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Nygard A.-B.,Copenhagen University | Cirera S.,Copenhagen University | Gilchrist M.J.,NIMR | Gorodkin J.,Copenhagen University | And 2 more authors.
BMC Research Notes

Background. Since at least half of the genes in mammalian genomes are subjected to alternative splicing, alternative pre-mRNA splicing plays an important contribution to the complexity of the mammalian proteome. Expressed sequence tags (ESTs) provide evidence of a great number of possible alternative isoforms. With the EST resource for the domestic pig now containing more than one million porcine ESTs, it is possible to identify alternative splice forms of the individual transcripts in this species from the EST data with some confidence. Results. The pig EST data generated by the Sino-Danish Pig Genome project has been assembled with publicly available ESTs and made available in the PigEST database. Using the Distiller package 2,515 EST clusters with candidate alternative isoforms were identified in the EST data with high confidence. In agreement with general observations in human and mouse, we find putative splice variants in about 30% of the contigs with more than 50 ESTs. Based on the criteria that a minimum of two EST sequences confirmed each splice event, a list of 100 genes with the most distinct tissue-specific alternative splice events was generated from the list of candidates. To confirm the tissue specificity of the splice events, 10 genes with functional annotation were randomly selected from which 16 individual splice events were chosen for experimental verification by quantitative PCR (qPCR). Six genes were shown to have tissue specific alternatively spliced transcripts with expression patterns matching those of the EST data. The remaining four genes had tissue-restricted expression of alternative spliced transcripts. Five out of the 16 splice events that were experimentally verified were found to be putative pig specific. Conclusions. In accordance with human and rodent studies we estimate that approximately 30% of the porcine genes undergo alternative splicing. We found a good correlation between EST predicted tissue-specificity and experimentally validated splice events in different porcine tissue. This study indicates that a cluster size of around 50 ESTs is optimal for in silico detection of alternative splicing. Although based on a limited number of splice events, the study supports the notion that alternative splicing could have an important impact on species differentiation since 31% of the splice events studied appears to be species specific. © 2010 Fredholm et al; licensee BioMed Central Ltd. Source

Rumeau P.,Toulouse University Hospital Center | Vigouroux N.,Toulouse University Hospital Center | Vigouroux N.,French National Center for Scientific Research | Boudet B.,Toulouse University Hospital Center | And 5 more authors.
3rd IEEE International Conference on Cognitive Infocommunications, CogInfoCom 2012 - Proceedings

Companion robots could have potential to help and improve the daily living of home-dwelling disabled elderly people and of their caregivers. Robots allow deployment with a lesser impact on the home of the user and mobility to bring communication or support where it's needed. As part of AAL DOMEO project we tested a doubt removal service to allow the main caregiver of a couple of nonagenarians with motor and cognitive impairment assess the status of her parents when she is in her own home and suspects a problem. We will present the methodology, including ethical aspects, and preliminary results. We will discuss the issues that arose from the confrontation of the technical requirements and the sociocultural background when a service based on cognitive infocommunications is required to cope with cognitive impairment and adapt to the requirements of patients and caregivers alike. © 2012 IEEE. Source

Feldblum P.J.,Family Health International | Lie C.-C.,Family Health International | Weaver M.A.,Family Health International | Van Damme L.,Family Health International | And 6 more authors.
Sexually Transmitted Diseases

Background: Analyzing pooled data from 4 recent microbicide trials, we aimed to determine characteristics of participants at higher risk of HIV and sexually transmitted infections (STIs), to inform targeted recruitment, preserved study power, and potentially smaller study sizes in future trials. Methods: We evaluated the relationships between participants? characteristics and the incidence of HIV, STIs, and reproductive tract infections (RTIs). We calculated incidence rates as the number of infection events divided by the person-years of observation. We applied Cox regression models to assess the relationships between baseline demographic, reproductive and behavioral factors and incident HIV, STIs and RTIs. Results: The pooled incidence rates for HIV, chlamydia, and gonorrhea were 2.1, 6.4 and 9.9 per 100 person-years, respectively. Proportions of participants with trichomoniasis, bacterial vaginosis (BV), and candidiasis were 0.06, 0.40, and 0.40, respectively. In final multivariable models, age and education were significantly (and inversely) associated with incident HIV; baseline chlamydia, baseline trichomoniasis, and younger age were associated with incident Chlamydia; and baseline gonorrhea infection, younger age, less education, nulliparous status, baseline chlamydia, and condom use for contraception were associated with incident gonorrhea. Three factors were associated with trichomoniasis: baseline trichomoniasis infection, baseline chlamydia, and baseline BV. CONCLUSIONS:: Only younger age was robustly associated with multiple STI outcomes in our multivariable analyses. Although there was little evidence of associations between baseline STIs and incident HIV, they were strongly associated with incident STIs. We found no evidence that measured baseline sexual behavior factors were associated with incident HIV or STIs. Copyright © 2010 American Sexually Transmitted Diseases Association All rights reserved. Source

Mbilinyi D.,NIMR | Daniel M.L.,University of Bergen | Lie G.T.,University of Bergen
BMC Health Services Research

Background: Health worker motivation can potentially affect the provision of health services. The HIV pandemic has placed additional strain on health service provision through the extra burden of increased testing and counselling, treating opportunistic infections and providing antiretroviral treatment. The aim of this paper is to explore the challenges generated by HIV care and treatment and their impact on health worker motivation in Mbeya Region, Tanzania. Methods. Thirty in-depth interviews were conducted with health workers across the range of health care professions in health facilities in two high HIV-prevalence districts of Mbeya Region, Tanzania. A qualitative framework analysis was adopted for data analysis. Results: The negative impact of HIV-related challenges on health worker motivation was confirmed by this study. Training seminars and workshops related to HIV contributed to the shortage of health workers in the facilities. Lower status workers were frequently excluded from training and were more severely affected by the consequent increase in workload as seminars were usually attended by higher status professionals who controlled access. Constant and consistent complaints by clients have undermined health workers' expectations of trust and recognition. Health workers were forced to take responsibility for dealing with problems arising from organisational inefficiencies within the health system. Conclusion: HIV-related challenges undermine motivation among health workers in Mbeya, Tanzania with the burden falling most heavily on lower status workers. Strained relations between health workers and the community they serve, further undermine motivation of health workers. © 2011 Mbilinyi et al; licensee BioMed Central Ltd. Source

James Briscoe has a BSc in Microbiology and Virology (from the University of Warwick, UK) and a PhD in Molecular and Cellular Biology (from the Imperial Cancer Research Fund, London, now Cancer Research UK). He started working on the development of the neural tube in the lab of Tom Jessel as a postdoctoral fellow, establishing that there was graded sonic hedgehog signaling in the ventral neural tube. He is currently a group leader and Head of Division in Developmental Biology at the MRC National Institute for Medical Research (which will become part of the Francis Crick Institute in April 2015). He is working to understand the molecular and cellular mechanisms of graded signaling in the vertebrate neural tube. We interviewed him about the development of ideas on morphogenetic gradients and his own work on modeling the development of the neural tube for our series on modeling in biology. © 2015 Briscoe. Source

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