Evaluation of the Environmental Impact of Milk Quotas

The aim of this study is to examine the environmental impacts of the different systems for allocation and transfer of milk quota under the Common Agricultural Policy (CAP) in individual Member States of the European Union (EU). In particular, it seeks to identify the ways in which differences in the implementation of milk quota regimes can impact on various sectoral and farm management trends and the environmental implications of these

A GIS of the extent of historical mining activities in Scotland: explanatory notes

As part of the secondment of BGS staff to SEPA to help implement the Water Framework Directive (WFD) in Scotland, BGS have been asked to provide an approximate outline of the extent of historical mining in Scotland. This will be used to help characterize pressures on Scottish groundwater as part of the initial characterization of groundwater bodies for the WFD. Initial characterization has to be completed by December 2004; for bodies deemed to be at risk there will be further characterization after 2004. A team of BGS geologists carried out the work during September 2003. The aim of the study was: “To delineate the extent of known and inferred historical and current shallow and dee

Rationality in context: An analogical perspective

At times, human behavior seems erratic and irrational. Therefore, when modeling human decision-making, it seems reasonable to take the remarkable abilities of humans into account with respect to rational behavior, but also their apparent deviations from the normative standards of rationality shining up in certain rationality tasks. Based on well-known challenges for human rationality, together with results from psychological studies on decision-making and from previous work in the field of computational modeling of analogy-making, I argue that the analysis and modeling of rational belief and behavior should also consider context-related cognitive mechanisms like analogy-making and coherence maximization of the background theory. Subsequently, I conceptually outline a high-level algorithmic approach for a Heuristic Driven Theory Projection-based system for simulating context-dependent human-style rational behavior. Finally, I show and elaborate on the close connections, but also on the significant differences, of this approach to notions of "ecological rationality"

Designing and implementing sample and data collection for an international genetics study: the Type 1 Diabetes Genetics Consortium (T1DGC)

Background and Purpose The Type 1 Diabetes Genetics Consortium (T1DGC) is an international project whose primary aims are to: (a) discover genes that modify type 1 diabetes risk; and (b) expand upon the existing genetic resources for type 1 diabetes research. The initial goal was to collect 2500 affected sibling pair (ASP) families worldwide

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Distinct gut virome profile of pregnant women with type 1 diabetes in the ENDIA study

Background:The importance of gut bacteria in human physiology, immune regulation, and disease pathogenesis is well established. In contrast, the composition and dynamics of the gut virome are largely unknown; particularly lacking are studies in pregnancy. We used comprehensive virome capture sequencing to characterize the gut virome of pregnant women with and without type 1 diabetes (T1D), longitudinally followed in the Environmental Determinants of Islet Autoimmunity study. Methods:In total, 61 pregnant women (35 with T1D and 26 without) from Australia were examined. Nucleic acid was extracted from serial fecal specimens obtained at prenatal visits, and viral genomes were sequenced by virome capture enrichment. The frequency, richness, and abundance of viruses were compared between women with and without T1D. Results:Two viruses were more prevalent in pregnant women with T1D: picobirnaviruses (odds ratio [OR], 4.2; 95% confidence interval [CI], 1.0-17.1; P = .046) and tobamoviruses (OR, 3.2; 95% CI, 1.1-9.3; P = .037). The abundance of 77 viruses significantly differed between the 2 maternal groups (≥2-fold difference; P < .02), including 8 Enterovirus B types present at a higher abundance in women with T1D. Conclusions:These findings provide novel insight into the composition of the gut virome during pregnancy and demonstrate a distinct profile of viruses in women with T1D.Ki Wook Kim, Digby W. Allen ... Simon C. Barry ... Lynne C Giles ... Megan A S Penno ... Rebecca L Thomson ... et al

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy