Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

BACKGROUND: There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible: whole-genome sequencing, whole-exome sequencing using exon capture methods, and RNA-Seq. While whole-genome sequencing is the most complete, it remains sufficiently expensive that cost effective alternatives are important. RESULTS: Here we provide a systematic exploration of how well RNA-Seq can identify human coding variants by comparing variants identified through high coverage whole-genome sequencing to those identified by high coverage RNA-Seq in the same individual. This comparison allowed us to directly evaluate the sensitivity and specificity of RNA-Seq in identifying coding variants, and to evaluate how key parameters such as the degree of coverage and the expression levels of genes interact to influence performance. We find that although only 40% of exonic variants identified by whole genome sequencing were captured using RNA-Seq; this number rose to 81% when concentrating on genes known to be well-expressed in the source tissue. We also find that a high false positive rate can be problematic when working with RNA-Seq data, especially at higher levels of coverage. CONCLUSIONS: We conclude that as long as a tissue relevant to the trait under study is available and suitable quality control screens are implemented, RNA-Seq is a fast and inexpensive alternative approach for finding coding variants in genes with sufficiently high expression levels

Systematic review of antiepileptic drugs’ safety and effectiveness in feline epilepsy

Understanding the efficacy and safety profile of antiepileptic drugs (AEDs) in feline epilepsy is a crucial consideration for managing this important brain disease. However, there is a lack of information about the treatment of feline epilepsy and therefore a systematic review was constructed to assess current evidence for the AEDs’ efficacy and tolerability in cats. The methods and materials of our former systematic reviews in canine epilepsy were mostly mirrored for the current systematic review in cats. Databases of PubMed, CAB Direct and Google scholar were searched to detect peer-reviewed studies reporting efficacy and/or adverse effects of AEDs in cats. The studies were assessed with regards to their quality of evidence, i.e. study design, study population, diagnostic criteria and overall risk of bias and the outcome measures reported, i.e. prevalence and 95% confidence interval of the successful and affected population in each study and in total

Dental practice satisfaction with preferred provider organizations

<p>Abstract</p> <p>Background</p> <p>Despite their increasing share of the dental insurance market, little is known about dental practices' satisfaction with preferred provider organizations (PPOs). This analysis examined practice satisfaction with dental PPOs and the extent to which satisfaction was a function of communications from the plan, claims handling and compensation.</p> <p>Methods</p> <p>Data were collected through telephone surveys with dental practices affiliated with MetLife between January 2002 and December 2004. Each respondent was asked a series of questions related to their satisfaction with a systematically selected PPO with which they were affiliated. Six different PPO plans had sufficient observations to allow for comparative analysis (total n = 4582). Multiple imputation procedures were used to adjust for item non-response.</p> <p>Results</p> <p>While the average level of overall satisfaction with the target plan fell between "very satisfied" and "satisfied," regression models revealed substantial differences in overall satisfaction across the 6 PPOs (p < .05). Statistically significant differences between plans in overall satisfaction were largely explained by differences in the perceived adequacy of compensation. However, differences in overall satisfaction involving two of the PPOs were also driven by satisfaction with claims handling.</p> <p>Conclusion</p> <p>Results demonstrate the importance of compensation to dental practice satisfaction with PPOs. However, these results also highlight the critical role of service-related factors in differentiating plans and suggest that there are important non-monetary dimensions of PPO performance that can be used to recruit and retain practices.</p

Age and Ethnicity among Hospitalized Alcoholics: A Nationwide Study

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65651/1/j.1530-0277.1992.tb00694.x.pd

Simulated effect of pneumococcal vaccination in the Netherlands on existing rules constructed in a non-vaccinated cohort predicting sequelae after bacterial meningitis

BACKGROUND: Previously two prediction rules identifying children at risk of hearing loss and academic or behavioral limitations after bacterial meningitis were developed. Streptococcus pneumoniae as causative pathogen was an important risk factor in both. Since 2006 Dutch children receive seven-valent conjugate vaccination against S. pneumoniae. The presumed effect of vaccination was simulated by excluding all children infected by S. pneumoniae with the serotypes included in the vaccine, from both previous collected cohorts (between 1990-1995). METHODS: Children infected by one of the vaccine serotypes were excluded from both original cohorts (hearing loss: 70 of 628 children; academic or behavioral limitations: 26 of 182 children). All identified risk factors were included in multivariate logistic regression models. The discriminative ability of both new models was calculated. RESULTS: The same risk factors as in the original models were significant. The discriminative ability of the original hearing loss model was 0.84 and of the new model 0.87. In the academic or behavioral limitations model it was 0.83 and 0.84 respectively. CONCLUSION: It can be assumed that the prediction rules will also be applicable on a vaccinated population. However, vaccination does not provide 100% coverage and evidence is available that serotype replacement will occur. The impact of vaccination on serotype replacement needs to be investigated, and the prediction rules must be validated externally

Increase in mammography detected breast cancer over time at a community based regional cancer center: a longitudinal cohort study 1990–2005

Background: Coincident with the advent of mammography screening, breast carcinoma in situ has increased in the US population. Methods: We conducted a prospective cohort study of all women presenting with primary breast cancer, aged 21-94, and biopsy confirmed Stage 0-IV from 1990-2005 identified and tracked by our registry. Clinical presentation characteristics including age, race, TNM stage, family and pregnancy history, histologic type and method of detection by patient (PtD), physician (PhysD) or mammography (MgD) were chart abstracted at time of diagnosis. Cases with unknown or other method of detection (n = 84), or unusual cell types (n = 26) were removed (n = 6074). Results: From 1990 to 1998 the percentage of PtD and MgD cases was roughly equivalent. In 1999 the percentage of MgD cases increased to 56% and PtD dropped to 37%, a significant 20% differential, constant to 2005 (Pearson chi square = 120.99, p less than .001). Overall, percent TNM stage 0 (breast carcinoma in situ) cases increased after 1990, percent stage I and III cases declined, and stage II and IV cases remained constant (Pearson chi square = 218.36, p less than .001). Increase in MgD over time differed by age group with an 8.5% increase among women age 40-49 and 12% increase among women age 50-95. Women age 21-39 rarely had MgD BC. In forward stepwise logistic regression modeling, significant predictors of MgD BC by order of entry were TNM stage, age at diagnosis, diagnosis year, and race (chi square = 1867.56, p less than .001). Conclusion: In our cohort the relative proportion of mammography detected breast cancer increased over time with a higher increase among women age 50+ and an increase of breast carcinoma in situ exclusively among MgD cases. The increase among women currently targeted by mammography screening programs (age = 50) combined with an increase of breast carcinoma in situ most often detected by mammography screening indicates a possible incidence shift to lower stage breast cancer as a result of mammographic detection.Kaplan Research Fun

Cholesterol treatment with statins: Who is left out and who makes it to goal?

<p>Abstract</p> <p>Background</p> <p>Whether patient socio-demographic characteristics (age, sex, race/ethnicity, income, and education) are independently associated with failure to receive indicated statin therapy and/or to achieve low density lipoprotein cholesterol (LDL-C) therapy goals are not known. We examined socio-demographic factors associated with a) eligibility for statin therapy among those not on statins, and b) achievement of statin therapy goals.</p> <p>Methods</p> <p>Adults (21-79 years) participating in the United States (US) National Health and Nutrition Examination Surveys, 1999-2006 were studied. Statin eligibility and achievement of target LDL-C was assessed using the US Third Adult Treatment Panel (ATP III) on Treatment of High Cholesterol guidelines.</p> <p>Results</p> <p>Among 6,043 participants not taking statins, 10.4% were eligible. Adjusted predictors of statin eligibility among statin non-users were being older, male, poorer, and less educated. Hispanics were less likely to be eligible but not using statins, an effect that became non-significant with adjustment for language usually spoken at home. Among 537 persons taking statins, 81% were at LDL-C goal. Adjusted predictors of goal failure among statin users were being male and poorer. These risks were not attenuated by adjustment for healthcare access or utilization.</p> <p>Conclusion</p> <p>Among person's not taking statins, the socio-economically disadvantaged are more likely to be eligible and among those on statins, the socio-economically disadvantaged are less likely to achieve statin treatment goals. Further study is needed to identify specific amenable patient and/or physician factors that contribute to these disparities.</p

Climatic Variability Leads to Later Seasonal Flowering of Floridian Plants

Understanding species responses to global change will help predict shifts in species distributions as well as aid in conservation. Changes in the timing of seasonal activities of organisms over time may be the most responsive and easily observable indicator of environmental changes associated with global climate change. It is unknown how global climate change will affect species distributions and developmental events in subtropical ecosystems or if climate change will differentially favor nonnative species. Contrary to previously observed trends for earlier flowering onset of plant species with increasing spring temperatures from mid and higher latitudes, we document a trend for delayed seasonal flowering among plants in Florida. Additionally, there were few differences in reproductive responses by native and nonnative species to climatic changes. We argue that plants in Florida have different reproductive cues than those from more northern climates. With global change, minimum temperatures have become more variable within the temperate-subtropical zone that occurs across the peninsula and this variation is strongly associated with delayed flowering among Florida plants. Our data suggest that climate change varies by region and season and is not a simple case of species responding to consistently increasing temperatures across the region. Research on climate change impacts need to be extended outside of the heavily studied higher latitudes to include subtropical and tropical systems in order to properly understand the complexity of regional and seasonal differences of climate change on species responses

Marital status and occupation in relation to short-term case fatality after a first coronary event - a population based cohort

<p>Abstract</p> <p>Background</p> <p>Although marital status and low occupation level has been associated with mortality, the relationship with case fatality rates (CFR) after a coronary event (CE) is unclear. This study explored whether incidence of CE and short-term CFR differ between groups defined in terms of marital status and occupation, and if this could be explained by biological and life-style risk factors.</p> <p>Methods</p> <p>Population-based cohort study of 33,224 subjects (67% men), aged 27 to 61 years, without history of myocardial infarction, who were enrolled between 1974 and 1992. Incidence of CE, and CFR (death during the first day or within 28 days after CE, including out-of-hospital deaths) was examined over a mean follow-up of 21 years.</p> <p>Results</p> <p>A total of 3,035 men (6.0 per 1000 person-years) and 507 women (2.4 per 1000) suffered a first CE during follow-up. CFR (during the 1^stday) was 29% in men and 23% in women. After risk factor adjustments, unmarried status in men, but not in women, was significantly associated with increased risk of suffering a CE [hazard ratios (HR) 1.10, 95% CI: 0.97-1.24; 1.42: 1.27-1.58 and 1.77: 1.31-2.40 for never married, divorced and widowed, respectively, compared to married]. Unmarried status, in both gender, was also related with an increased CFR (1^stday), taking potential confounders into account (odds ratio (OR) 2.14, 95% CI: 1.63-2.81; 1.91: 1.50-2.43 and 1.49: 0.77-2.89 for never married, divorced and widowed, respectively, compared to married men. Corresponding figures for women was 2.32: 0.93-5.81; 1.87: 1.04-3.36 and 2.74: 1.03-7.28. No differences in CFR (1^stday) were observed between occupational groups in neither gender.</p> <p>Conclusions</p> <p>In this population-based Swedish cohort, short-term CFR was significantly related to unmarried status in men and women. This relationship was not explained by biological-, life-style factors or occupational level.</p

EVOTECH® endoscope cleaner and reprocessor (ECR) simulated-use and clinical-use evaluation of cleaning efficacy

<p>Abstract</p> <p>Background</p> <p>The objective of this study was to perform simulated-use testing as well as a clinical study to assess the efficacy of the EVOTECH^®Endoscope Cleaner and Reprocessor (ECR) cleaning for flexible colonoscopes, duodenoscopes, gastroscopes and bronchoscopes. The main aim was to determine if the cleaning achieved using the ECR was at least equivalent to that achieved using optimal manual cleaning.</p> <p>Methods</p> <p>Simulated-use testing consisted of inoculating all scope channels and two surface sites with Artificial Test Soil (ATS) containing 10⁸cfu/mL of <it>Enterococcus faecalis, Pseudomonas aeruginosa </it>and <it>Candida albicans</it>. Duodenoscopes, colonoscopes, and bronchoscopes (all Olympus endoscopes) were included in the simulated use testing. Each endoscope type was tested in triplicate and all channels and two surface sites were sampled for each scope. The clinical study evaluated patient-used duodenoscopes, bronchoscopes, colonoscopes, and gastroscopes (scopes used for emergency procedures were excluded) that had only a bedside flush prior to being processed in the ECR (i.e. no manual cleaning). There were 10 to 15 endoscopes evaluated post-cleaning and to ensure the entire ECR cycle was effective, 5 endoscopes were evaluated post-cleaning and post-high level disinfection. All channels and two external surface locations were sampled to evaluate the residual organic and microbial load. Effective cleaning of endoscope surfaces and channels was deemed to have been achieved if there was < 6.4 μg/cm²of residual protein, < 1.8 μg/cm²of residual hemoglobin and < 4 Log₁₀viable bacteria/cm². Published data indicate that routine manual cleaning can achieve these endpoints so the ECR cleaning efficacy must meet or exceed these to establish that the ECR cleaning cycle could replace manual cleaning</p> <p>Results</p> <p>In the clinical study 75 patient-used scopes were evaluated post cleaning and 98.8% of surfaces and 99.7% of lumens met or surpassed the cleaning endpoints set for protein, hemoglobin and bioburden residuals. In the simulated-use study 100% of the Olympus colonoscopes, duodenoscopes and bronchoscopes evaluated met or surpassed the cleaning endpoints set for protein, and bioburden residuals (hemoglobin was not evaluated).</p> <p>Conclusions</p> <p>The ECR cleaning cycle provides an effective automated approach that ensures surfaces and channels of flexible endoscopes are adequately cleaned after having only a bedside flush but no manual cleaning. It is crucial to note that endoscopes used for emergency procedures or where reprocessing is delayed for more than one hour MUST still be manually cleaned prior to placing them in the ECR.</p