The Los Alamos hepatitis C sequence database.
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MOTIVATION: The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide. RESULTS: The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of approximately 280 visits per day from distinct IP addresses. AVAILABILITY: The HCV website can be accessed via http://hcv.lanl.gov and http://hcv-db.org. (+info)
Local adaptation in the rock pocket mouse (Chaetodipus intermedius): natural selection and phylogenetic history of populations.
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Elucidating the causes of population divergence is a central goal of evolutionary biology. Rock pocket mice, Chaeotdipus intermedius, are an ideal system in which to study intraspecific phenotypic divergence because of the extensive color variation observed within this species. Here, we investigate whether phenotypic variation in color is correlated with local environmental conditions or with phylogenetic history. First, we quantified variation in pelage color (n=107 mice) and habitat color (n=51 rocks) using a spectrophotometer, and showed that there was a correlation between pelage color and habitat color across 14 sampled populations (R2=0.43). Analyses of mtDNA sequences from these same individuals revealed strong population structure in this species across its range, where most variation (63%) was partitioned between five geographic regions. Using Mantel tests, we show that there is no correlation between color variation and mtDNA phylogeny, suggesting that pelage coloration has evolved rapidly. At a finer geographical scale, high levels of gene flow between neighboring melanic and light populations suggest the selection acting on color must be quite strong to maintain habitat-specific phenotypic distributions. Finally, we raise the possibility that, in some cases, migration between populations of pocket mice inhabiting different lava flows may be responsible for similar melanic phenotypes in different populations. Together, the results suggest that color variation can evolve very rapidly over small geographic scales and that gene flow can both hinder and promote local adaptation. (+info)
Geographic variation in the treatment of localized breast cancer.
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BACKGROUND: Breast-conserving surgery followed by radiation therapy is as effective as modified radical mastectomy in treating women with localized breast cancer, as demonstrated by clinical trials reported during the 1980s. The extent to which breast-conserving surgery has been adopted in various regions of the United States is not known. METHODS: We assessed variations in the use of breast-conserving surgery from 1983 to 1986 in 18,399 non-Hispanic white, 324 Hispanic, and 1174 black women with breast cancer in nine areas of the United States, using data from the Surveillance, Epidemiology, and End-Results Program of the National Cancer Institute. RESULTS: The proportion of white women with localized breast cancer who underwent breast-conserving surgery ranged from 9.2 percent (Iowa) to 32.1 percent (Seattle) in 1983-1984 and from 19.6 percent (Iowa) to 41.5 percent (Seattle) in 1985-1986. Between 1983 and 1986, the use of breast-conserving surgery increased in each area, but the relative rankings of the areas changed little. The frequency of the use of breast-conserving surgery in black and Hispanic women was comparable to that in white women. The proportion of women who received radiation therapy after breast-conserving surgery also varied geographically and increased from 1983 to 1986 in all areas. Older women in all areas and black women in Atlanta and Detroit were less likely than other women to receive radiotherapy after breast-conserving surgery. CONCLUSIONS: There is marked variation in the United States in the use of breast-conserving surgery for localized breast cancer. The variation is not explained by demographic factors, although race and age affect the use of radiotherapy after breast-conserving surgery. (+info)
Association of body composition and weight history with breast cancer prognostic markers: divergent pattern for Hispanic and non-Hispanic White women.
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Body composition and weight gain are breast cancer risk factors that may influence prognosis. The Health, Eating, Activity, and Lifestyle Study was designed to evaluate the relations of body composition, weight history, hormones, and lifestyle factors to prognosis for women with breast cancer. In the cross-sectional analysis of this cohort study specific to 150 Hispanic and 466 non-Hispanic White women in New Mexico diagnosed between 1996 and 1999, the authors hypothesized that obesity measures are associated with baseline prognostic markers and that these associations are modified by ethnicity. Ethnic-stratified multiple logistic regression analyses showed divergent results for a tumor size of 1.0 cm or more and, to a lesser extent, positive lymph node status. Among Hispanics, the highest quartile for body mass index (29.5 vs. <22.5 kg/m2: odds ratio (OR) = 0.16, 95% confidence interval (CI): 0.03, 0.84) and for waist circumference (> or =95.0 vs. <78.5 cm: OR = 0.09, 95% CI: 0.01, 0.78) was significantly associated with a reduced tumor size. In contrast, for overweight and obese non-Hispanic White women, there was an increased association with obesity-related measures, particularly striking for the highest quartile of waist circumference (OR = 2.76, 95% CI: 1.45, 5.26). These findings suggest that Hispanics may have a different breast cancer phenotype than non-Hispanic Whites, which associates differently with body composition and weight history. (+info)
Measuring patient safety in ambulatory care: potential for identifying medical group drug-drug interaction rates using claims data.
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OBJECTIVE: To evaluate the feasibility of using health-plan administrative data to measure potential drug-drug interaction (DDI) rates in the ambulatory setting at the medical-group level and to assess the potential use of DDI rates in performance measurement, quality improvement, and research in patient safety. STUDY DESIGN: We combined administrative and pharmacy claims data from 2 large health plans to calculate the rates at which member users of selected chronic medications were potentially exposed to a second drug known to pose a risk of harmful interactions. METHODS: We divided 44 medication combinations with risk of adverse interactions into those with DDIs of moderate/severe clinical significance and those with DDIs of mild significance. We then calculated yearly rates of potential DDIs in continuously enrolled members aged 19 and older from 1998 through 2001. Rates were calculated for all members, overall base-medication users, and, individual medical groups responsible for their care. RESULTS: The analytic data set included 756 047 patient-years of data and 110 to 123 medical groups per year. During the 4-year interval, one or more unique potential DDIs occurred in 6.2% to 6.7% of base-drug users and 2.0% to 2.3% of all adult health-plan members per year. Medical-group mean user rates were slightly lower (5.33%-5.81%), with wide variance (SD = 2.6%-3.1%) and high stability over time. CONCLUSION: Potential DDI rates calculated from health-plan data have promise for measurement in patient medication safety. This readily available and inexpensive evaluation tool has potential for monitoring, improvement, and research purposes if further studies validate their relationship to actual adverse events. (+info)
The Latin American Social Medicine database.
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BACKGROUND: Public health practitioners and researchers for many years have been attempting to understand more clearly the links between social conditions and the health of populations. Until recently, most public health professionals in English-speaking countries were unaware that their colleagues in Latin America had developed an entire field of inquiry and practice devoted to making these links more clearly understood. The Latin American Social Medicine (LASM) database finally bridges this previous gap. DESCRIPTION: This public health informatics case study describes the key features of a unique information resource intended to improve access to LASM literature and to augment understanding about the social determinants of health. This case study includes both quantitative and qualitative evaluation data. Currently the LASM database at The University of New Mexico http://hsc.unm.edu/lasm brings important information, originally known mostly within professional networks located in Latin American countries to public health professionals worldwide via the Internet. The LASM database uses Spanish, Portuguese, and English language trilingual, structured abstracts to summarize classic and contemporary works. CONCLUSION: This database provides helpful information for public health professionals on the social determinants of health and expands access to LASM. (+info)
Use of complementary therapies among primary care clinic patients with arthritis.
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INTRODUCTION: Use of complementary and alternative medicine (CAM) for chronic conditions has increased in recent years. There is little information, however, on CAM use among adults with clinic-confirmed diagnoses, including arthritis, who are treated by primary care physicians. METHODS: To assess the frequency and types of CAM therapy used by Hispanic and non-Hispanic white women and men with osteoarthritis, rheumatoid arthritis, or fibromyalgia, we used stratified random selection to identify 612 participants aged 18-84 years and seen in university-based primary care clinics. Respondents completed an interviewer-administered survey in English or Spanish. RESULTS: Nearly half (44.6%) of the study population was of Hispanic ethnicity, 71.4% were women, and 65.0% had annual incomes of less than 25,000 dollars. Most (90.2%) had ever used CAM for arthritis, and 69.2% were using CAM at the time of the interview. Current use was highest for oral supplements (mainly glucosamine and chondroitin) (34.1%), mind-body therapies (29.0%), and herbal topical ointments (25.1%). Fewer participants made current use of vitamins and minerals (16.6%), herbs taken orally (13.6%), a CAM therapist (12.7%), CAM movement therapies (10.6%), special diets (10.1%), or copper jewelry or magnets (9.2%). Those with fibromyalgia currently used an average of 3.9 CAM therapies versus 2.4 for those with rheumatoid arthritis and 2.1 for those with osteoarthritis. Current CAM use was significantly associated with being female, being under 55 years of age, and having some college education. CONCLUSION: Hispanic and non-Hispanic white arthritis patients used CAM to supplement conventional treatments. Health care providers should be aware of the high use of CAM and incorporate questions about its use into routine assessments and treatment planning. (+info)
New Mexico's capacity for increasing the prevalence of colorectal cancer screening with screening colonoscopies.
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INTRODUCTION: Colorectal cancer screening rates are low throughout the United States. Colonoscopy has been recommended as a cost-effective strategy for colorectal cancer screening and prevention. We evaluated New Mexico's capacity to increase the prevalence of colorectal cancer screening using colonoscopy. METHODS: We identified New Mexican gastroenterologists from state licensing data and from endoscopic manufacturers. We surveyed gastroenterologists on their weekly number of colonoscopies, capacity for additional screening colonoscopies, and barriers to increasing capacity. We used census data, published data on the yield of screening colonoscopy, and professional society guidelines for cancer/polyp surveillance to estimate the additional colonoscopies required to increase the state's prevalence of endoscopic screening. RESULTS: Forty gastroenterologists, representing all 11 group practices in the state, and nine of 12 solo practitioners responded. They estimated that their weekly procedure capacity could be increased by 41%, from 832 to 1174 colonoscopies. We estimated an annual capacity increase of 14,880 procedures, which could increase the prevalence of endoscopic colorectal cancer screening from the current 35% to about 50% over five years. Lack of support staff, space, and physicians were barriers to increasing screening. CONCLUSION: Implementing a screening colonoscopy strategy could achieve the goal of a higher level of colorectal screening. However, achieving more universal screening would require additional testing modalities. (+info)