The 1999 Center for Simulation of Dynamic Response in Materials Annual Technical Report

Introduction: This annual report describes research accomplishments for FY 99 of the Center for Simulation of Dynamic Response of Materials. The Center is constructing a virtual shock physics facility in which the full three dimensional response of a variety of target materials can be computed for a wide range of compressive, ten- sional, and shear loadings, including those produced by detonation of energetic materials. The goals are to facilitate computation of a variety of experiments in which strong shock and detonation waves are made to impinge on targets consisting of various combinations of materials, compute the subsequent dy- namic response of the target materials, and validate these computations against experimental data

VIS: the visible imager for Euclid

Euclid-VIS is a large format visible imager for the ESA Euclid space mission in their Cosmic Vision program, scheduled for launch in 2019. Together with the near infrared imaging within the NISP instrument it forms the basis of the weak lensing measurements of Euclid. VIS will image in a single r+i+z band from 550-900 nm over a field of view of ~0.5 deg2. By combining 4 exposures with a total of 2240 sec, VIS will reach to V=24.5 (10{\sigma}) for sources with extent ~0.3 arcsec. The image sampling is 0.1 arcsec. VIS will provide deep imaging with a tightly controlled and stable point spread function (PSF) over a wide survey area of 15000 deg2 to measure the cosmic shear from nearly 1.5 billion galaxies to high levels of accuracy, from which the cosmological parameters will be measured. In addition, VIS will also provide a legacy imaging dataset with an unprecedented combination of spatial resolution, depth and area covering most of the extra-Galactic sky. Here we will present the results of the study carried out by the Euclid Consortium during the Euclid Definition phase.Comment: 10 pages, 6 figure

Analysis of the anti-cancer effects of cincau extract (Premna oblongifolia merr) and other types of non- digestible fibre using faecal fermentation supernatants and Caco-2 cells as a model of the human colon

© 2017 by the authors. Green cincau (Premna oblongifolia Merr) is an Indonesian food plant with a high dietary fibre content. Research has shown that dietary fibre mixtures may be more beneficial for colorectal cancer prevention than a single dietary fibre type. The aim of this study was to investigate the effects of green cincau extract on short chain fatty acid (SCFA) production in anaerobic batch cultures inoculated with human faecal slurries and to compare these to results obtained using different dietary fibre types (pectin, inulin, and cellulose), singly and in combination. Furthermore, fermentation supernatants (FSs) were evaluated in Caco-2 cells for their effect on cell viability, differentiation, and apoptosis. Cincau increased total SCFA concentration by increasing acetate and propionate, but not butyrate concentration. FSs from all dietary fibre sources, including cincau, reduced Caco-2 cell viability. However, the effects of all FSs on cell viability, cell differentiation, and apoptosis were not simply explainable by their butyrate content. In conclusion, products of fermentation of cincau extracts induced cell death, but further work is required to understand the mechanism of action. This study demonstrates for the first time that this Indonesian traditional source of dietary fibre may be protective against colorectal cancer

Infant feeding counselling in Uganda in a changing environment with focus on the general population and HIV-positive mothers - a mixed method approach

<p>Abstract</p> <p>Background</p> <p>Health workers' counselling practices are essential to improve infant feeding practices. This paper will assess how infant feeding counselling was done and experienced by counsellors and mothers in Eastern Uganda in the context of previous guidelines. This has implications for implementation of the new infant feeding guidelines from 2009.</p> <p>Methods</p> <p>This paper combines qualitative and quantitative data from Mbale District in Eastern Uganda. Data was collected from 2003 to 2005 in a mixed methods approach. This includes: key-informant interviews among eighteen health workers in the public hospital, health clinics and non-governmental organisations working with people living with HIV, fifteen focus group discussions in the general population and among clients from an HIV clinic, two cross-sectional surveys including 727 mothers from the general population and 235 HIV-positive mothers.</p> <p>Results</p> <p>The counselling sessions were often improvised. Health workers frequently had pragmatic approaches to infant feeding as many clients struggled with poverty, stigma and non-disclosure of HIV. The feasibility of the infant feeding recommendations was perceived as challenging among health workers, both for HIV-positive mothers and in the general population. Group counselling with large groups was common in the public health service. Some extra infant feeding teaching capacities were mobilised for care-takers of undernourished children. A tendency to simplify messages giving one-sided information was seen. Different health workers presented contradicting simplified perspectives in some cases. Outdated training was a common concern with many health workers not being given courses or seminars on infant feeding since professional graduation. Other problems were minimal staffing, lack of resources, and programs being started and subsequently stopped abruptly. Many of the HIV-counsellors in the non-governmental organisations got extended training in counselling which seemed to be beneficial.</p> <p>Conclusions</p> <p>Health workers were faced with challenges related to workload, resources, scientific updating, and also a need to adjust to frequent changes in programs, recommendations and guidelines. The clients were faced with difficult choices, poverty, lack of education and stigma. Feasibility of the recommendations was a major concern. Systematic approaches to update health workers should be a priority.</p

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

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

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment