Evaluation of trauma patterns in blast injuries using multiple correspondence analysis.

Anthropology features little in published literature about blast injuries. Contributions through case studies and experimental research are beginning to expand our understanding of the effect these injuries have on the human skeleton. This study examines blast injury and gunshot related fractures through multiple correspondence analysis (MCA) with the aim of establishing injury patterns between the two types of trauma. Using a sample of 491 individuals from Bosnia, MCA is employed to identify which body regions differentiate between blast or gunshot related fractures. Cranial fractures were more closely associated with gunshot related cases. Post-cranial fractures were associated with blast-related cases. A differentiation in post-cranial and cranial fractures between gunshot and blast related cases was revealed in the samples. The high prevalence of extremity trauma in blast is similar to previous work, but the smaller amount of cranial blast-related fractures differs from previous studies and from what is found in gunshot-related cases. Differentiation of blast and gunshot wound injuries can be made on the human skeleton and can be used to possibly interpret injury mechanism in large skeletal assemblages as well as single cases

Pseudorapidity Dependence of Particle Production and Elliptic Flow in Asymmetric Nuclear Collisions of p+Al, p+Au, d+Au, and ^{3}He+Au at sqrt[s_{NN}]=200 GeV.

Asymmetric nuclear collisions of p+Al, p+Au, d+Au, and ^{3}He+Au at sqrt[s_{NN}]=200  GeV provide an excellent laboratory for understanding particle production, as well as exploring interactions among these particles after their initial creation in the collision. We present measurements of charged hadron production dN_{ch}/dη in all such collision systems over a broad pseudorapidity range and as a function of collision multiplicity. A simple wounded quark model is remarkably successful at describing the full data set. We also measure the elliptic flow v_{2} over a similarly broad pseudorapidity range. These measurements provide key constraints on models of particle emission and their translation into flow

Attempting to distinguish between endogenous and contaminating cytokeratins in a corneal proteomic study

<p>Abstract</p> <p>Background</p> <p>The observation of cytokeratins (CK's) in mass spectrometry based studies raises the question of whether the identified CK is a true endogenous protein from the sample or simply represents a contaminant. This issue is especially important in proteomic studies of the corneal epithelium where several CK's have previously been reported to mark the stages of differentiation from corneal epithelial stem cell to the differentiated cell.</p> <p>Methods</p> <p>Here we describe a method to distinguish very likely endogenous from uncertain endogenous CK's in a mass spectrometry based proteomic study. In this study the CK identifications from 102 human corneal samples were compared with the number of human CK identifications found in 102 murine thymic lymphoma samples.</p> <p>Results</p> <p>It was anticipated that the CK's that were identified with a frequency of <5%, <it>i.e. </it>in less than one spot for every 20 spots analysed, are very likely to be endogenous and thereby represent a 'biologically significant' identification. CK's observed with a frequency >5% are uncertain endogenous since they may represent true endogenous CK's but the probability of contamination is high and therefore needs careful consideration. This was confirmed by comparison with a study of mouse samples where all identified human CK's are contaminants.</p> <p>Conclusions</p> <p>CK's 3, 4, 7, 8, 11, 12, 13, 15, 17, 18, 19, 20 and 23 are very likely to be endogenous proteins if identified in a corneal study, whilst CK's 1, 2e, 5, 6A, 9, 10, 14 and 16 may be endogenous although some are likely to be contaminants in a proteomic study. Further immunohistochemical analysis and a search of the current literature largely supported the distinction.</p

Redefining risk research priorities for nanomaterials

Chemical-based risk assessment underpins the current approach to responsible development of nanomaterials (NM). It is now recognised, however, that this process may take decades, leaving decision makers with little support in the near term. Despite this, current and near future research efforts are largely directed at establishing (eco)toxicological and exposure data for NM, and comparatively little research has been undertaken on tools or approaches that may facilitate near-term decisions, some of which we briefly outline in this analysis. We propose a reprioritisation of NM risk research efforts to redress this imbalance, including the development of more adaptive risk governance frameworks, alternative/complementary tools to risk assessment, and health and environment surveillance

The estimated prevalence of exposure to asthmagens in the Australian workforce

Background: There is very little information available on a national level as to the number of people exposed to specific asthmagens in workplaces. Methods: We conducted a national telephone survey in Australia to investigate the prevalence of current occupational exposure to 277 asthmagens, assembled into 27 groups. Demographic and current job information were obtained. A web-based tool, OccIDEAS, was used to collect job task information and assign exposure to each asthmagen group. Results: In the Australian Workplace Exposure Study – Asthma (AWES- Asthma) we interviewed 4878 participants (2441 male and 2437 female). Exposure to at least one asthmagen was more common among men (47 %) than women (40 %). Extrapolated to the Australian population, approximately 2.8 million men and 1.7 million women were estimated to be exposed. Among men, the most common exposures were bioaerosols (29 %) and metals (27 %), whilst the most common exposures among women were latex (25 %) and industrial cleaning and sterilising agents (20 %). Conclusions: This study provides information about the prevalence of exposure to asthmagens in Australian workplaces which will be useful in setting priorities for control and prevention of occupational asthma

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