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BACKGROUND - High-throughput technologies such as flow and mass cytometry have the potential to illuminate cellular networks. However, analyzing the data produced by these technologies is challenging. Visualization is needed to help researchers explore this data.
RESULTS - We developed a web-based software program, NetworkPainter, to enable researchers to analyze dynamic cytometry data in the context of pathway diagrams. NetworkPainter provides researchers a graphical interface to draw and "paint" pathway diagrams with experimental data, producing animated diagrams which display the activity of each network node at each time point.
CONCLUSION - NetworkPainter enables researchers to more fully explore multi-parameter, dynamical cytometry data.
BACKGROUND - Patient portal adoption has rapidly increased over the last decade. Most patient portal research has been done in primary care or medical specialties, and few studies have examined their use in surgical patients or for recruiting research subjects. No known studies have compared portal messaging with other approaches of recruitment.
OBJECTIVES - This case report describes our experience with patient portal versus telephone recruitment for a study involving long-term follow up of surgical patients.
METHODS - Participants were recruited for a study of recurrence after ventral hernia repair through telephone calls and patient portal messaging based on registration status with the portal. Potential subjects who did not have a portal account or whose portal messages were returned after 5 days were called. The proportion of participants enrolled with each method was determined and demographics of eligible patients, portal users, and participants were compared.
RESULTS - 1359 patients were eligible for the hernia study, and enrollment was 35% (n=465). Most participants were recruited by telephone (84%, n=391); 16% (n=74) were recruited through portal messaging. Forty-four percent of eligible participants had a registered portal account, and 14% of users responded to the recruitment message. Portal users were younger than non-users (55 vs. 58 years, p<0.001); participants recruited through the portal versus telephone were also younger (54 vs. 59 years, p=0.001). Differences in the sex and racial distributions between users and non-users and between portal and telephone recruits were not significant.
CONCLUSIONS - Portal versus telephone recruitment for a surgical research study demonstrated modest portal recruitment rates and similar demographics between recruitment methods. Published studies of portal-only recruitment in primary care or medical-specialty patient populations have demonstrated higher enrollment rates, but this case study demonstrates that portal recruitment for research studies in the surgical population is feasible, and it offers convenience to patients and researchers.
OBJECTIVE - To identify sources of general and mental health information for rural women to inform the development of public health nursing interventions that consider preferences for obtaining information.
DESIGN AND SAMPLE - One thousand women (mean age = 57 years; 96.9% White) living in primarily nonmetropolitan areas of Western Kentucky participated via a random-digit-dial survey.
MEASURES - Data were collected on demographics, sources of health information, depression, and stigma.
RESULTS - Most participants preferred anonymous versus interpersonal sources for both general (68.1%) and mental health (69.4%) information. All participants reported at least one source of general health information, but 20.8% indicated not seeking or not knowing where to seek mental health information. The Internet was the most preferred anonymous source. Few women cited health professionals as the primary information source for general (11.4%) or mental (9.9%) health. Public stigma was associated with preferring anonymous sources and not seeking information.
CONCLUSIONS - Public health nurses should understand the high utilization of anonymous sources, particularly for mental health information, and focus efforts on helping individuals to navigate resources to ensure they obtain accurate information about symptoms, effective treatments, and obtaining care. Reducing stigma should remain a central focus of prevention and education in rural areas.
© 2014 Wiley Periodicals, Inc.
Pulmonary arterial hypertension (PAH) is a major progressive form of pulmonary hypertension (PH) with more than 4800 patients in the United States. In the last two decades, many studies have identified numerous genes associated with this disease. However, there is no comprehensive research resource for PAH or other PH types that integrates various genetic studies and their related biological information. Thus, the number of associated genes, and their strength of evidence, is unclear. In this study, we tested the hypothesis that a web-based knowledgebase could be used to develop a biological map of highly interrelated, functionally important genes in PAH. We developed the pulmonary arterial hypertension knowledgebase (PAHKB, ), a comprehensive database with a user-friendly web interface. PAHKB extracts genetic data from all available sources, including those from association studies, genetic mutation, gene expression, animal model, supporting literature, various genomic annotations, gene networks, cellular and regulatory pathways, as well as microRNAs. Moreover, PAHKB provides online tools for data browsing and searching, data integration, pathway graphical presentation, and gene ranking. In the current release, PAHKB contains 341 human PH-related genes (293 protein coding and 48 non-coding genes) curated from over 1000 PubMed abstracts. Based on the top 39 ranked PAH-related genes in PAHKB, we constructed a core biological map. This core map was enriched with the TGF-beta signaling pathway, focal adhesion, cytokine-cytokine receptor interaction, and MAPK signaling. In addition, the reconstructed map elucidates several novel cancer signaling pathways, which may provide clues to support the application of anti-cancer therapeutics to PAH. In summary, we have developed a system for the identification of core PH-related genes and identified critical signaling pathways that may be relevant to PAH pathogenesis. This system can be easily applied to other pulmonary diseases.
The vaccine safety advice network is a collaborative pilot project between Vanderbilt University Medical Center, the Tennessee Department of Health, and the Centers for Disease Control and Prevention to assess the feasibility of addressing vaccine safety questions posed by healthcare providers in near real-time. Using a two-tier response system and an electronic database for query submission, the pilot project received ten queries in three and one half months. Two of three pre-specified benchmarks for program evaluation, addressing queries within 24 h of receipt and 100% provider satisfaction, were met; one benchmark, the percentage of questions addressed by Tier 1 staff, was not met. Limitations included few submitted queries primarily involving children in the pilot period, "after-only" program evaluation, and limited geographic generalizability. The study demonstrates a successful partnership between federal, state and academic institutions and a feasible method to respond to healthcare provider inquiries about vaccine safety in near real-time.
Copyright © 2014 Elsevier Ltd. All rights reserved.
Copy number variation (CNV) is one of the most prevalent genetic variations in the genome, leading to an abnormal number of copies of moderate to large genomic regions. High-throughput technologies such as next-generation sequencing often identify thousands of CNVs involved in biological or pathological processes. Despite the growing demand to filter and classify CNVs by factors such as frequency in population, biological features, and function, surprisingly, no online web server for CNV annotations has been made available to the research community. Here, we present CNVannotator, a web server that accepts an input set of human genomic positions in a user-friendly tabular format. CNVannotator can perform genomic overlaps of the input coordinates using various functional features, including a list of the reported 356,817 common CNVs, 181,261 disease CNVs, as well as, 140,342 SNPs from genome-wide association studies. In addition, CNVannotator incorporates 2,211,468 genomic features, including ENCODE regulatory elements, cytoband, segmental duplication, genome fragile site, pseudogene, promoter, enhancer, CpG island, and methylation site. For cancer research community users, CNVannotator can apply various filters to retrieve a subgroup of CNVs pinpointed in hundreds of tumor suppressor genes and oncogenes. In total, 5,277,234 unique genomic coordinates with functional features are available to generate an output in a plain text format that is free to download. In summary, we provide a comprehensive web resource for human CNVs. The annotated results along with the server can be accessed at http://bioinfo.mc.vanderbilt.edu/CNVannotator/.
OBJECTIVE - To determine mediators of 12-month outcomes of Internet interventions for youth with type 1 diabetes transitioning to adolescence.
METHODS - In this multisite clinical trial, 320 youth were randomized to one of two Internet-based interventions: Coping skills (TEENCOPE™) or diabetes education (Managing Diabetes). Mediators of the interventions' effects on glycosylated hemoglobin and quality of life were examined. Data were collected at baseline and at 3, 6, and 12 months.
RESULTS - Self-efficacy mediated treatment effects on quality of life in both interventions. For TEENCOPE™, stress reactivity, primary control coping, and secondary control coping mediated treatment effects, whereas for Managing Diabetes, social acceptance mediated treatment effects. There were no significant effects of either intervention on glycosylated hemoglobin.
CONCLUSIONS - 2 Internet interventions for youth with type 1 diabetes resulted in improved quality of life by different mechanisms, suggesting components of both diabetes education and coping skills may help to achieve better outcomes in youth with type 1 diabetes.
Genome-wide association studies (GWAS) have rapidly become a powerful tool in genetic studies of complex diseases and traits. Traditionally, single marker-based tests have been used prevalently in GWAS and have uncovered tens of thousands of disease-associated SNPs. Network-assisted analysis (NAA) of GWAS data is an emerging area in which network-related approaches are developed and utilized to perform advanced analyses of GWAS data in order to study various human diseases or traits. Progress has been made in both methodology development and applications of NAA in GWAS data, and it has already been demonstrated that NAA results may enhance our interpretation and prioritization of candidate genes and markers. Inspired by the strong interest in and high demand for advanced GWAS data analysis, in this review article, we discuss the methodologies and strategies that have been reported for the NAA of GWAS data. Many NAA approaches search for subnetworks and assess the combined effects of multiple genes participating in the resultant subnetworks through a gene set analysis. With no restriction to pre-defined canonical pathways, NAA has the advantage of defining subnetworks with the guidance of the GWAS data under investigation. In addition, some NAA methods prioritize genes from GWAS data based on their interconnections in the reference network. Here, we summarize NAA applications to various diseases and discuss the available options and potential caveats related to their practical usage. Additionally, we provide perspectives regarding this rapidly growing research area.
PURPOSE - Survival from Wilms Tumor (WT) exceeds 90% at 5 years in developed nations, whereas at last report, 2-year event-free survival (EFS) in Kenya reached only 35%. To clarify factors linked to these poor outcomes in Kenya, we established a comprehensive web-based WT registry, comprised of patients from the four primary hospitals treating childhood cancers.
MATERIALS AND METHODS - WT patients diagnosed between January 2008 and January 2012 were identified. Files were abstracted for demographic characteristics, treatment regimens, and enrollment in the Kenyan National Hospital Insurance Fund (NHIF). Children under 15 years of age having both a primary kidney tumor on imaging and concordant histology consistent with WT were included.
RESULTS - Two-year event-free survival (EFS) was 52.7% for all patients (n=133), although loss to follow up (LTFU) was 50%. For the 33 patients who completed all scheduled standard therapy, 2-year EFS was 94%. Patients enrolled in NHIF tended to complete more standard therapy and had a lower hazard of death (Cox 0.192, p < 0.001).
CONCLUSION - Survival of Kenyan WT patients has increased slightly since last report. Notably, WT patients completing all phases of standard therapy experienced 2-year survival approaching the benchmarks of developed nations. Efforts in Kenya should be made to enhance compliance with WT treatment through NHIF enrollment.
Copyright © 2013 Elsevier Inc. All rights reserved.