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Biomedical subjects

A Farmer

Publications and source records attributed to A Farmer.

At least 55 records · Page 3Linked to original sources
PubMed1999

Establishing a method of vector contamination identification in database sequences.

MOTIVATION: The nucleotide sequence databases are invaluable tools both for the private and the academic research communities, from the retrieval of sequences to homology searching. Several issues related to data quality, such as the existence of sequencing artifacts and errors, are facing the databases. We investigated a major source of these errors, i.e. the presence of vector-contaminated sequences. RESULTS: Using a panel of 180 vector polylinker sequences, we found 0.36% or 3029 vector-matching sequences in GenBank Release 95-96, with an average vector-matching length of 72 nucleotides. The number of vector-contaminated sequences has been growing with the database; however, the percent contamination has remained approximately constant at an average of 0.28% from 1982 to 1996. AVAILABILITY: Access to the database of vector polylinker sequences via sequence similarity searching is available at http://seqsim.ncgr.org/vector/ CONTACT: gas@molinfo.com

Animals↗
PubMed1998

The Genome Sequence DataBase (GSDB): improving data quality and data access.

In 1997 the primary focus of the Genome Sequence DataBase (GSDB; www. ncgr.org/gsdb ) located at the National Center for Genome Resources was to improve data quality and accessibility. Efforts to increase the quality of data within the database included two major projects; one to identify and remove all vector contamination from sequences in the database and one to create premier sequence sets (including both alignments and discontiguous sequences). Data accessibility was improved during the course of the last year in several ways. First, a graphical database sequence viewer was made available to researchers. Second, an update process was implemented for the web-based query tool, Maestro. Third, a web-based tool, Excerpt, was developed to retrieve selected regions of any sequence in the database. And lastly, a GSDB flatfile that contains annotation unique to GSDB (e.g., sequence analysis and alignment data) was developed. Additionally, the GSDB web site provides a tool for the detection of matrix attachment regions (MARs), which can be used to identify regions of high coding potential. The ultimate goal of this work is to make GSDB a more useful resource for genomic comparison studies and gene level studies by improving data quality and by providing data access capabilities that are consistent with the needs of both types of studies.

Base Sequence↗
PubMed1998

Psychomotor performance: investigating the dose-response relationship for caffeine and theophylline in elderly volunteers.

OBJECTIVE: The aim of the study was to investigate the dose-response relationship for psychomotor performance, caffeine and theophylline in healthy elderly volunteers. METHODS: In a randomized, double-blind, placebo-controlled, six-period cross-over study we compared the effect of three doses of theophylline (predicted peak concentrations of 3, 6 mg. 1(-1) and 12 mg . 1(-1), two doses of caffeine (predicted peak concentrations of 4.5 mg. 1(-1) and 9 mg. 1 (-1) and placebo on ten healthy elderly volunteers. Psychomotor performance was measured using a continuous attention task, symbol digit substitution test and choice reaction time. Subjective effects were assessed using visual analogue scales. Following drug administration, subjects received the test battery at 30-min intervals, up to 150 min. Maximum and mean effects from baseline on each variable were included in the analysis. RESULTS: Significant improvement on the continuous attention task was seen at the lowest concentration of caffeine and theophylline used, while at higher concentrations there was a non-significant trend towards placebo scores. There was little effect of either drug on the subjective effects measured by visual analogue scales. CONCLUSION: Caffeine and theophylline increase psychomotor performance measures of attention at low plasma concentrations in healthy elderly volunteers. This effect is not increased by higher drug concentrations and there is trend towards a return to placebo scores. The lack of effect of both caffeine and theophylline on subjective measures is consistent with previous studies of caffeine in the elderly.

Aged↗
PubMed1998

Unusual presentation of mycosis fungoides as pigmented purpura with malignant thymoma.

Thymoma is known to be associated with many lymphoreticular and nonlymphoreticular tumors. A woman who presented with patch stage mycosis fungoides with skin lesions resembling a pigmented purpura was found to have an anterior mediastinal mass on routine staging evaluation. A core needle biopsy of the mass revealed a lymphocyte predominant malignant thymoma. Review of the literature reveals many diseases with dermatologic manifestations associated with thymoma; however, malignant thymoma coexisting with mycosis fungoides has not previously been reported.

Adult↗
PubMed1997

The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes.

The Genome Sequence DataBase (GSDB) has completed its conversion to an improved relational database. The new database, GSDB 1.0, is fully operational and publicly available. Data contributions, including both original sequence submissions and community annotation, are being accomplished through the use of a graphical client-server interface tool, the GSDB Annotator, and via GIO (GSDB Input/Output) files. Data retrieval services are being provided through a new Web Query Tool and direct SQL. All methods of data contribution and data retrieval fully support the new data types that have been incorporated into GSDB, including discontiguous sequences, multiple sequence alignments, and community annotation.

Animals↗
PubMed1997

Association studies of bipolar disorder at the human serotonin transporter gene (hSERT; 5HTT).

The human serotonin transporter gene (hSERT) is a strong candidate for involvement in the pathogenesis of mood disorder and, using a UK Caucasian case-control sample, Collier et al found a significant association between bipolar disorder and the 12 allele of the VNTR polymorphism in intron 2 of this gene. In a European collaborative sample, Collier et al found a significant association between affective disorder and a functional deletion polymorphism in the promoter of hSERT. We have undertaken association studies using these polymorphisms in a British Caucasian sample comprising 171 DSM-IV bipolar probands, 80 DSM-IV major depression probands and 121 unrelated controls matched to bipolar probands for age, sex and ethnicity. We found no association between the promoter deletion and affective disorder but our findings with the VNTR polymorphism are similar to those of Collier and colleagues: we found a significant excess of the 12 repeat allele in bipolar probands (P = 0.031, one-tall) with a suggestion of a gene dosage effect (using genotypes bearing no 12 repeat allele as baseline, the increased risks conferred by genotypes bearing 12 repeat alleles were: heterozygote, OR = 1.24; homozygote, OR = 1.76). Our findings add to the evidence that variation at or near hSERT influences susceptibility to bipolar disorder in the British Caucasian population.

Adult↗
PubMed1997

Primary care physician-reported secondary and tertiary stroke prevention practices. A comparison between the United States and the United Kingdom.

BACKGROUND AND PURPOSE: Stroke is a major healthcare problem in both the United States (US) and the United Kingdom (UK). Little comparative data are available concerning how generalist physicians in the two countries approach the management of patients at high risk of stroke. METHODS: Contemporaneous surveys of random samples of primary care physician-reported stroke prevention practices were performed in the US and UK from 1993 to 1994. The US National Survey of Physician Practices for the Secondary and Tertiary Prevention of Ischemic Stroke included 254 noninternist primary care physicians. The UK Survey of the Care of Patients With Stroke in General Practice obtained responses from 661 general practitioners. The two surveys used many of the same questions, allowing for direct comparisons of reported stroke prevention practices between American and British physicians. RESULTS: More than 80% of American physicians reported a variety of services (24-hour electrocardiography, echocardiography, brain CT scan, brain MR scan, carotid ultrasonography, cerebral angiography) as readily available. These same services were readily available to less than 10% of physicians in the UK (P < .001 for each comparison). Although physicians in the UK reported prescribing lower doses of aspirin for stroke prevention than physicians in the US, the proportions of physicians using aspirin were not different. In contrast, almost 70% of physicians in the US responded that they always or often anticoagulate patients with nonvalvular atrial fibrillation compared with 7% of British physicians (P < .001). Whereas 70% of American versus 14% of British physicians reported obtaining carotid ultrasound studies in patients with asymptomatic bruits (P < .001), physicians in the UK more commonly reported referring this type of patient to neurologists (46% versus 21%, P < .001). For patients with recent carotid-distribution transient ischemic attack or minor stroke, physicians in the US more commonly reported referral to neurologists (55% versus 45%, P = .022), referral to surgeons (39% versus 19%, P < .001), the performance of carotid ultrasonography (80% versus 11%, P < .001), echocardiography (45% versus 5%, P < .001), 24-hour electrocardiography (49% versus 4%, P < .001), brain CT scan (72% versus 3%, P < .001), and the prescription of anticoagulants (53% versus 4%, P < .001). CONCLUSIONS: These data show significant differences in stroke prevention practices as reported by primary care physicians practicing in the US and UK. Some of these differences may be related to the relative availability of specific services in the two countries, potentially leading to overutilization in the US and underutilization in the UK in certain circumstances.

Atrial Fibrillation↗