Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives

The use of induced pluripotent stem cells (iPSC) derived from independent patients and sources holds considerable promise to improve the understanding of development and disease. However, optimized use of iPSC depends on our ability to develop methods to efficiently qualify cell lines and protocols, monitor genetic stability, and evaluate self-renewal and differentiation potential. To accomplish these goals, 57 stem cell lines from 10 laboratories were differentiated to 7 different states, resulting in 248 analyzed samples. Cell lines were differentiated and characterized at a central laboratory using standardized cell culture methodologies, protocols, and metadata descriptors. Stem cell and derived differentiated lines were characterized using RNA-seq, miRNA-seq, copy number arrays, DNA methylation arrays, flow cytometry, and molecular histology. All materials, including raw data, metadata, analysis and processing code, and methodological and provenance documentation are publicly available for re-use and interactive exploration at https://www.synapse.org/pcbc. The goal is to provide data that can improve our ability to robustly and reproducibly use human pluripotent stem cells to understand development and disease

The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community

The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data. All of these data are freely available at http://www.aspgd.org. We welcome feedback from users and the research community at [email protected]

WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization

In this paper we present the open-source WikiPathways app for Cytoscape http://apps.cytoscape.org/apps/wikipathways) that can be used to import biological pathways for data visualization and network analysis. an open, collaborative biological pathway database that provides fully pathway diagrams for manual download or through web services. The app allows users to load pathways in two different views: as an ideal for data visualization and as a simple network to perform analysis. An example pathway and dataset are used to demonstrate the functionality of the WikiPathways app and how they can be combined and together with other apps. More than 3000 downloads in the first 12 following its release in August 2013 highlight the importance and app in the network biology field

Improving Access and Inclusion in Employment for People with Disabilities: Implementation of Workplace Adjustments in ‘Best-Practice’ Organisations

The Centre for Workplace Leadership (CWL), in consultation with the Australian Network on Disability (AND) and with funding from the Hallmark Disability Research Initiative at the University of Melbourne, embarked on research to: disseminate information about best practice in implementing workplace adjustments; make a meaningful contribution to disability rights advocacy in the employment sphere; facilitate meaningful engagement between academic enquiry and business practice; and aid the pursuit of self-determination and full and equal participation in society by people with disabilities. To achieve these aims, we conducted interviews of managers and employees with disabilities in ‘best-practice’ organisations in Australia

Population-level impact of active tuberculosis case finding in an Asian megacity.

BACKGROUND: The potential population-level impact of private-sector initiatives for tuberculosis (TB) case finding in Southeast Asia remains uncertain. In 2011, the Indus Hospital TB Control Program in Karachi, Pakistan, undertook an aggressive case-finding campaign that doubled notification rates, providing an opportunity to investigate potential population-level effects. METHODS: We constructed an age-structured compartmental model of TB in the intervention area. We fit the model using field and literature data, assuming that TB incidence equaled the estimated nationwide incidence in Pakistan (primary analysis), or 1.5 times greater (high-incidence scenario). We modeled the intervention as an increase in the rate of formal-sector TB diagnosis and evaluated the potential impact of sustaining this rate for five years. RESULTS: In the primary analysis, the five-year intervention averted 24% (95% uncertainty range, UR: 18-30%) of five-year cumulative TB cases and 52% (95% UR: 45-57%) of cumulative TB deaths. Corresponding reductions in the high-incidence scenario were 12% (95% UR: 8-17%) and 27% (95% UR: 21-34%), although the absolute number of lives saved was higher. At the end of five years, TB notification rates in the primary analysis were below their 2010 baseline, incidence had dropped by 45%, and annual mortality had fallen by 72%. About half of the cumulative impact on incidence and mortality could be achieved with a one-year intervention. CONCLUSIONS: Sustained, multifaceted, and innovative approaches to TB case-finding in Asian megacities can have substantial community-wide epidemiological impact

Transmission Model of Tuberculosis in Karachi, Pakistan.

<p>Boxes represent compartments in the model, and arrows represent rates of flow, which are modeled as ordinary differential equations. Not shown here, but included in the model, are 9 age classes and TB-specific mortality occurring from each active TB compartment.</p