Petro-mineralogical controls on coda attenuation in volcanic rock samples

ACKNOWLEDGEMENTS We thank Dr John Millett (Volcanic Basin Petroleum Research VBPR) for providing the rock samples, Dr Maxim Lebedev (Curtin University) for helping us with the acquisition of the µCT images, and Prof Andrew Putnis for his insights in the mineralogical description of the samples. We also thank the Aberdeen-Curtin Alliance (http://aberdeencurtinalliance.org/) for providing funding for this research. Part of this study was undertaken using the TIMA instrumentation (ARC LE140100150) at the John de Laeter Center, Curtin University. This work was supported by resources provided by the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. DATA AVAILABILITY The data underlying this paper are available in Mendeley Data, at http://dx.doi.org/10.17632/ysmt4kcjtn.2. Results-related data are available in the paper and its online supplementary material.Peer reviewedPublisher PD

Data ingestion pipeline and data marts to empower UK researchers, academics, and business and economic decision makers

The data integration problem from the voluminous data generated from different sources in disparate formats coupled with a large number of diverse requirements related to the data have made the need for a reconciliation of them into a unique model, the identification of relationships, and the enabling of data analytics processes extremely vital. In light of the unabated growth of data volume and the need for data sharing across various stakeholders there is a requirement for the design and implementation of a data ingestion pipeline with a set of data marts. In this paper, we present a data ingestion pipeline which empowers hitherto impeded data users to easily access shared big data sources. We aim to improve the effectiveness and efficiency of open 993source data sharing capability so that researchers, academics, policy makers, businesses and government departments can all benefit from the use of these sophisticated data management techniques. In this work, we propose a novel data ingestion pipeline and data marts approach to utilise data generated from big data systems and effectively integrate them to a unified form, ready for use. Currently, the data ingestion pipeline focuses on UK data, as our primary aim is to support the City of London and the various communities within it. An additional benefit is the potential for developing collaboration across disciplines to tackle the economic and social challenges faced by cities in innovative ways

IL‐4 induces proliferation in prostate cancer PC3 cells under nutrient‐depletion stress through the activation of the JNK‐pathway and survivin up‐regulation

Interleukin (IL)‐4 plays a critical role in the regulation of immune responses and has been detected at high levels in the tumor microenvironment of cancer patients where it correlates with the grade of malignancy. The direct effect of IL‐4 on cancer cells has been associated with increased cell survival; however, its role in cancer cell proliferation and related mechanisms is still unclear. Here it was shown that in a nutrient‐depleted environment, IL‐4 induces proliferation in prostate cancer PC3 cells. In these cells, under nutrient‐depletion stress, IL‐4 activates mitogen‐activated protein kinases (MAPKs), including Erk, p38, and JNK. Using MAP‐signaling‐specific inhibitors, it was shown that IL‐4‐induced proliferation is mediated by JNK activation. In fact, JNK‐inhibitor‐V (JNKi‐V) stunted IL‐4‐mediated cell proliferation. Furthermore, it was found that IL‐4 induces survivin up‐regulation in nutrient‐depleted cancer cells. Using survivin‐short‐hairpin‐RNAs (shRNAs), it was demonstrated that in this milieu survivin expression above a threshold limit is critical to the mechanism of IL‐4‐mediated proliferation. In addition, the significance of survivin up‐regulation in a stressed environment was assessed in prostate cancer mouse xenografts. It was found that survivin knockdown decreases tumor progression in correlation with cancer cell proliferation. Furthermore, under nutrient depletion stress, IL ‐4 could induce proliferation in cancer cells from multiple origins: MDA‐MB‐231 (breast), A253 (head and neck), and SKOV‐3 (ovarian). Overall, these findings suggest that in a tumor microenvironment under stress conditions, IL‐4 triggers a simultaneous activation of the JNK‐pathway and the up‐regulation of survivin turning on a cancer proliferation mechanism. J. Cell. Biochem. 113: 1569–1580, 2012. © 2011 Wiley Periodicals, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90542/1/24025_ftp.pd

Transcription factors OVOL1 and OVOL2 induce the mesenchymal to epithelial transition in human cancer

Cell plasticity regulated by the balance between the mesenchymal to epithelial transition (MET) and the opposite program, EMT, is critical in the metastatic cascade. Several transcription factors (TFs) are known to regulate EMT, though the mechanisms of MET remain unclear. We demonstrate a novel function of two TFs, OVOL1 and OVOL2, as critical inducers of MET in human cancers. Our findings indicate that the OVOL-TFs control MET through a regulatory feedback loop with EMT-inducing TF ZEB1, and the regulation of mRNA splicing by inducing Epithelial Splicing Regulatory Protein 1 (ESRP1). Using mouse prostate tumor models we show that expression of OVOL-TFs in mesenchymal prostate cancer cells attenuates their metastatic potential. The role of OVOL-TFs as inducers of MET is further supported by expression analyses in 917 cancer cell lines, suggesting their role as crucial regulators of epithelial-mesenchymal cell plasticity in cancer

Perspectives on Linkage Involving Indigenous data

Topic: Perspectives on Linkage Involving Indigenous data Indigenous populations across the globe are reaffirming their sovereignty rights in the collection and use of Indigenous data. The Indigenous data sovereignty movement has been widely influential and can be unsettling for those who routinely use population-level linked data that include Indigenous identifiers. Ethical policies that stipulate community engagement for access, interpretation and dissemination of Indigenous data create an enabling environment through the critical process of negotiating and navigating data access in partnership with communities. This session will be designed to create space for leading Indigenous voices to set the tone for the discussion around Indigenous population data linkage. Objectives: • To provide participants with an opportunity to build on the themes of Indigenous Data Sovereignty presented in the keynote session as they apply to diverse Indigenous populations. • To explore approaches to the linkage of Indigenous-identified population data across four countries, including First Nations in three Canadian regions. • To share practical applications of Indigenous data sovereignty on data linkage and analysis and discussion. • To center Indigenous-driven data linkage and research. Facilitator: Jennifer Walker. Canada Research Chair in Indigenous Health, Laurentian University and Indigenous Lead, Institute for Clinical Evaluative Sciences. Collaborators: • Alberta: Bonnie Healy, Tina Apsassin, Chyloe Healy and William Wadsworth (Alberta First Nations Information Governance Centre) • Ontario: Carmen R. Jones (Chiefs of Ontario) and Jennifer Walker (Institute for Clinical Evaluative Sciences) • British Columbia: Jeff Reading (Providence Health Centre) and Laurel Lemchuk-Favel (First Nations Health Authority) • Australia: Raymond Lovett (Australian National University) • Aotearoa / New Zealand: Donna Cormack (University of Otago) • United States: Stephanie Rainie and Desi Rodriguez-Lonebear (University of Arizona) Session format: 90 minutes Collaborators will participate in a round-table introduction to the work they are doing. Collaborators will discuss the principles underlying their approaches to Indigenous data linkage as well as practical and concrete solutions to challenges. Questions to guide the discussion will be pre-determined by consensus among the collaborators and the themes will include: data governance, community engagement, Indigenous-led linkage and analysis of data, and decision-making regarding access to linked data. Other participants attending the session will be encouraged to listen and will have an opportunity to engage in the discussion and ask questions. Intended output or outcome: The key outcome of the session will be twofold. First, those actively working with Indigenous linked data will have an opportunity for an in-depth and meaningful dialogue about their work, which will promote international collaboration and sharing of ideas. Second, those with less experience and knowledge of the principles of Indigenous data sovereignty and their practical application will have an opportunity to listen to Indigenous people who are advancing the integration of Indigenous ways of knowing into data linkage and analysis. The output of the session will be a summary paper highlighting both the diversity and commonalities of approaches to Indigenous data linkage internationally. Areas where consensus exists, opportunities for collaboration, and challenges will be highlighted

Immunogenicity of COVID ‐19 vaccines in patients with follicular lymphoma receiving frontline chemoimmunotherapy

Summary: Immune responses to primary COVID‐19 vaccination were investigated in 58 patients with follicular lymphoma (FL) as part of the PETReA trial of frontline therapy (EudraCT 2016–004010‐10). COVID‐19 vaccines (BNT162b2 or ChAdOx1) were administered before, during or after cytoreductive treatment comprising rituximab (depletes B cells) and either bendamustine (depletes CD4+ T cells) or cyclophosphamide‐based chemotherapy. Blood samples obtained after vaccine doses 1 and 2 (V1, V2) were analysed for antibodies and T cells reactive to the SARS‐CoV‐2 spike protein using the Abbott Architect and interferon‐gamma ELISpot assays respectively. Compared to 149 healthy controls, patients with FL exhibited lower antibody but preserved T‐cell responses. Within the FL cohort, multivariable analysis identified low pre‐treatment serum IgA levels and V2 administration during induction or maintenance treatment as independent determinants of lower antibody and higher T‐cell responses, and bendamustine and high/intermediate FLIPI‐2 score as additional determinants of a lower antibody response. Several clinical scenarios were identified where dichotomous immune responses were estimated with >95% confidence based on combinations of predictive variables. In conclusion, the immunogenicity of COVID‐19 vaccines in FL patients is influenced by multiple disease‐ and treatment‐related factors, among which B‐cell depletion showed differential effects on antibody and T‐cell responses

Variation in Reproductive Success Across Captive Populations: Methodological Differences, Potential Biases and Opportunities

Our understanding of fundamental organismal biology has been disproportionately influenced by studies of a relatively small number of model\u27 species extensively studied in captivity. Laboratory populations of model species are commonly subject to a number of forms of past and current selection that may affect experimental outcomes. Here, we examine these processes and their outcomes in one of the most widely used vertebrate species in the laboratory - the zebra finch (Taeniopygia guttata). This important model species is used for research across a broad range of fields, partly due to the ease with which it can be bred in captivity. However despite this perceived amenability, we demonstrate extensive variation in the success with which different laboratories and studies bred their subjects, and overall only 64% of all females that were given the opportunity, bred successfully in the laboratory. We identify and review several environmental, husbandry, life-history and behavioural factors that potentially contribute to this variation. The variation in reproductive success across individuals could lead to biases in experimental outcomes and drive some of the heterogeneity in research outcomes across studies. The zebra finch remains an excellent captive animal system and our aim is to sharpen the insight that future studies of this species can provide, both to our understanding of this species and also with respect to the reproduction of captive animals more widely. We hope to improve systematic reporting methods and that further investigation of the issues we raise will lead both to advances in our fundamental understanding of avian reproduction as well as to improvements in future welfare and experimental efficiency