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J D Thompson

Publications and source records attributed to J D Thompson.

At least 73 records · Page 4Linked to original sources
PubMed1999

A comprehensive comparison of multiple sequence alignment programs.

In recent years improvements to existing programs and the introduction of new iterative algorithms have changed the state-of-the-art in protein sequence alignment. This paper presents the first systematic study of the most commonly used alignment programs using BAliBASE benchmark alignments as test cases. Even below the 'twilight zone' at 10-20% residue identity, the best programs were capable of correctly aligning on average 47% of the residues. We show that iterative algorithms often offer improved alignment accuracy though at the expense of computation time. A notable exception was the effect of introducing a single divergent sequence into a set of closely related sequences, causing the iteration to diverge away from the best alignment. Global alignment programs generally performed better than local methods, except in the presence of large N/C-terminal extensions and internal insertions. In these cases, a local algorithm was more successful in identifying the most conserved motifs. This study enables us to propose appropriate alignment strategies, depending on the nature of a particular set of sequences. The employment of more than one program based on different alignment techniques should significantly improve the quality of automatic protein sequence alignment methods. The results also indicate guidelines for improvement of alignment algorithms.

Algorithms↗
PubMed1999

Cryptic dioecy and leaky dioecy in endemic species of Dombeya (Sterculiaceae) on La Reunion.

The high frequency of dioecy on oceanic islands such as Hawaii and New Zealand has attracted a great deal of attention from plant evolutionary biologists. One reason suggested for the high prevalence of dioecy on oceanic islands is that taxa considered truly dioecious may have occasional hermaphrodite flowers, i.e., show leaky dioecy. In this study, we quantified the presence and distribution of leaky dioecy in a group of congeneric endemic species of the genus Dombeya (Sterculiaceae) on La Réunion island (Indian Ocean). All eight species show cryptic dioecy. Five species show strict dioecy and three species show leaky dioecy due to the presence of male trees that set fruit. Species with strict dioecy and large populations tend to occur in mid- to high-altitude moist tropical cloud forest, whereas species in smaller populations at lower altitude and in semidry tropical forest tend to show leaky dioecy. Two reasons for this differential distribution of strict dioecy and leaky dioecy are discussed. First, environmental variation along the altitudinal gradient, biotic and/or abiotic, may influence the breeding system. Second, leaky dioecy may be favored in lowland populations due to the small size and disturbed nature of such populations.

Journal Article↗
PubMed1998

BRCA1 mutations and breast cancer in the general population: analyses in women before age 35 years and in women before age 45 years with first-degree family history.

CONTEXT: Studies of high-risk families with multiple early-onset cases of breast cancer have been useful for assessing the type and spectrum of germline mutations on the BRCA1 gene, but do not provide guidance to women with modest family history profiles. Thus, studies of women from the general population are needed to determine the BRCA1 mutation frequency in women perceived to be at high risk, and to develop profiles of those most likely to be carriers. OBJECTIVE: To characterize frequency and spectrum of germline BRCA1 mutations in 2 categories of women identified via population-based studies hypothesized to be at increased risk of carrying such mutations: those diagnosed as having breast cancer before age 35 years and those diagnosed before age 45 years who have first-degree breast cancer family history. DESIGN: Study subjects were drawn from 2 population-based case-control studies of breast cancer in young women on the basis of their family history or their age of diagnosis. Cases were younger than 35 years or were younger than 45 years with first-degree family history at the time of breast cancer diagnosis and were ascertained via a population-based cancer registry, and controls (women without breast cancer) were identified via random-digit dialing. SETTING: Three counties in western Washington State. MAIN OUTCOME MEASURE: BRCA1 germline mutations in study subjects identified in DNA from peripheral blood lymphocytes by single-strand conformation polymorphism analysis using primer pairs that span the BRCA1 coding region and intron-exon boundaries. RESULTS: Of 193 women diagnosed as having breast cancer before age 35 years, none of whom were selected on the basis of family history status, 12 (6.2%, 95% confidence interval [CI], 3.2%-10.6%) had germline BRCA1 mutations. In 208 women diagnosed before age 45 years who had first-degree breast cancer family history, 15 (7.2%, 95% CI,4.1%-11.6%) had germline mutations in BRCA1. In both groups, there were variations in mutation frequency noted by age and by family history. Mutation frequency decreased with increasing age of diagnosis. Higher proportions of mutations were seen in cases with at least 1 relative diagnosed as having breast cancer before age 45 years, in cases with greater numbers of affected relatives, and those with ovarian cancer family history. Mutation frequency did not vary by bilateral breast cancer family history. No frameshift or nonsense mutations were observed in 71 control women with a first-degree family history, although missense changes of unknown significance were seen in cases and controls. CONCLUSIONS: Women with BRCA1 germline mutations lacked a common family history profile. Also, a large proportion of the women with a first-degree breast cancer family history and women diagnosed as having breast cancer before age 35 years did not carry germline BRCA1 mutations. Hence, while early-onset disease and a strong breast cancer family history may be useful guidelines for checking BRCA1 status, these findings on women drawn from the general population suggest that it may be difficult to develop BRCA1 mutation screening criteria among women with modest family history profiles.

Adult↗
PubMed1997

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.

Algorithms↗
PubMed1997

Head injury and risk of Alzheimer's disease by apolipoprotein E genotype.

Head injury and apolipoprotein E (APOE)-epsilon 4 (e4) genotype have each been associated with increased risk of Alzheimer's disease. If APOE-e4 affects neuronal viability and branching, and if response to head injury differs in e4 patients, then the association between head injury and Alzheimer's disease may vary with the presence of the e4 allele. The authors examined this association in a case-control study conducted between 1987 and 1995 among enrollees of the Group Health Cooperative of Puget Sound, a health maintenance organization in Seattle, Washington. Proxy informants reported prior head injury with loss of consciousness for 32 of 349 patients with probable Alzheimer's disease and for 16 of 342 control subjects of similar age and sex who had been randomly selected from the same population (odds ratio (OR) = 2.1, 95% confidence interval (CI) 1.1-3.8). Elevated risk was observed among men (OR = 4.2, 95% CI 1.5-11.5) but not among women (OR = 1.1, 95% CI 0.5-2.6). No significant variation in the head injury-Alzheimer's disease risk relation by APOE-e4 genotype was found among 230 cases and 309 controls (OR = 3.1 (95% CI 0.7-14.6) for persons with at least one e4 allele and OR = 2.0 (95% CI 0.8-5.2) for those without e4). Neither age, education, race, type of proxy informant, nor duration of relationship with the proxy confounded the association. Head injury with loss of consciousness, although uncommon in this sample, was associated with increased risk of Alzheimer's disease. APOE-e4 was an independent risk factor which neither modified nor confounded the association. Susceptibility to Alzheimer's disease as conferred by APOE-e4 does not appear to increase the risk associated with head injury.

Aged↗
PubMed1997

Analysis of a monophosphoryl lipid A immunostimulant preparation from Salmonella minnesota R595 by high-performance liquid chromatography.

MPL immunostimulant, a 4'-monophosphoryl lipid A (MLA) preparation obtained from the lipopolysaccharide of Salmonella minnesota R595, is being developed for several clinical indications. MPL comprises a mixture of MLA congeners that contain 4, 5, and 6 fatty acids. In this paper, we report a new high-performance liquid chromatography (HPLC) method for analyzing the congener composition and purity of MPL. MPL is first derivatized with dinitrobenzyloxyamine (DNBA), resulting in incorporation of the dinitrobenzyl chromophore at the reducing end of all MLA congeners. DNBA-MPL is then analyzed by reversed-phase HPLC on a Waters NovaPak C18, 4 microns particle size, 300 mm x 3.9 mm column. Optimal separation of DNBA-MLA species is obtained using a linear gradient of 10% to 80% isopropanol-water (95:5, v/v), 5 mM tetrabutylammonium dihydrogenphosphate (TBAP), in acetonitrile-water (95:5, v/v), 5 mM.TBAP, over 45 min. A synthetic compound, corresponding to a hexaacyl MLA congener, is used for determination of the detector response factor, allowing the MLA content of MPL (i.e., purity) to be determined. Overall, this method provides better separation, higher sensitivity, and is faster and saler than previous methods used for the analysis of MPL.

Adjuvants, Immunologic↗
PubMed1997

Evaluation of a model for improving emergency medical and trauma services for children in rural areas.

STUDY OBJECTIVE: To evaluate the effectiveness of a rural emergency medical and trauma services project in increasing the knowledge and confidence of emergency care personnel in the management of acutely ill and injured children. METHODS: This prospective, quasi-experimental study used an untreated control group design with pretest and posttest of pre-hospital and hospital-based emergency care personnel in two rural counties in central Ohio. Project evaluation compared 50 emergency care providers from the intervention county with 43 emergency care providers from the control county. Changes in knowledge and confidence of these personnel in the assessment and management of pediatric emergencies were compared. RESULTS: Providers in the intervention county demonstrated a significantly greater increase in test scores regarding knowledge of pediatric emergencies than did providers in the control county (P = .001). Significantly greater improvement was also seen when comparisons of test scores were made for field (P = .02) and hospital (P = .03) emergency care personnel separately. Self-reports on a visual analog scale indicated that providers in the project intervention county had a significantly greater decrease in anxiety than did control subjects when presented a scenario of a child experiencing a respiratory arrest (P = .01). On the basis of scores from a five-point Likert scale, emergency personnel in the intervention county had a greater increase in confidence regarding management of the pediatric airway (P = .0003) and a greater increase in the belief that they had adequate pediatric training (P = .000001) after participating in the project than emergency personnel in the control county. CONCLUSION: The rural pediatric emergency medical and trauma services project was effective in increasing the knowledge and confidence of emergency care personnel in the management of acutely ill and injured children. This project offers a model that can be replicated in other rural areas nationally.

Child↗
PubMed1997

Shortening in femoral shaft fractures in children treated with spica cast.

Early spica cast treatment is one method used for children's femoral shaft fractures; it is increasingly advocated as treatment that allows early hospital discharge. The outcome of early spica cast treatment in 100 children, ages 2 to 10 years, with uncomplicated and isolated closed femoral shaft fractures treated at Johns Hopkins Hospital between October 1987 and March 1994 were analyzed. The objective was to identify those children who can be treated safely and dependably with early spica casting without excessive shortening of the fracture fragments. Eighty-one (81%) children had an acceptable outcome and 19 (19%) had an unacceptable outcome by the definition of more than 25 mm of fracture fragment overlap after clinical healing. A new clinical test, the telescope test, was statistically significant for correlation with spica cast outcome. Age, gender, fracture, location, mechanism of injury, fracture type, and resting radiograph of fracture fragment overlap were not statistically significant. The telescope test had a sensitivity of 80% and a specificity of 85% for predicting outcome. The relative risk for failure of spica cast treatment with a positive telescope test was 20.4 (95% confidence limits = 2.7-225.1). Children 2 to 10 years of age with uncomplicated femoral shaft fractures and a negative telescope test can be treated appropriately in most cases with early application of a spica cast.

Casts, Surgical↗
PubMed1997

Alzheimer's disease and history of blood transfusion by apolipoprotein-E genotype.

Some dementias, such as Creutzfeldt-Jakob disease, may result from transmissible agents. To assess the possibility of a blood-borne transmissible agent in Alzheimer's disease (AD), we compared informant-reported history of blood transfusions among 326 newly recognized probable AD cases and 330 control subjects of similar age and sex, randomly selected from the same health maintenance organization population. Since risk of AD is increased in persons with apolipoprotein E epsilon 4 (APOE-e4) alleles, we examined whether the transfusion-AD relationship varies by APOE genotype. Transfusion was more frequent among controls (17.9%) than cases (12.0%) in the overall group (crude odds ratio = 0.62; 95% confidence interval = 0.40, 0.97). Similar risks were seen for transfusions occurring < or = or > 10 years before the reference year. Stratified analysis by APOE-e4 genotype showed no effect modification. Logistic regression adjusting for age, sex, education, and presence of e4 did not change the transfusion-AD association. We conclude that a history of blood transfusion is not associated with increased risk of AD, nor does consideration of APOE-e4 status modify that conclusion.

Aged↗
PubMed1997

Pullout strengths of cannulated and noncannulated cancellous bone screws.

The pullout strengths of large diameter cannulated and noncannulated cancellous screws were tested in a synthetic polyurethane foam. The foam was fabricated to have mechanical properties equivalent to human cancellous bone and was characterized by compression testing before screw pullout. Long and short thread commercially available screws from four manufacturers were tested. In screws with short threads (16-22 mm), there was no difference in holding power among the four cannulated screw designs. However, the short thread noncannulated screw performed significantly better than the short thread cannulated screw with the lowest pullout strength. There were statistically significant differences in holding power among the different long thread (32-40 mm) cannulated screw designs. Additionally, the long thread noncannulated screw had better holding power than several of the long thread cannulated screws. No differences in pullout strengths between comparably sized cannulated and noncannulated screws produced by the same manufacturer were found, and all long thread screws had significantly greater holding power than all short thread screws. There was no demonstrable effect on holding power when screws were inserted with or without tapping. Thread surface area was found to be a reasonable predictor of holding power.

Bone Screws↗
PubMed1996

PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames.

DNA translation frames can be disrupted for several reasons, including: (i) errors in sequence determination; (ii) RNA processing, such as intron removal and guide RNA editing; (iii) less commonly, polymerase frameshifting during transcription or ribosomal frameshifting during translation. Frameshifts frequently confound computational activities involving homologous sequences, such as database searches and inferences on structure, function or phylogeny made from multiple alignments. A dynamic alignment algorithm is reported here which compares a protein profile (a residue scoring matrix for one or more aligned sequences) against the three translation frames of a DNA strand, allowing frameshifting. The algorithm has been incorporated into a new package, WiseTools, for comparison of biological sequences. A protein profile can be compared against either a DNA sequence or a protein sequence. The program PairWise may be used interactively for alignment of any two sequence inputs. SearchWise can perform combinations of searches through DNA or protein databases by a protein profile or DNA sequence. Routine application of the programs has revealed a set of database entries with frameshifts caused by errors in sequence determination.

Algorithms↗
PubMed1996

BRCA1 mutations in a population-based sample of young women with breast cancer.

BACKGROUND: Inherited mutations in the BRCA1 gene are associated with a high risk of breast and ovarian cancer in some families. However, little is known about the contribution of BRCA1 mutations to breast cancer in the general population. We analyzed DNA samples from women enrolled in a population-based study of early-onset breast cancer to assess the spectrum and frequency of germ-line BRCA1 mutations in young women with breast cancer. METHODS: We studied 80 women in whom breast cancer was diagnosed before the age of 35, and who were not selected on the basis of family history. Genomic DNA was studied for BRCA1 mutations by analysis involving single-strand conformation polymorphisms and with allele-specific assays. Alterations were defined by DNA sequencing. RESULTS: Germ-line BRCA1 mutations were identified in 6 of the 80 women. Four additional rare sequence variants of unknown functional importance were also identified. Two of the mutations and three of the rare sequence variants were found among the 39 women who reported no family history of breast or ovarian cancer. None of the mutations and only one of the rare variants was identified in a reference population of 73 unrelated subjects. CONCLUSIONS: Alterations in BRCA1 were identified in approximately 10 percent of this cohort of young women with breast cancer. The risk of harboring a mutation was not limited to women with family histories of breast or ovarian cancer. These results represent a minimal estimate of the frequency of BRCA1 mutations in this population. Comprehensive methods of identifying BRCA1 mutations and understanding their importance will be needed before testing of women in the general population can be undertaken.

Adult↗
PubMed1996

Apolipoprotein E in Alzheimer's disease risk and case detection: a case-control study.

The objective of this study was to describe the association between the epsilon 4 allele of the apolipoprotein E gene (APOE E4) and Alzheimer's disease (AD) and to evaluate APOE E4 genotyping as a test for AD. The study base of this case-control study included about 23,000 persons 60 year of age or greater (a large health maintenance organization); the demographic characteristics of this group are similar to those of the surrounding area. Analysis focused on 234 Caucasian probable AD patients first identified between 1987 and 1993; and 304 cognitively intact controls of similar age, sex, and race who were randomly selected from the same study base. All cases were examined and diagnosed by study physicians using standard protocols. All subjects participate in continuing annual follow-up testing to verify their cognitive status. APOE genotypes were determined from blood samples using standard laboratory methods. Subject characteristics and diagnoses were obtained from interviews, diagnostic examination, or medical record review. Heterozygous E4 individuals had a crude odds ratio of 3.1 (2.1-4.5) for AD compared to those with no E4, while homozygous E4 subjects had an odds ratio of 34.3 (8.0-146.3) for AD. As an indicator of AD, having one E4 allele showed a sensitivity of 0.52 and a specificity of 0.74. Homozygous E4 genotype had a sensitivity of 0.23 and a specificity of 0.99 (when compared to non-E4 genotypes). Cardiovascular disease differed in cases and controls, but did not confound or modify the APOE E4-AI) association. In this study base, the APOE E4 allele was a significant risk factor. However, considering either homozygous or heterozygous E4 genotype as a screen or diagnostic marker for AD would miss many true cases and could misclassify many normals as AD.

Aged↗