404 research outputs found
The effects of distraction and a brief intervention on auditory and visual-spatial working memory in college students with attention deficit hyperactivity disorder
Medication related problems in ICU survivors: learning from a multi-centre programme
No abstract available
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
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
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
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
The Rapid ASKAP Continuum Survey I: Design and First Results
The Rapid ASKAP Continuum Survey (RACS) is the first large-area survey to be
conducted with the full 36-antenna Australian Square Kilometre Array Pathfinder
(ASKAP) telescope. RACS will provide a shallow model of the ASKAP sky that will
aid the calibration of future deep ASKAP surveys. RACS will cover the whole sky
visible from the ASKAP site in Western Australia, and will cover the full ASKAP
band of MHz. The RACS images are generally deeper than the existing
NRAO VLA Sky Survey (NVSS) and Sydney University Molonglo Sky Survey (SUMSS)
radio surveys and have better spatial resolution. All RACS survey products will
be public, including radio images (with arcsecond resolution) and
catalogues of about three million source components with spectral index and
polarisation information. In this paper, we present a description of the RACS
survey and the first data release of 903 images covering the sky south of
declination made over a 288 MHz band centred at 887.5 MHz.Comment: 24 pages, 17 figures, 4 tables. For associated data see
https://data.csiro.au/collections/domain/casdaObservation/results/PRAS110%20-%20The%20Rapid%20ASKAP%20Continuu
Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial
Background
Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy
Self-reported safety belt use among emergency department patients in Boston, Massachusetts
BACKGROUND: Safety belt use is 80% nationally, yet only 63% in Massachusetts. Safety belt use among potentially at-risk groups in Boston is unknown. We sought to assess the prevalence and correlates of belt non-use among emergency department (ED) patients in Boston. METHODS: A cross-sectional survey with systematic sampling was conducted on non-urgent ED patients age ≥18. A closed-ended survey was administered by interview. Safety belt use was defined via two methods: a single-item and a multiple-item measure of safety belt use. Each was scored using a 5-point frequency scale. Responses were used to categorize safety belt use as 'always' or less than 'always'. Outcome for multivariate logistic regression analysis was safety belt use less than 'always'. RESULTS: Of 478 patients approached, 381 (80%) participated. Participants were 48% female, 48% African-American, 40% White, median age 39. Among participants, 250 (66%) had been in a car crash; 234 (61%) had a valid driver's license, and 42 (11%) had been ticketed for belt non-use. Using two different survey measures, a single-item and a multiple-item measure, safety belt use 'always' was 51% and 36% respectively. According to separate regression models, factors associated with belt non-use included male gender, alcohol consumption >5 drinks in one episode, riding with others that drink and drive, ever receiving a citation for belt non-use, believing that safety belt use is 'uncomfortable', and that 'I just forget', while 'It's my usual habit' was protective. CONCLUSION: ED patients at an urban hospital in Boston have considerably lower self-reported safety belt use than state or national estimates. An ED-based intervention to increase safety belt use among this hard-to-reach population warrants consideration
MRSA in Conventional and Alternative Retail Pork Products
In order to examine the prevalence of Staphylococcus aureus on retail pork, three hundred ninety-five pork samples were collected from a total of 36 stores in Iowa, Minnesota, and New Jersey. S. aureus was isolated from 256 samples (64.8%, 95% confidence interval [CI] 59.9%–69.5%). S. aureus was isolated from 67.3% (202/300) of conventional pork samples and from 56.8% (54/95) of alternative pork samples (labeled “raised without antibiotics” or “raised without antibiotic growth promotants”). Two hundred and thirty samples (58.2%, 95% CI 53.2%–63.1%) were found to carry methicillin-sensitive S. aureus (MSSA). MSSA was isolated from 61.0% (183/300) of conventional samples and from 49.5% (47/95) of alternative samples. Twenty-six pork samples (6.6%, 95% CI 4.3%–9.5%) carried methicillin-resistant S. aureus (MRSA). No statistically significant differences were observed for the prevalence of S. aureus in general, or MSSA or MRSA specifically, when comparing pork products from conventionally raised swine and swine raised without antibiotics, a finding that contrasts with a prior study from the Netherlands examining both conventional and “biologic” meat products. In our study spa types associated with “livestock-associated” ST398 (t034, t011) were found in 26.9% of the MRSA isolates, while 46.2% were spa types t002 and t008—common human types of MRSA that also have been found in live swine. The study represents the largest sampling of raw meat products for MRSA contamination to date in the U.S. MRSA prevalence on pork products was higher than in previous U.S.-conducted studies, although similar to that in Canadian studies
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