Estimating and evaluating the statistics of gapped local-alignment scores

We present a novel maximum-likelihood-based algorithm for estimating the distribution of alignment scores from the scores of unrelated sequences in a database search. Using a new method for measuring the accuracy of p-values, we show that our maximum-likelihood-based algorithm is more accurate than existing regression-based and lookup table methods. We explore a more sophisticated way of modeling and estimating the score distributions (using a two-component mixture model and expectation maximization), but conclude that this does not improve significantly over simply ignoring scores with small E-values during estimation. Finally, we measure the classification accuracy of p-values estimated in different ways and observe that inaccurate p-values can, somewhat paradoxically, lead to higher classification accuracy. We explain this paradox and argue that statistical accuracy, not classification accuracy, should be the primary criterion in comparisons of similarity search methods that return p-values that adjust for target sequence length.

Checklist of health promotion environments at worksites (CHEW): Development and measurement characteristics

Purpose. Health promotion policy frameworks, recent theorizing, and research all emphasize understanding and mobilizing environmental influences to change particular health-related behaviors in specific settings. The workplace is a key environmental setting. The Checklist of Health Promotion Environments at Worksites (CHEW) was designed as a direct observation instrument to assess characteristics of worksite environments that are known to influence health-related behaviors. Methods. The CHEW is a 112-item checklist of workplace environment features hypothesized to be associated, both positively and negatively, with physical activity, healthy eating, alcohol consumption, and smoking. The three environmental domains assessed are (1) physical characteristics of the worksite, (2) features of the information environment, and (3) characteristics of the immediate neighborhood around the workplace. The conceptual rationale and development studies for the CHEW are described, and data from observational studies of 20 worksites are reported. Results. The data on CHEW-derived environmental attributes showed generally good reliability and identified meaningful sets of variables that plausibly may influence health-related behaviors. With the exception of one information environment attribute, intraclass correlation coefficients ranged from 0.80 to 1.00. Descriptive statistics on selected physical and information environment characteristics indicated that vending machines, showers, bulletin boards, and signs prohibiting smoking were common across worksites. Bicycle racks, visible stairways, and signs related to alcohol consumption, nutrition, and health. promotion were relatively uncommon. Conclusions. These findings illustrate the types of data on environmental attributes that can be derived, their relevance for program planning, and how they can characterize variability across worksites. The CHEW is a promising observational measure that has the potential to assess environmental influences on health behaviors and to evaluate workplace health promotion programs.

Usefulness of B-type natriuretic peptide in hypertensive patients with exertional dyspnea and normal left ventricular ejection fraction and correlation with new echocardiographic indexes of systolic and diastolic function

B-type natriuretic peptide (BNP) levels increase in systolic heart failure (HF). However, the value of BNP in hypertensive patients with suspected diastolic HF (symptoms suggestive of HF but normal ejection fraction) and its relation to myocardial function in these patients is unclear. We prospectively studied 72 ambulatory hypertensive subjects (40 women, mean age 58 +/- 8 years) with exertional dyspnea and ejection fraction greater than or equal to50%. Diastolic function was evaluated with transmitral and pulmonary venous Doppler, mitral annular velocities (pulsed-wave tissue Doppler), and flow propagation velocity (color M-mode). Systolic function was assessed with strain and strain rate derived from color tissue Doppler imaging. BNP was related to myocardial function and the presence or absence of global diastolic dysfunction. By conventional Doppler criteria, 34 patients had normal left ventricular diastolic function and 38 had isolated diastolic dysfunction. BNP values were higher in patients with diastolic dysfunction (46 +/- 48 vs 20 +/- 20 pg/ml, p = 0.004) and were related independently to blood pressure, systolic strain rate, left atrial function (p < 0.01 for all), and age (p = 0.015). Patients with diastolic dysfunction and pseudonormal filling had higher BNP levels compared with impaired relaxation (89 +/- 47 vs 35 +/- 42 pg/ml, p = 0.001). However, 79% of patients with diastolic dysfunction had BNP levels within the normal range. We conclude that in ambulatory hypertensive patients with symptoms suggestive of mild HF and normal ejection fraction, BNP is related to atrial and ventricular systolic parameters, blood pressure, and age. Although elevated in the presence of diastolic dysfunction, the BNP level mostly is in the normal range and, therefore, has limited diagnostic value in stable patients with suspected diastolic HF. (C) 2003 by Excerpta Medica, Inc.

Poor correlation of mid-femoral measurements by CT and hip measurements by DXA in the elderly

Background and aims: Hip fracture is a devastating event in terms of outcome in the elderly, and the best predictor of hip fracture risk is hip bone density, usually measured by dual X-ray absorptiometry (DXA). However, bone density can also be ascertained from computerized tomography (CT) scans, and mid-thigh scans are frequently employed to assess the muscle and fat composition of the lower limb. Therefore, we examined if it was possible to predict hip bone density using mid-femoral bone density. Methods: Subjects were 803 ambulatory white and black women and men, aged 70-79 years, participating in the Health, Aging and Body Composition (Health ABC) Study. Bone mineral content (BMC, g) and volumetric bone mineral density (vBMD, mg/cm(3)) of the mid-femur were obtained by CT, whereas BMC and areal bone mineral density (aBMD, g/cm(2)) of the hip (femoral neck and trochanter) were derived from DXA. Results: In regression analyses stratified by race and sex, the coefficient of determination was low with mid-femoral BMC, explaining 6-27% of the variance in hip BMC, with a standard error of estimate (SEE) ranging from 16 to 22% of the mean. For mid-femur vBMD, the variance explained in hip aBMD was 2-17% with a SEE ranging from 15 to 18%. Adjusting aBMD to approximate volumetric density did not improve the relationships. In addition, the utility of fracture prediction was examined. Forty-eight subjects had one or more fractures (various sites) during a mean follow-up of 4.07 years. In logistic regression analysis, there was no association between mid-femoral vBMD and fracture (all fractures), whereas a 1 SD increase in hip BMD was associated with reduced odds for fracture of similar to60%. Conclusions: These results do not support the use of CT-derived mid-femoral vBMD or BMC to predict DXA-measured hip bone mineral status, irrespective of race or sex in older adults. Further, in contrast to femoral neck and trochanter BMD, mid-femur vBMD was not able to predict fracture (all fractures). (C) 2003, Editrice Kurtis.