DEHP, BBP, and DINP all altered sexual differentiation, whereas DOTP, DEP, or DMP were ineffective at this dose.
1,020 citations
TL;DR: It is demonstrated that several of the compounds that regulate mouse and human CAR, including natural steroids, bind directly to the receptors and suggest that CAR, like PXR, is a steroid receptor that is capable of recognizing structurally diverse compounds.
809 citations
TL;DR: This paper uses change management data from a very large, long-lived software system to explore the extent to which measurements from the change history are successful in predicting the distribution over modules of these incidences of faults.
Abstract: This paper is an attempt to understand the processes by which software ages. We define code to be aged or decayed if its structure makes it unnecessarily difficult to understand or change and we measure the extent of decay by counting the number of faults in code in a period of time. Using change management data from a very large, long-lived software system, we explore the extent to which measurements from the change history are successful in predicting the distribution over modules of these incidences of faults. In general, process measures based on the change history are more useful in predicting fault rates than product metrics of the code: For instance, the number of times code has been changed is a better indication of how many faults it will contain than is its length. We also compare the fault rates of code of various ages, finding that if a module is, on the average, a year older than an otherwise similar module, the older module will have roughly a third fewer faults. Our most successful model measures the fault potential of a module as the sum of contributions from all of the times the module has been changed, with large, recent changes receiving the most weight.
TL;DR: Data indicate that DEHP disrupts male rat sexual differentiation by reducing T to female levels in the fetal male rat during a critical stage of reproductive tract differentiation.
TL;DR: Results indicate that compounds with a selective PPARα activation profile reduce insulin resistance without having adverse effects on body weight and adipose tissue mass in animal models of IR.
TL;DR: Alosetron was well tolerated and clinically effective in alleviating pain and bowel-related symptoms in this population of women with IBS.
TL;DR: In vivo studies indicated that the 3-day uterotrophic assay in prepubertal rats was the best method for detecting estrogenic activity when compared with all other end points, based upon the dose-response data for ethynyl estradiol and 4-tert-octylphenol.
TL;DR: The crystal structures of the PPARγ and RXRα LBDs complexed to the RXR ligand 9- cis -retinoic acid (9cRA), the PParγ agonist rosiglitazone or GI262570, and coactivator peptides are reported to provide a molecular understanding of the ability of RXR to heterodimerize with many nuclear receptors.
TL;DR: It is concluded that ambient air particles are capable of inducing a mild inflammation in the lower respiratory tract, as well as an increased concentration of blood fibrinogen.
Abstract: We tested the hypothesis that exposure of healthy volunteers to concentrated ambient particles (CAPS) is associated with an influx of inflammatory cells into the lower respiratory tract. Thirty-eight volunteers were exposed to either filtered air or particles concentrated from the immediate environment of the Environmental Protection Agency (EPA) Human Studies Facility in Chapel Hill, North Carolina. Particle concentrations in the chamber during the exposures ranged from 23.1 to 311.1 microgram/m(3). While in the exposure chamber, volunteers alternated between moderate exercise (15 min) and rest (15 min) for a total exposure time of 2 h. There were no symptoms noted by volunteers after the exposure. Similarly, there were no decrements in pulmonary function. Eighteen hours after exposure, analysis of cells and fluid obtained by bronchoalveolar lavage showed a mild increase in neutrophils in both the bronchial and alveolar fractions in those individuals exposed to CAPS (8.44 +/- 1.99 and 4.20 +/- 1.69%, respectively, in those with the greatest exposure) relative to filtered air (2.69 +/- 0.55 and 0.75 +/- 0.28%, respectively). Blood obtained 18 h after exposure to CAPS contained significantly more fibrinogen relative to samples obtained before exposure. We conclude that ambient air particles are capable of inducing a mild inflammation in the lower respiratory tract, as well as an increased concentration of blood fibrinogen.
TL;DR: In this paper, a study of thermal conductivities perpendicular to the interfaces in Si/Ge superlattices is presented, where a diffusive transport analysis suggests a low-frequency cutoff in the spectrum of heat-conducting phonons, which is comparable to that estimated from applying the Anderson criterion to the potential localization of phonon waves.
Abstract: A study of thermal conductivities perpendicular to the interfaces in ${\mathrm{Bi}}_{2}{\mathrm{Te}}_{3}{/\mathrm{S}\mathrm{b}}_{2}{\mathrm{Te}}_{3}$ superlattices is presented The lattice thermal conductivities in these short-period superlattices are less than those in homogeneous solid-solution alloys and exhibit a minimum for a period of \ensuremath{\sim}50 \AA{} For periods less than 50 \AA{}, the adjoining layers of the superlattice apparently become coupled and, in effect, make their thermal conductivities approach that of an alloy Using the mean free path from kinetic theory, a diffusive transport analysis suggests a low-frequency cutoff $({\ensuremath{\omega}}_{\mathrm{cutoff}})$ in the spectrum of heat-conducting phonons A physical model based on the coherent backscattering of phonon waves at the superlattice interfaces is outlined for the reduction of lattice thermal conductivity; this suggests conditions of localizationlike behavior for the low-frequency phonons The ${\ensuremath{\omega}}_{\mathrm{cutoff}}$ from the diffusive transport model is comparable to that estimated from applying the Anderson criterion to the potential localization of phonon waves The general behavior of localizationlike effects is not unique to ${\mathrm{Bi}}_{2}{\mathrm{Te}}_{3}{/\mathrm{S}\mathrm{b}}_{2}{\mathrm{Te}}_{3}$ superlattices; it is also apparent in the thermal conductivities of Si/Ge superlattices These superlattice structures offer a scope for studying the phonon localization phenomena while the lattice thermal conductivity reduction could lead to high-performance thermoelectric materials
TL;DR: In this article, the current Eulerian models are found to represent well the primary processes impacting the evolution of trace species in most cases, though some exceptions may exist, such as concentrated power plant plumes, which are treated only approximately.
TL;DR: The role of SA and JA signaling in influencing O3-induced cell death has been confirmed and an antagonistic relationship between JA- and SA-signaling pathways in controlling the magnitude of O2-induced HR-like cell death is demonstrated.
Abstract: Recent studies suggest that cross-talk between salicylic acid (SA)‐, jasmonic acid (JA)‐, and ethylene-dependent signaling pathways regulates plant responses to both abiotic and biotic stress factors. Earlier studies demonstrated that ozone (O 3 ) exposure activates a hypersensitive response (HR)‐like cell death pathway in the Arabidopsis ecotype Cvi-0. We now have confirmed the role of SA and JA signaling in influencing O 3 -induced cell death. Expression of salicylate hydroxylase (NahG) in Cvi-0 reduced O 3 -induced cell death. Methyl jasmonate (Me-JA) pretreatment of Cvi-0 decreased O 3 -induced H 2 O 2 content and SA concentrations and completely abolished O 3 -induced cell death. Cvi-0 synthesized as much JA as did Col-0 in response to O 3 exposure but exhibited much less sensitivity to exogenous Me-JA. Analyses of the responses to O 3 of the JA-signaling mutants jar1 and fad3/7/8 also demonstrated an antagonistic relationship between JA- and SA-signaling pathways in controlling the magnitude of O 3 -induced HR-like cell death.
TL;DR: It is demonstrated that HSC activation is associated with the reductions in PPARγ expression and PPAR-responsive element binding in vivo and is reversed by the treatment withPPARγ ligands in vitro, which implicate diminished PParγ signaling in molecular mechanisms underlying activation of HSC in liver fibrogenesis and the potential therapeutic value of PPARβ ligands for liver fibrosis.
TL;DR: It is demonstrated that multiple factors may come between a prescription of an inhaled corticosteroid and the arrival of that medicine at its target organ, the lung.
TL;DR: For this 10-day prenatal (embryonic and fetal) exposure to DBP, the NOAEL and LOAEL (lowest-observed-adverse-effect level) were 50 and 100 mg/kg/day, respectively, this is currently the lowest NoAEL described for the toxicity of DBP.
TL;DR: Chronicity of depression appears to affect women more seriously than men, as manifested by an earlier age of onset, greater family history of affective disorders, greater symptom reporting, poorer social adjustment and poorer quality of life.
TL;DR: The pedigree disequilibrium test (PDT) is presented, demonstrating validity of the test when the asymptotic distribution is used to assess the significance, and suggesting there may be advantages to using the PDT even if the data consist of independent families without extended family information.
Abstract: Family-based tests of linkage disequilibrium are usually based on nuclear family data including affected individuals and their parents or their unaffected siblings. A problem with these tests is that they are not valid tests of association when data from related nuclear families from larger pedigrees are used. One way to ensure validity when testing for association is to select a single nuclear family from each extended pedigree in the sample. When data are available for larger pedigrees, it would be desirable to have a valid test of linkage disequilibrium that can use all potentially informative data. In this paper we present such a test: the Pedigree Disequilibrium Test (PDT). The PDT can use data from related nuclear families from extended pedigrees and remains valid when there is population substructure. Power simulations demonstrate that, when extended pedigree data are available, gains in power can be obtained by using the PDT rather than existing methods that only use a subset of the data. The PDT can also be more powerful than current methods when the data consist of a sample of independent nuclear families or sibships.
TL;DR: It is shown that AKT activation and activity are markedly increased in androgen-independent, prostate-specific antigen-positive prostate cancer cells (LNAI cells) established from xenograft tumors of the androgens-dependent LNCaP cell line, suggesting increased AKT activity in prostate tumor progression and androgen independence.
TL;DR: It is found that a high density of markers will be necessary in order to have a good chance of including SNPs with detectable levels of allelic association with the disease mutation, and statistical analysis based on haplotypes can provide additional information with respect to tests of significance and fine localization of complex disease genes.
Abstract: There has been great interest in the prospects of using single-nucleotide polymorphisms (SNPs) in the search for complex disease genes, and several initiatives devoted to the identification and mapping of SNPs throughout the human genome are currently underway. However, actual data investigating the use of SNPs for identification of complex disease genes are scarce. To begin to look at issues surrounding the use of SNPs in complex disease studies, we have initiated a collaborative SNP mapping study around APOE, the well-established susceptibility gene for late-onset Alzheimer disease (AD). Sixty SNPs in a 1.5-Mb region surrounding APOE were genotyped in samples of unrelated cases of AD, in controls, and in families with AD. Standard tests were conducted to look for association of SNP alleles with AD, in cases and controls. We also used family-based association analyses, including recently developed methods to look for haplotype association. Evidence of association ( P ≤.05) was identified for 7 of 13 SNPs, including the APOE-4 polymorphism, spanning 40 kb on either side of APOE. As expected, very strong evidence for association with AD was seen for the APOE-4 polymorphism, as well as for two other SNPs that lie APOE. Haplotype analysis using family data increased significance over that seen in single-locus tests for some of the markers, and, for these data, improved localization of the gene. Our results demonstrate that associations can be detected at SNPs near a complex disease gene. We found that a high density of markers will be necessary in order to have a good chance of including SNPs with detectable levels of allelic association with the disease mutation, and statistical analysis based on haplotypes can provide additional information with respect to tests of significance and fine localization of complex disease genes.
TL;DR: It is found that amino- and carboxyl-terminal truncated forms of TTP, as well as a 77 amino acid fragment that contained both zinc fingers, could bind to the TNFα ARE in cell-free cross-linking and gel shift assays and stimulate the apparent deadenylation and/or breakdown of TNF α mRNA in intact cells.
TL;DR: In cell-surface labelling experiments, mature TACE was detected on the cell surface but immunofluorescence data indicate that TACE is predominantly localized to a perinuclear compartment similar to that described for tumour necrosis factor (TNF)alpha, raising the possibility that Tace-mediated ectodomain shedding may occur in an intracellular compartment in addition to the cellsurface.
Abstract: Tumour necrosis factor alpha convertase (TACE) is a metalloprotease/disintegrin involved in the ectodomain shedding of several proteins, a process thought to be important in inflammation, rheumatoid arthritis and murine development. The characterization of the intracellular maturation and subcellular localization of endogenous TACE is decribed in the present study. Similarly to other proteolytically active metalloprotease/disintegrins, two forms of TACE are found in cells; a full-length precursor and a mature form lacking the prodomain. Prodomain removal occurs in a late Golgi compartment, consistent with the proposed role of a furin type proprotein convertase in this process. An additional form of TACE, lacking the pro and cytoplasmic domains, is detected when cell lysates are prepared in the presence of EDTA instead of a hydroxamate-based metalloprotease inhibitor or 1,10-phenanthroline. This form appears to be generated by mature TACE cleaving its own cytoplasmic tail and may explain why little mature TACE has been detected in previous studies. In cell-surface labelling experiments, mature TACE was detected on the cell surface but immunofluorescence data indicate that TACE is predominantly localized to a perinuclear compartment similar to that described for tumour necrosis factor (TNF)alpha. This raises the possibility that TACE-mediated ectodomain shedding may occur in an intracellular compartment in addition to the cell surface.