The presence of intratumoral T cells correlates with improved clinical outcome in advanced ovarian carcinoma.

No abstract

Our analysis indicates information content-based measures outperform graph structure-based measures for stratifying protein interactions. Measures in terms of GO biological process and molecular function annotations can be used alone or together for the validation of protein interactions involved in the pathways. However, GO cellular component-derived measures may not have the ability to separate true positives from noise. Furthermore, we demonstrate that the functional similarity of proteins within known regulatory pathways decays rapidly as the path length between two proteins increases. Several logistic regression models are built to estimate the confidence of both direct and indirect interactions within a pathway, which may be used to score putative pathways inferred from a scaffold of molecular interactions.

Fourier-transform infrared spectroscopy is a valuable method for the study of protein conformation in solution primarily because of the sensitivity to conformation of the amide I band (1700-1620 cm-1) which arises from the backbone C = O stretching vibration. Combined with resolution-enhancement techniques such as derivative spectroscopy and self-deconvolution, plus the application of iterative curve-fitting techniques, this method provides a wealth of information concerning protein secondary structure. Further extraction of conformational information from the amide I band is dependent upon discerning the correlations between specific conformational types and component bands in the amide I region. In this paper, we report spectra-structure correlations derived from conformational perturbations in bovine trypsin which arise from autolytic processing, zymogen activation, and active-site inhibition. IR spectra were collected for the single-chain (beta-trypsin) and once-cleaved, double-chain (alpha-trypsin) forms as well as at various times during the course of autolysis and also for zymogen, trypsinogen, and beta-trypsin inhibited with diisopropyl fluorophosphate. Spectral differences among the various molecular forms were interpreted in light of previous biochemical studies of autolysis and the known three-dimensional structures of the zymogen, the active enzyme, and the DIP-inhibited form. Our spectroscopic results from these proteins in D2O imply that certain loop structures may absorb in the region of 1655 cm-1. Previously, amide I' infrared bands near 1655 cm-1 have been interpreted as arising solely from alpha-helices. These new data suggest caution in interpreting this band. We have also proposed that regions of protein molecules which are known from crystallographic experiments to be disordered absorb in the 1645 cm-1 region and that type II beta-turns absorb in the region of 1672-1685 cm-1. Our results also corroborate assignment of the low-frequency component of extended strands to bands below 1636 cm-1. Additionally, the results of multiple measurements have allowed us to estimate the variability present in component band areas calculated by curve fitting the resolution-enhanced IR spectra. We estimate that this approach to data analysis and interpretation is sensitive to changes of 0.01 unit or less in the relative integrated intensities of component bands in spectra whose peaks are well resolved.

OBJECTIVE:To assess the relation between body mass index (BMI) levels and various lifestyle variables related to physical activity and specific characteristics of a healthy eating pattern, using baseline cross-sectional data from the Wellness IN the Rockies project. SUBJECTS: A total of 928 males and 889 females, aged 18-99 y, recruited from six rural communities in Wyoming, Montana, and Idaho. MEASUREMENTS: Using BMI as the criterion, overweight was defined as a BMI X25 kg/m 2 and obesity was defined as a BMI X30 kg/m 2 . All participants in this study completed a questionnaire that elicited sociodemographic information, self-reported height and weight, and data related to specific dietary intakes, eating-related behaviors, and physical activity behaviors and perceptions. RESULTS: Prevalence of overweight was 70% in men and 59% in women. Increased likelihood of overweight or obesity was associated with greater frequency of the following: drinking sweetened beverages such as soft drinks/soda pop, ordering supersized portions, eating while doing other activities, and watching television. Other predictors were lower frequency of participation in physical activity and the perception of not getting as much exercise as needed. CONCLUSIONS: The increased probability of having a high BMI in individuals who more often eat while doing another activity appears to be a novel finding that will need to be substantiated by additional research. The finding that the vast majority of overweight and obese respondents believed that they do not get as much exercise as needed strengthens the assertion that finding ways to increase participation in physical activity should remain a high priority in obesity prevention and intervention efforts at the community and individual levels.