GEODE – Sharing Occupational Data Through The Grid

The ESRC funded Grid Enabled Occupational Data Environment (GEODE) project is conceived to facilitate and virtualise occupational data access through a grid environment. Through GEODE it is planned that occupational data users from the social sciences can access curated datasets, share micro datasets, and perform statistical analysis within a secure virtual community. The Michigan Data Documentation Initiative (DDI) is used to annotate the datasets with social science specific metadata to provide for better semantics and indexes. GEODE uses the Globus Toolkit and the Open Grid Service Architecture – Data Access and Integration (OGSA-DAI) software as the Grid middleware to provide data access and integration. Users access and use occupational data sets through a GEODE web portal. This portal interfaces with the Grid infrastructure and provides useroriented data searches and services. The processing of CAMSIS (Cambridge Social Interaction and Stratification) measures is used as an illustrative example of how GEODE provides services for linking occupational information. This paper provides an overview of the GEODE work and lessons learned in applying Grid technologies in this domain

Development of a Grid Enabled Occupational Data Environment

The GEODE project is developing user-oriented Grid-based services, accessible via a portal, for social scientists who require and use 'occupational information' within their research. There are many complexities associated with social scientists’ use of data on individual occupations. These arise for example from the availability of numerous alternative occupational classifications, and the use of different occupational definitions across countries. This paper describes how the GEODE project is developing an online service which acts as a facility supporting access to numerous occupational information resources. This is achieved through an integrated Grid service which uses a Globus Toolkit 4 infrastructure and OGSA-DAI (Database Access and Integration) middleware to provide the necessary data indexing and matching services, accessed through a user-oriented front-end portal (using GridSphere). The paper discusses issues in the implementation and organization of these services

Metadata Creation, Transformation and Discovery for Social Science Data Management: The DAMES Project Infrastructure

This paper discusses the use of metadata, underpinned by DDI (Data Documentation Initiative), to support social science data management. Social science data management refers broadly to the discovery, preparation, and manipulation of social science data for the purposes of research and analysis. Typical tasks include recoding variables within a dataset, and linking data from different sources. A description is given of the DAMES project (Data Management through e-Social Science), a UK project which is building resources and services to support quantitative social science data management activities. DAMES provides generic facilities for performing (and recording) operations on data. Specific resources include support for analysis through micro-simulation, and support for access to specialist data on occupations, educational qualifications, measures of ethnicity and immigration, social care, and mental health. The DAMES project tools and services can generate, use, transform, and search metadata that describe social science datasets (including microdata from social survey datasets and aggregate-level macrodata). On DAMES, these metadata are described by various standards including DDI Version 2, DDI Version 3, JSDL (Job Submission Definition Language), and the purpose-designed JFDL (Job Flow Definition Language). The paper describes how DAMES uses metadata with a range of resources that are integrated with a job execution infrastructure, a Web portal, and a tool for data fusion

Realization of a universal hydrodynamic semiconductor in ultra-clean dual-gated bilayer graphene

Hydrodynamic electronic transport is of fundamental interest due to its presence in strongly correlated materials and connections to areas outside of condensed matter physics; its study will be facilitated by identifying ambipolar hydrodynamic materials in which collisions between thermally activated electrons and holes determine conductivity. Here we present a comprehensive experimental and theoretical study of hydrodynamics in bilayer graphene, and consider the effects of an induced bandgap. For zero bandgap, conductivity at charge neutrality is temperature-independent; its magnitude determined by Planckian dissipation. With a bandgap, conductivity at charge neutrality collapses onto a universal curve. These results demonstrate that electron-hole collision limited transport in bilayer graphene can be readily detected at room temperature using straightforward DC conductivity measurements, providing an easily accessible platform for hydrodynamic investigations

Clear Cell Renal Cell Carcinoma is linked to Epithelial‐to‐Mesenchymal Transition and to Fibrosis

Clear cell renal cell carcinoma (ccRCC) represents the most common type of kidney cancer with high mortality in its advanced stages. Our study aim was to explore the correlation between tumor epithelial‐to‐mesenchymal transition (EMT) and patient survival. Renal biopsies of tumorous and adjacent nontumorous tissue were taken with a 16 g needle from our patients (n = 26) undergoing partial or radical nephrectomy due to ccRCC. RNA sequencing libraries were generated using Illumina TruSeq® Access library preparation protocol and TruSeq Small RNA library preparation kit. Next generation sequencing (NGS) was performed on Illumina HiSeq2500. Comparative analysis of matched sample pairs was done using the Bioconductor Limma/voom R‐package. Liquid chromatography‐tandem mass spectrometry and immunohistochemistry were applied to measure and visualize protein abundance. We detected an increased generic EMT transcript score in ccRCC. Gene expression analysis showed augmented abundance of AXL and MMP14, as well as down‐regulated expression of KL (klotho). Moreover, microRNA analyses demonstrated a positive expression correlation of miR‐34a and its targets MMP14 and AXL. Survival analysis based on a subset of genes from our list EMT‐related genes in a publicly available dataset showed that the EMT genes correlated with ccRCC patient survival. Several of these genes also play a known role in fibrosis. Accordingly, recently published classifiers of solid organ fibrosis correctly identified EMT‐affected tumor samples and were correlated with patient survival. EMT in ccRCC linked to fibrosis is associated with worse survival and may represent a target for novel therapeutic interventions.Peer reviewe

Genetic and Epigenetic Factors at <i>COL2A1</i> and <i>ABCA4</i> Influence Clinical Outcome in Congenital Toxoplasmosis

Background: Primary Toxoplasma gondii infection during pregnancy can be transmitted to the fetus. At birth, infected infants may have intracranial calcification, hydrocephalus, and retinochoroiditis, and new ocular lesions can occur at any age after birth. Not all children who acquire infection in utero develop these clinical signs of disease. Whilst severity of disease is influenced by trimester in which infection is acquired by the mother, other factors including genetic predisposition may contribute. Methods and Findings: In 457 mother-child pairs from Europe, and 149 child/parent trios from North America, we show that ocular and brain disease in congenital toxoplasmosis associate with polymorphisms in ABCA4 encoding ATP-binding cassette transporter, subfamily A, member 4. Polymorphisms at COL2A1 encoding type II collagen associate only with ocular disease. Both loci showed unusual inheritance patterns for the disease allele when comparing outcomes in heterozygous affected children with outcomes in affected children of heterozygous mothers. Modeling suggested either an effect of mother's genotype, or parent-of-origin effects. Experimental studies showed that both ABCA4 and COL2A1 show isoform-specific epigenetic modifications consistent with imprinting. Conclusions: These associations between clinical outcomes of congenital toxoplasmosis and polymorphisms at ABCA4 and COL2A1 provide novel insight into the molecular pathways that can be affected by congenital infection with this parasite.</p

Genetic and Epigenetic Factors at COL2A1 and ABCA4 Influence Clinical Outcome in Congenital Toxoplasmosis

Background: Primary Toxoplasma gondii infection during pregnancy can be transmitted to the fetus. At birth, infected infants may have intracranial calcification, hydrocephalus, and retinochoroiditis, and new ocular lesions can occur at any age after birth. Not all children who acquire infection in utero develop these clinical signs of disease. Whilst severity of disease is influenced by trimester in which infection is acquired by the mother, other factors including genetic predisposition may contribute.Methods and Findings: In 457 mother-child pairs from Europe, and 149 child/parent trios from North America, we show that ocular and brain disease in congenital toxoplasmosis associate with polymorphisms in ABCA4 encoding ATP-binding cassette transporter, subfamily A, member 4. Polymorphisms at COL2A1 encoding type II collagen associate only with ocular disease. Both loci showed unusual inheritance patterns for the disease allele when comparing outcomes in heterozygous affected children with outcomes in affected children of heterozygous mothers. Modeling suggested either an effect of mother's genotype, or parent-of-origin effects. Experimental studies showed that both ABCA4 and COL2A1 show isoform-specific epigenetic modifications consistent with imprinting.Conclusions: These associations between clinical outcomes of congenital toxoplasmosis and polymorphisms at ABCA4 and COL2A1 provide novel insight into the molecular pathways that can be affected by congenital infection with this parasite

Comparing very low birth weight versus very low gestation cohort methods for outcome analysis of high risk preterm infants

Background: Compared to very low gestational age (\u3c32 weeks, VLGA) cohorts, very low birth weight (\u3c1500 g; VLBW) cohorts are more prone to selection bias toward small-for-gestational age (SGA) infants, which may impact upon the validity of data for benchmarking purposes. Method: Data from all VLGA or VLBW infants admitted in the 3 Networks between 2008 and 2011 were used. Two-thirds of each network cohort was randomly selected to develop prediction models for mortality and composite adverse outcome (CAO: mortality or cerebral injuries, chronic lung disease, severe retinopathy or necrotizing enterocolitis) and the remaining for internal validation. Areas under the ROC curves (AUC) of the models were compared. Results: VLBW cohort (24,335 infants) had twice more SGA infants (20.4% vs. 9.3%) than the VLGA cohort (29,180 infants) and had a higher rate of CAO (36.5% vs. 32.6%). The two models had equal prediction power for mortality and CAO (AUC 0.83), and similarly for all other cross-cohort validations (AUC 0.81-0.85). Neither model performed well for the extremes of birth weight for gestation (\u3c1500 g and ≥32 weeks, AUC 0.50-0.65; ≥1500 g and \u3c32 weeks, AUC 0.60-0.62). Conclusion: There was no difference in prediction power for adverse outcome between cohorting VLGA or VLBW despite substantial bias in SGA population. Either cohorting practises are suitable for international benchmarking

Psychological distress is related to poor health behaviours in COPD and non-COPD patients: Evidence from the CanCOLD study

Background Patients with psychiatric disorders (depression, anxiety) are more likely to have poor health behaviours, including higher smoking and lower physical activity (PA) levels. Smoking is a major risk factor for Chronic Obstructive Pulmonary Disease (COPD), and PA is critical for COPD management. However, no studies have assessed associations between psychological distress and these behaviours among patients with vs without COPD. This is a sub-analysis of the CanCOLD study that assessed the relationships between psychological disorders (depression, anxiety) and poor health behaviours (smoking, PA). Methods 717 COPD and 797 matched non-COPD individuals from the CanCOLD study, completed the Hospital Anxiety Depression Scale (HADS) to assess anxiety and depression. Smoking behaviour was self-reported pack-years smoking. The CHAMPS PA questionnaire determined calorific expenditure as a PA measure. Regressions determined relationships between anxiety/depression and health behaviours, adjusting for age, sex, BMI, GOLD stage and COPD status. Results Across the whole sample, we observed relationships between depression (β = 1.107 ± 0.197; 95%CI = 0.691–1.462; p < .001) and anxiety (β = 0.780 ± 0.170; 95%CI = 0.446–1.114; p < .001) and pack years. Higher depression (β = −0.220 ± 0.028; 95%CI = −0.275 to −0.165; p < .001) and anxiety (β = −0.091 ± 0.025; 95%CI = −0.139 to −0.043; p < .001) scores were related to lower PA. These associations were comparable across COPD and non-COPD patients. Conclusions Results showed that higher levels of anxiety and depression were related to higher cumulative smoking and lower levels of PA in patients with and without COPD, suggesting symptoms of psychological distress is similarly associated with poorer health behaviours in COPD and non-COPD individuals. Future studies need to determine if treating symptoms of psychological distress can improve health behaviours and outcomes in this population

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin