GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

Abstract Background: Most successful computational approaches for protein function prediction integrate multiple genomics and proteomics data sources to make inferences about the function of unknown proteins. The most accurate of these algorithms have long running times, making them unsuitable for real-time protein function prediction in large genomes. As a result, the predictions of these algorithms are stored in static databases that can easily become outdated. We propose a new algorithm, GeneMANIA, that is as accurate as the leading methods, while capable of predicting protein function in real-time. Results: We use a fast heuristic algorithm, derived from ridge regression, to integrate multiple functional association networks and predict gene function from a single process-specific network using label propagation. Our algorithm is efficient enough to be deployed on a modern webserver and is as accurate as, or more so than, the leading methods on the MouseFunc I benchmark and a new yeast function prediction benchmark; it is robust to redundant and irrelevant data and requires, on average, less than ten seconds of computation time on tasks from these benchmarks. Conclusion: GeneMANIA is fast enough to predict gene function on-the-fly while achieving state-of-the-art accuracy. A prototype version of a GeneMANIA-based webserver is available at http://morrislab.med.utoronto.ca/prototype

Continuity of medication management in Medicaid patients with chronic comorbid conditions: An examination by mental health status

Patients with serious mental illness (SMI) often have comorbid cardiometabolic conditions (CMCs) that may increase the number of prescribers involved in treatment. This study examined whether patients with SMI (depression and schizophrenia) and comorbid CMCs experience greater discontinuity of prescribing than patients with CMCs alone

Invasive Pneumococcal Pneumonia and Respiratory Virus Co-infections

Each year, especially in the winter, many get sick and some die of invasive pneumococcal pneumonia. Does this type of pneumonia increase in the winter because people are in closer contact indoors?  Or are people more susceptible to this bacterial disease after having had a seasonal respiratory virus infection?  A season-by-season analysis found an association between pneumococcal pneumonia and two viruses (influenza and respiratory syncytial virus). The association varied by season and was strongest when the predominant influenza virus subtype was H3N2. Vaccination against influenza and RSV should also help protect against pneumococcal pneumonia

Prostitution, Condom Use, and Invasive Squamous Cell Cervical Cancer in Thailand

Cervical cancer is probably caused by a sexually transmitted agent. A case-control study was conducted in three hospitals in Thailand to investigate further the role of male sexual behavior, particularly regarding sexual contacts with prostitutes, in the development of this disease. Data were obtained from interviews with 225 married women with invasive squamous cell cervical carcinoma and 791 hospitalized controls, all of whom reported having only one sexual partner, and from interviews with their husbands. Risk of cervical cancer was strongly related to the women's husbands having visited prostitutes without using a condom when the husbands were less than 30 years old. A strong increasing trend in risk in relation to decreasing frequency of the husbands' condom use with prostitutes was observed, and a weaker increasing trend in risk with husbands' estimated lifetime total number of visits to prostitutes was found. The average latent period between the women's likely initial exposure to a sexually transmitted oncogenic agent and her diagnosis of invasive cervical cancer was about a quarter of a century. Regular use of condoms by customers of prostitutes could reduce the number of invasive cervical cancer cases in the general population of Thailand by at least one fourth. Am J Epidemiol 1996; 143: 779-8

‘Growing your own’: a multi-level modelling approach to understanding personal food growing trends and motivations in Europe

Growing food for personal and family consumption is a significant global activity, but one that has received insufficient academic attention, particularly in developed countries. This paper uses data from the European Quality of Life Survey (EQLS) to address three areas of particular concern: the prevalence of growing your own food and how this has changed over time; the individual and household context in which growing takes place; and whether those who grow their own food are happier than those who do not. Results showed that there was a marked increase in growing your own food in Europe, in the period 2003–2007. This increase is largely associated with poorer households and thus, possibly, economic hardship. In the UK however the increase in growing your own food is predominantly associated with older middle class households. Across Europe, whether causal or not, those who grew their own were happier than those who did not. The paper therefore concludes that claims about the gentrification of growing your own may be premature. Despite contrary evidence from the UK, the dominant motive across Europe appears to be primarily economic — to reduce household expenditure whilst ensuring a supply of fresh food

Multifaceted value profiles of forest owner categories in South Sweden: The river helge å catchment as a case study

Forest landscapes provide benefits from a wide range of goods, function and intangible values. But what are different forest owner categories\u27 profiles of economic use and non-use values? This study focuses on the complex forest ownership pattern of the River Helge å catchment including the Kristianstad Vattenrike Biosphere Reserve in southern Sweden. We made 89 telephone interviews with informants representing the four main forest owner categories. Our mapping included consumptive and non-consumptive direct use values, indirect use values, and non-use values such as natural and cultural heritage. While the value profiles of non-industrial forest land owners and municipalities included all value categories, the forest companies focused on wood production, and the Swedish Environmental Protection Agency on nature protection. We discuss the challenges of communicating different forest owners\u27 economic value profiles among stakeholders, the need for a broader suite of forest management systems, and fora for collaborative planning. © 2013 The Author(s)