Binning Metagenomic Data by CSSR

Metagenomics is the study of microbes in their natural environments without the need for isolation and lab cultivation. The DNA fragments obtained from sequencing of a sample of mixed species requires taxonomic characterization called binning. My research concerns binning of metagenomic data using a novel approach. Each genomic sequence was codified based on their Cistronic Stop Signal Ratio (CSSR) values. Since the genic CSSR values of phylogenetically related organisms often share a definable pattern, a neural network was trained to recognize the genic CSSR patterns of known species.The trained neural network was then used to cluster the CSSR values from the metagenomic data. To show the validity of this method, a total of 15,000 genic CSSR values were calculated from five different bacterial species. The data was randomly mixed and a neural network was used to recognize the originality of these genes, based on their unique CSSR values. Results showed that better than 95% of the genes were correctly binned to the rightful species. The metagenomic sequences from the fecal samples of 124 individuals were reanalyzed based on the CSSR - neural network method by training the genic values of a set of known enteric bacteria. The resulting clusters were discussed

Defensive Disclosure under Antitrust Enforcement

We formulate a simple model of optimal defensive disclosure by a monopolist facing uncertain antitrust enforcement and test its implications using unique data on defensive disclosures and patents by IBM during 1955-1989. Our results indicate that stronger antitrust enforcement leads to more defensive disclosure, that quality inventions are disclosed defensively, and that defensive disclosure served as an alternative but less successful mechanism to patenting at IBM in appropriating returns from R&D

Factors Influencing Physical Activity Behavior among Iranian Women with Type 2 Diabetes Using the Extended Theory of Reasoned Action

BackgroundFindings of most studies indicate that the only way to control diabetes and prevent its debilitating effects is through the continuous performance of self-care behaviors. Physical activity is a non-pharmacological method of diabetes treatment and because of its positive effects on diabetic patients, it is being increasingly considered by researchers and practitioners. This study aimed at determining factors influencing physical activity among diabetic women in Iran, using the extended theory of reasoned action in Iran.MethodsA sample of 352 women with type 2 diabetes, referring to a Diabetes Clinic in Khoy, Iran, participated in the study. Appropriate instruments were designed to measure the desired variables (knowledge of diabetes, personal beliefs, subjective norms, perceived self-efficacy, behavioral intention and physical activity behavior). The reliability and validity of the instruments were examined and approved. Statistical analyses of the study were conducted by inferential statistical techniques (independent t-test, correlations and regressions) using the SPSS package.ResultsThe findings of this investigation indicated that among the constructs of the model, self efficacy was the strongest predictor of intentions among women with type 2 diabetes and both directly and indirectly affected physical activity. In addition to self efficacy, diabetic patients' physical activity also was influenced by other variables of the model and sociodemographic factors.ConclusionOur findings suggest that the high ability of the theory of reasoned action extended by self-efficacy in forecasting and explaining physical activity can be a base for educational intervention. Educational interventions based on the proposed model are necessary for improving diabetics' physical activity behavior and controlling disease

The decline of science in corporate R&D

Research summary: In this article, we document a shift away from science by large corporations between 1980 and 2006. We find that publications by company scientists have declined over time in a range of industries. We also find that the value attributable to scientific research has dropped, whereas the value attributable to technical knowledge (as measured by patents) has remained stable. These trends are unlikely to be driven principally by changes in publication practices. Furthermore, science continues to be useful as an input into innovation. Our evidence points to a reduction of the private benefits of internal research. Large firms still value the golden eggs of science (as reflected in patents), but seem to be increasingly unwilling to invest in the golden goose itself (the internal scientific capabilities). Managerial summary: There is a widespread belief among commentators that large American corporations are withdrawing from research. Large corporations may still collaborate with universities and acquire promising science-based start-ups, but their labs increasingly focus on developing existing knowledge and commercializing it, rather than creating new knowledge. In this article, we combine firm-level financial information with a large and comprehensive data set on firm publications, patents and acquisitions to quantify the withdrawal from science by large American corporations between 1980 and 2006. This withdrawal is associated with a decline in the private value of research activities, even though scientific knowledge itself remains important for corporate invention. We discuss the managerial and policy implications of our findings

Immunoglobulin gene insertions and deletions in the affinity maturation of HIV-1 broadly reactive neutralizing antibodies.

CAPRISA, 2014.Abstract available in pdf