NETWORK TOPOLOGY IN HUMAN PROTEIN INTERACTION DATA PREDICTS FUNCTIONAL ASSOCIATION

High-throughput assays, such as yeast two-hybrid system, have generated a huge amount of protein-protein interaction (PPI) data in the past decade. This tremendously increases the need for developing reliable methods to systematically and automatically suggest protein functions and relationships between them. With the available PPI data, it is now possible to study the functions and relationships in the context of a large-scale network. To data, several network-based schemes have been provided to effectively annotate protein functions on a large scale. However, due to those inherent noises in high-throughput data generation, new methods and algorithms should be developed to increase the reliability of functional annotations. Previous work in a yeast PPI network (Samanta and Liang, 2003) has shown that the local connection topology, particularly for two proteins sharing an unusually large number of neighbors, can predict functional associations between proteins, and hence suggest their functions. One advantage of the work is that their algorithm is not sensitive to noises (false positives) in high-throughput PPI data. In this study, we improved their prediction scheme by developing a new algorithm and new methods which we applied on a human PPI network to make a genome-wide functional inference. We used the new algorithm to measure and reduce the influence of hub proteins on detecting functionally associated proteins. We used the annotations of the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) as independent and unbiased benchmarks to evaluate our algorithms and methods within the human PPI network. We showed that, compared with the previous work from Samanta and Liang, our algorithm and methods developed in this study improved the overall quality of functional inferences for human proteins. By applying the algorithms to the human PPI network, we obtained 4,233 significant functional associations among 1,754 proteins. Further comparisons of their KEGG and GO annotations allowed us to assign 466 KEGG pathway annotations to 274 proteins and 123 GO annotations to 114 proteins with estimated false discovery rates of <21% for KEGG and <30% for GO. We clustered 1,729 proteins by their functional associations and made pathway analysis to identify several subclusters that are highly enriched in certain signaling pathways. Particularly, we performed a detailed analysis on a subcluster enriched in the transforming growth factor β signaling pathway (P<10-50) which is important in cell proliferation and tumorigenesis. Analysis of another four subclusters also suggested potential new players in six signaling pathways worthy of further experimental investigations. Our study gives clear insight into the common neighbor-based prediction scheme and provides a reliable method for large-scale functional annotations in this post-genomic era.

Family Preservation and Support: Past, Present, and Future

As the family preservation and support movement evolves rapidly, this article overviews the past, present and future of this approach to policy and services. Building upon several decades of practice experience and research, and now federally funded, program designers are searching for ways to implement system wide change with an array of services all from a family focus, and strengths perspective. Critical issues facing the movement are discussed and a set of benchmarks to judge our future success is presented.

Advancing the theory of collective empowerment: A qualitative study

In order to fully describe the construct of empowerment and to determine possible measures for this construct in racially and ethnically diverse neighborhoods, a qualitative study based on Grounded Theory was conducted at both the individual and collective levels. Participants for the study included 49 grassroots experts on community empowerment who were interviewed through semi-structured interviews and focus groups. The researcher also conducted field observations as part of the research protocol.^ The results of the study identified benchmarks of individual and collective empowerment and hundreds of possible markers of collective empowerment applicable in diverse communities. Results also indicated that community involvement is essential in the selection and implementation of proper measures. Additional findings were that the construct of empowerment involves specific principles of empowering relationships and particular motivational factors. All of these findings lead to a two dimensional model of empowerment based on the concepts of relationships among members of a collective body and the collective body's desire for socio-political change.^ These results suggest that the design, implementation, and evaluation of programs that foster empowerment must be based on collaborative ventures between the population being served and program staff because of the interactive, synergistic nature of the construct. In addition, empowering programs should embrace specific principles and processes of individual and collective empowerment in order to maximize their effectiveness and efficiency. And finally, the results suggest that collaboratively choosing markers to measure the processes and outcomes of empowerment in the main systems and populations living in today's multifaceted communities is a useful mechanism to determine change. ^

Evaluating minimal important differences for the FACT-Melanoma quality of life questionnaire

Objectives. Minimal Important Differences (MIDs) establish benchmarks for interpreting mean differences in clinical trials involving quality of life outcomes and inform discussions of clinically meaningful change in patient status. As such, the purpose of this study was to assess MIDs for the Functional Assessment of Cancer Therapy–Melanoma (FACT-M). ^ Methods. A prospective validation study of the FACT-M was performed with 273 patients with stage I to IV melanoma. FACT-M, Karnofsky Performance Status (KPS), and Eastern Cooperative Oncology Group Performance Status (ECOG-PS) scores were obtained at baseline and 3 months following enrollment. Anchor- and distribution-based methods were used to assess MIDs, and the correspondence between MID ranges derived from each method was evaluated. ^ Results. This study indicates that an approximate range for MIDs of the FACT-M subscales is between 5 to 8 points for the Trial Outcome Index, 4 to 5 points for the Melanoma Combined Subscale, 2 to 4 points for the Melanoma Subscale, and 1 to 2 points for the Melanoma Surgery Subscale. Each method produced similar but not identical ranges of MIDs. ^ Conclusions. The properties of the anchor instrument employed to derive MIDs directly affect resulting MID ranges and point values. When MIDs are offered as supportive evidence of a clinically meaningful change, the anchor instrument used to derive thresholds should be clearly stated along with evidence supporting the choice of anchor instrument as the most appropriate for the domain of interest. In this analysis, the KPS was a more appropriate measure than the ECOG-PS for assessing MIDs. ^

Evaluation of a wellness program at a large private sector petrochemical company in Texas

The study purpose was to analyze the effects Integrated Health Solutions (IHS), an employee wellness program that has been implemented for one year on the corporate campus of a major private sector petrochemical company in Houston, TX, has on employee health. ^ Chronic diseases are the leading causes of morbidity and mortality in the United States and are the most preventable of all health problems. The costs of chronic diseases in the working-age adult population include not only health problems and a decrease in quality of life, but also an increase the cost of health care and costs to businesses and employers, both directly and indirectly. These emerging costs to employers as well as the fact that adults now spend the majority of waking hours at the office have increased the interest in worksite health promotion programs that address many of the behavioral factors that lead to chronic conditions. Therefore, implementing and evaluating programs that are aimed at promoting health and decreasing the prevalence of chronic diseases at worksites is very important. ^ Data came from existing data that were collected by IHS staff during employee biometric screenings at the company in 2010 and 2011. Data from employees who participated in screenings in both 2010 and 2011 were grouped into a cohort by IHS staff. ^ One-tailed t-tests were conducted to determine if there were significant improvements in the biometric measures of body fat percentage, BMI, waist circumference, systolic and diastolic blood pressures, total, HDL, and LDL cholesterol levels, triglycerides, blood glucose levels, and cardiac risk ratios. Sensitivity analysis was conducted to determine if there were differences in program outcomes when stratified by age, gender, job type, and time between screenings. ^ Mean differences for the variables from 2010 to 2011 were small and not always in the desired direction for health improvement indicators. Through conducting t-tests, it was found that there were significant improvements in HDL, cardiac risk ratio, and glucose levels. There were significant increases in cholesterol, LDL, and diastolic blood pressures. For the IHS program, it appears that gender, job type, and time between screenings were possible modifiers of program effectiveness. When program outcome measures were stratified by these factors, results suggest that corporate employees had better outcomes than field employees, males had better outcomes overall than females, and more positive program effects were seen for employees with less time between their two screenings. ^ Recommendations for the program based on the results include ensuring validity of instruments and initial and periodic training of measurement procedures and equipment handling, using normative data or benchmarks to decrease chances for biased estimates of program effectiveness, measuring behaviors as well as biometric and physiologic statuses and changes, and collecting level of engagement data.^