Development of a cloud-based Bioinformatics Training Platform

First published online: April 15, 2016The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP.Jerico Revote, Nathan S. Watson-Haigh, Steve Quenette, Blair Bethwaite, Annette McGrath and Catherine A. Shan

Low density of CD3+, CD4+ and CD8+ cells is associated with increased risk of relapse in squamous cell cervical cancer

The purpose of this study was to investigate the prognostic value of the primary in situ cellular immune response in cervical squamous cell carcinoma. A study of 102 women treated for stage IB and IIA disease, between 1990 and 2000, was performed. Paraffin-embedded cervical tissue processed at the time of diagnosis was immunostained for CD3+ (T cells), CD4+ (T helper/regulatory T cells) and CD8+ (cytotoxic T cells) cells. Immune cell profile densities were estimated using stereology. Both intra- and peritumoural cell densities were estimated. Using Cox's proportional hazards regression modelling we found an increase in cell density to decrease the risk of relapse for all three cell types. The density of peritumoural CD3+ cells seems to have the strongest potential for predicting relapse. An increase in CD3+ cell density from 795 to 2043 cells per mm2 (25–75 percentile) reduced the hazard ratio to 0.27

CD1a-positive infiltrating-dendritic cell density and 5-year survival from human breast cancer

© Churchill LivingstoneInfiltrating CD1a+ dendritic cells (DCs) have been associated with increased survival in a number of human cancers. This study investigated DC infiltration within breast cancers and the association with survival. Classical established prognostic factors, of tumour size, lymph node status, histological grade, lympho-vascular invasion, the KI-67 (MIB-1) fraction and the Nottingham Prognostic Index (NPI) were also compared. A total of 48 breast cancer patients were followed from the time of surgery and CD1a density analysis for 5 years or until death. Our data set validated previous studies, which show a relationship between survival and the NPI (P<0.001), tumour size (P<0.01) and lymph node status (P<0.05). Although more patients were alive at the 5-year time point in the group with higher CD1a DC density than the lower CD1a DC group, this failed to reach statistical significance at the P=0.05 level. Analysis at 10 years postsurgery is required to investigate the association further.B.J.Coventry and J. Morto

Eosinophils in glioblastoma biology

Glioblastoma multiforme (GBM) is the most common primary brain tumor in adults. The development of this malignant glial lesion involves a multi-faceted process that results in a loss of genetic or epigenetic gene control, un-regulated cell growth, and immune tolerance. Of interest, atopic diseases are characterized by a lack of immune tolerance and are inversely associated with glioma risk. One cell type that is an established effector cell in the pathobiology of atopic disease is the eosinophil. In response to various stimuli, the eosinophil is able to produce cytotoxic granules, neuromediators, and pro-inflammatory cytokines as well as pro-fibrotic and angiogenic factors involved in pathogen clearance and tissue remodeling and repair. These various biological properties reveal that the eosinophil is a key immunoregulatory cell capable of influencing the activity of both innate and adaptive immune responses. Of central importance to this report is the observation that eosinophil migration to the brain occurs in response to traumatic brain injury and following certain immunotherapeutic treatments for GBM. Although eosinophils have been identified in various central nervous system pathologies, and are known to operate in wound/repair and tumorstatic models, the potential roles of eosinophils in GBM development and the tumor immunological response are only beginning to be recognized and are therefore the subject of the present review

Grid interoperability: an experiment in bridging Grid islands

In the past decade Grid computing has matured considerably. A number of groups have built, operated, and expanded large testbed and production Grids. These Grids have inevitably been designed to meet the needs of a limited set of initial stakeholders, resulting in varying and sometimes adhoc specifications. As the use of e-Science becomes more common, this inconsistency is increasingly problematic for the growing set of applications requiring more resources than a single Grid can offer, as spanning these Grid islands is far from trivial. Thus, Grid interoperability is attracting much interest as researchers try to build bridges between separate Grids. Recently we ran a case study that tested interoperation between several Grids, during which we recorded and classified the issues that arose. In this paper we provide empirical evidence supporting existing interoperability efforts, and identify current and potential barriers to Grid interoperability

A reflection on the origins, evolution, and future of PRAGMA

All of the papers in this special collection have been shaped by and/or have helped shape PRAGMA. This paper, a reflection on PRAGMA, will provide additional technical, scientific and human context to many of these papers. We hope to illustrate that it is the people who set directions by following their interests or posing questions, who make progress by honoring their commitments, and who build community by establishing open communications and trust