Implementation of GenePattern within the Stanford Microarray Database

Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability

TB database: an integrated platform for tuberculosis research

The effective control of tuberculosis (TB) has been thwarted by the need for prolonged, complex and potentially toxic drug regimens, by reliance on an inefficient vaccine and by the absence of biomarkers of clinical status. The promise of the genomics era for TB control is substantial, but has been hindered by the lack of a central repository that collects and integrates genomic and experimental data about this organism in a way that can be readily accessed and analyzed. The Tuberculosis Database (TBDB) is an integrated database providing access to TB genomic data and resources, relevant to the discovery and development of TB drugs, vaccines and biomarkers. The current release of TBDB houses genome sequence data and annotations for 28 different Mycobacterium tuberculosis strains and related bacteria. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives. TBDB currently hosts data for nearly 1500 public tuberculosis microarrays and 260 arrays for Streptomyces. In addition, TBDB provides access to a suite of comparative genomics and microarray analysis software. By bringing together M. tuberculosis genome annotation and gene-expression data with a suite of analysis tools, TBDB (http://www.tbdb.org/) provides a unique discovery platform for TB research

TB database: an integrated platform for tuberculosis research

The effective control of tuberculosis (TB) has been thwarted by the need for prolonged, complex and potentially toxic drug regimens, by reliance on an inefficient vaccine and by the absence of biomarkers of clinical status. The promise of the genomics era for TB control is substantial, but has been hindered by the lack of a central repository that collects and integrates genomic and experimental data about this organism in a way that can be readily accessed and analyzed. The Tuberculosis Database (TBDB) is an integrated database providing access to TB genomic data and resources, relevant to the discovery and development of TB drugs, vaccines and biomarkers. The current release of TBDB houses genome sequence data and annotations for 28 different Mycobacterium tuberculosis strains and related bacteria. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives. TBDB currently hosts data for nearly 1500 public tuberculosis microarrays and 260 arrays for Streptomyces. In addition, TBDB provides access to a suite of comparative genomics and microarray analysis software. By bringing together M. tuberculosis genome annotation and gene-expression data with a suite of analysis tools, TBDB (http://www.tbdb.org/) provides a unique discovery platform for TB research

Developing lay health worker policy in South Africa: a qualitative study

<p>Abstract</p> <p>Background</p> <p>Over the past half decade South Africa has been developing, implementing and redeveloping its Lay Health Worker (LHW) policies. Research during this period has highlighted challenges with LHW programme implementation. These challenges have included an increased burden of care for female LHWs. The aim of this study was to explore contemporary LHW policy development processes and the extent to which issues of gender are taken up within this process.</p> <p>Methods</p> <p>The study adopted a qualitative approach to exploring policy development from the perspective of policy actors. Eleven policy actors (policy makers and policy commentators) were interviewed individually. Data from the interviews were analysed thematically.</p> <p>Results</p> <p>Considerations of LHW working conditions drove policy redevelopment. From the interviews it seems that gender as an issue never reached the policy making agenda. Although there was strong recognition that the working conditions of LHWs needed to be improved, poor working conditions were not necessarily seen as a gender concern. Our data suggests that in the process of defining the problem which the redeveloped policy had to address, gender was not included. There was no group or body who brought the issue of gender to the attention of policy developers. As such the issue of gender never entered the policy debates. These debates focused on whether it was appropriate to have LHWs, what LHW programme model should be adopted and whether or not LHWs should be incorporated into the formal health system.</p> <p>Conclusion</p> <p>LHW policy redevelopment focused on resolving issues of LHW working conditions through an active process involving many actors and strong debates. Within this process the issue of gender had no champion and never reached the LHW policy agenda. Future research may consider how to incorporate the voices of ordinary women into the policy making process.</p

Mouse SPNS2 Functions as a Sphingosine-1-Phosphate Transporter in Vascular Endothelial Cells

Sphingosine-1-phosphate (S1P), a sphingolipid metabolite that is produced inside the cells, regulates a variety of physiological and pathological responses via S1P receptors (S1P1–5). Signal transduction between cells consists of three steps; the synthesis of signaling molecules, their export to the extracellular space and their recognition by receptors. An S1P concentration gradient is essential for the migration of various cell types that express S1P receptors, such as lymphocytes, pre-osteoclasts, cancer cells and endothelial cells. To maintain this concentration gradient, plasma S1P concentration must be at a higher level. However, little is known about the molecular mechanism by which S1P is supplied to extracellular environments such as blood plasma. Here, we show that SPNS2 functions as an S1P transporter in vascular endothelial cells but not in erythrocytes and platelets. Moreover, the plasma S1P concentration of SPNS2-deficient mice was reduced to approximately 60% of wild-type, and SPNS2-deficient mice were lymphopenic. Our results demonstrate that SPNS2 is the first physiological S1P transporter in mammals and is a key determinant of lymphocyte egress from the thymus

The evolution of HIV policy in Vietnam: from punitive control measures to a more rights-based approach

Aim: Policymaking in Vietnam has traditionally been the preserve of the political elite, not open to the scrutiny of those outside the Communist Party. This paper aims to analyse Vietnam&#x0027;s HIV policy development in order to describe and understand the policy content, policy-making processes, actors and obstacles to policy implementation. Methods: Nine policy documents on HIV were analysed and 17 key informant interviews were conducted in Hanoi and Quang Ninh Province, based on a predesigned interview guide. Framework analysis, a type of qualitative content analysis, was applied for data analysis. Results: Our main finding was that during the last two decades, developments in HIV policy in Vietnam were driven in a top-down way by the state organs, with support and resources coming from international agencies. Four major themes were identified: HIV policy content, the policy-making processes, the actors involved and human resources for policy implementation. Vietnam&#x0027;s HIV policy has evolved from one focused on punitive control measures to a more rights-based approach, encompassing harm reduction and payment of health insurance for medical costs of patients with HIV-related illness. Low salaries and staff reluctance to work with patients, many of whom are drug users and female sex workers, were described as the main barriers to low health staff motivation. Conclusion: Health policy analysis approaches can be applied in a traditional one party state and can demonstrate how similar policy changes take place, as those found in pluralistic societies, but through more top-down and somewhat hidden processes. Enhanced participation of other actors, like civil society in the policy process, is likely to contribute to policy formulation and implementation that meets the diverse needs and concerns of its population

Attrition among Human Immunodeficiency Virus (HIV)- Infected Patients Initiating Antiretroviral Therapy in China, 2003–2010

BACKGROUND: Mortality and morbidity from HIV have dramatically decreased in both high- and low-income countries. However, some patients may not benefit from combination antiretroviral therapy (cART) because of inadequate access to HIV care, including attrition after care initiation. METHODOLOGY/PRINCIPAL FINDINGS: The study population included all HIV-infected patients receiving cART through the Chinese National Free Antiretroviral Treatment Program from 1 January 2003 to 31 December 2010 (n = 106,542). We evaluated retention in HIV care and used multivariable Cox proportional hazard models to identify independent factors predictive of attrition. The cumulative probability of attrition from cART initiation was 9% at 12 months, 13% at 18 months, 16% at 24 months and 24% at 60 months. A number of factors were associated with attrition, including younger age, male gender, and being single or divorced. Patients with higher CD4 cell counts at cART initiation were more likely to drop out of HIV care. The proportion of patients remaining in HIV care increased in more recent calendar years and among patients who initiated modern cART regimens. CONCLUSIONS/SIGNIFICANCE: Retention in HIV care is essential for optimizing individual and public health outcomes. Attrition, even the degree observed in our study, can lead to premature morbidity and mortality, and possibly affect further transmission of HIV and HIV resistant drug variants. Effective strategies to promote retention in HIV care programs are needed. In China these strategies may include focusing particularly on younger male patients and those with higher CD4 cell counts at therapy initiation

A proposal for a CT driven classification of left colon acute diverticulitis

Computed tomography (CT) imaging is the most appropriate diagnostic tool to confirm suspected left colonic diverticulitis. However, the utility of CT imaging goes beyond accurate diagnosis of diverticulitis; the grade of severity on CT imaging may drive treatment planning of patients presenting with acute diverticulitis. The appropriate management of left colon acute diverticulitis remains still debated because of the vast spectrum of clinical presentations and different approaches to treatment proposed. The authors present a new simple classification system based on both CT scan results driving decisions making management of acute diverticulitis that may be universally accepted for day to day practice