Collaborative e-science architecture for Reaction Kinetics research community

This paper presents a novel collaborative e-science architecture (CeSA) to address two challenging issues in e-science that arise from the management of heterogeneous distributed environments: (i) how to provide individual scientists an integrated environment to collaborate with each other in distributed, loosely coupled research communities where each member might be using a disparate range of tools; and (ii) how to provide easy access to a range of computationally intensive resources from a desktop. The Reaction Kinetics research community was used to capture the requirements and in the evaluation of the proposed architecture. The result demonstrated the feasibility of the approach and the potential benefits of the CeSA

A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer.

BACKGROUND: Molecular profiling of the tumour immune microenvironment (TIME) has enabled the rational choice of immunotherapies in some adult cancers. In contrast, the TIME of paediatric cancers is relatively unexplored. We speculated that a more refined appreciation of the TIME in childhood cancers, rather than a reliance on commonly used biomarkers such as tumour mutation burden (TMB), neoantigen load and PD-L1 expression, is an essential prerequisite for improved immunotherapies in childhood solid cancers. METHODS: We combined immunohistochemistry (IHC) with RNA sequencing and whole-genome sequencing across a diverse spectrum of high-risk paediatric cancers to develop an alternative, expression-based signature associated with CD8+ T-cell infiltration of the TIME. Furthermore, we explored transcriptional features of immune archetypes and T-cell receptor sequencing diversity, assessed the relationship between CD8+ and CD4+ abundance by IHC and deconvolution predictions and assessed the common adult biomarkers such as neoantigen load and TMB. RESULTS: A novel 15-gene immune signature, Immune Paediatric Signature Score (IPASS), was identified. Using this signature, we estimate up to 31% of high-risk cancers harbour infiltrating T-cells. In addition, we showed that PD-L1 protein expression is poorly correlated with PD-L1 RNA expression and TMB and neoantigen load are not predictive of T-cell infiltration in paediatrics. Furthermore, deconvolution algorithms are only weakly correlated with IHC measurements of T-cells. CONCLUSIONS: Our data provides new insights into the variable immune-suppressive mechanisms dampening responses in paediatric solid cancers. Effective immune-based interventions in high-risk paediatric cancer will require individualised analysis of the TIME.Chelsea Mayoh, Andrew J. Gifford, Rachael Terry, Loretta M. S. Lau, Marie Wong, Padmashree Rao, Tyler Shai, Hee, Federica Saletta, Dong, Anh Khuong, Quang, Vicky Qin, Marion K. Mateos, Deborah Meyran, Katherine E. Miller, Aysen Yuksel, Emily V. A. Mould, Rachel Bowen, James, Dinisha Govender, Akanksha Senapati, Nataliya Zhukova, Natacha Omer, Hetal Dholaria, Frank Alvaro, Heather Tapp, Yonatan Diamond, Luciano Dalla Pozza, Andrew S. Moore, Wayne Nicholls, Nicholas G. Gottardo, Geoffrey McCowage, Jordan R. Hansford, Seong, Lin Khaw, Paul J. Wood, Daniel Catchpoole, Catherine E. Cottrell, Elaine R. Mardis, Glenn M. Marshall, Vanessa Tyrrell, Michelle Haber, David S. Ziegler, Orazio Vittorio, Joseph A. Trapani, Mark J. Cowley, Paul J. Neeson, and Paul G. Eker

Use of Virtual Science Park resource rooms to support group work in a learning environment

This paper presents a detailed evaluation on the acceptability of a range of synchronous and asynchronous collaborative tools provided within the Virtual Science Park (VSP) for group work in a learning environment. In this study, the VSP was used to provide a web-based 'Resource Room' adopting the familiar 'folder' metaphor for structuring and linking resources, and a number of different user interfaces for interaction and sharing information. A list of criteria is established for the evaluation. By using scenario testing and structured questionnaires, qualitative feedback was collected from 43 Masters students. The findings reinforce and add to the concerns highlighted in other studies, in particular, the importance for shared awareness, privacy, conventions for interaction and the provision of an effective multimedia environment. More attention will be needed in these areas for effective use of these groupware tools