151 research outputs found

    Sensitivity analysis and simulations of surface heating for hypersonic cavity flows

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    Hypersonic flow over cavities results in instabilities and discontinuities that affect the surface properties, and potentially results in surface damage. Simulations were performed using semi-structured 2D meshes in FUN3D with the Spalart-Allmaras and Menter Shear Stress Transport turbulence models at a freestream Mach number of 10. The geometry includes a flat plate and four cavities with length-to-height (L/H) ratios of 0.17, 5, 15, and 30. The surface heating is found to have a strong sensitivity to freestream Reynolds numbers and some sensitivity to a change in the wall temperature. The cavity flow results are compared to Nestler et al.’s experimental data and Holifield’s CFD results. The cavities with an L/H greater than 1 presented a good match to the experimental data for both heating and pressure. The flow did not fully develop at the bottom of the L/H 0.17 gap, resulting in less accurate results close to the cavity floor

    The Relationship Between Project-Based Learning and Rigor in STEM-Focused High Schools

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    Project-based learning (PjBL) is an approach often favored in STEM classrooms, yet some studies have shown that teachers struggle to implement it with academic rigor. This paper explores the relationship between PjBL and rigor in the classrooms of ten STEM-oriented high schools. Utilizing three different data sources reflecting three different perceptions—student surveys, teacher logs, and classroom observations—the study examines the extent to which PjBL and rigor co-occur. Across all three measures, the results show that use of PjBL is associated with higher levels of rigor. However, the study also shows that academic rigor can be present in the absence of PjBL, and that PjBL can be implemented with low levels of rigor. The paper concludes with implications for practice

    The transformation of agro-climatic resources of the Altai region under changing climate conditions

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    © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This research examines the transformation of the agro-climatic conditions of the Altai region as a result of climate change. The climate of the Altai region in Russia is sharply continental and characterized by dry air and significant weather variability, both in individual seasons and years. The current study is determined by the lack of detailed area-related analytical generalizations for the territory of the Altai region over the past 30 years. Most of the published data dealing with an integrated analysis of the agro-climatic conditions in the Altai region date back to the late 1960s and early 1970s; in most cases, this data is from climate reference-books based on the generalized data from the first half of the 20th century. To make accurate forecasts and to efficiently manage agricultural production in the Altai region, area-related data on the state and dynamics of agro-climatic changes have been analysed. The results reveal that in the period between 1964 and 2017, significant climatic changes occurred in the territory of the Altai region. These climatic changes affected the growing season length, which increased due to a shift in the dates of the air temperature transition above 10 °C, to earlier dates in spring and to later dates in autumn. Furthermore, the current study also revealed that the foothills of the Altai Mountains are the most moistened parts of the region and the Kulunda lowland is the most arid part. In the Altai region, the accumulated temperatures and amounts of precipitation during the growing season increased significantly, and the values of integrated coefficients and indices that reflect the moisture supply conditions for the territory also changed significantly. Based upon the results, a schematic map of the current precipitation distribution on the Altai region’s territory has been generated. These results and this map may be used to conduct more detailed studies in the field of agro-climatology and to update the current borders of agro-climatic areas and revision of the agro-climatic zonation scheme

    An In Silico Approach for Evaluating a Fraction-Based, Risk Assessment Method for Total Petroleum Hydrocarbon Mixtures

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    Both the Massachusetts Department of Environmental Protection (MADEP) and the Total Petroleum Hydrocarbon Criteria Working Group (TPHCWG) developed fraction-based approaches for assessing human health risks posed by total petroleum hydrocarbon (TPH) mixtures in the environment. Both organizations defined TPH fractions based on their expected environmental fate and by analytical chemical methods. They derived toxicity values for selected compounds within each fraction and used these as surrogates to assess hazard or risk of exposure to the whole fractions. Membership in a TPH fraction is generally defined by the number of carbon atoms in a compound and by a compound's equivalent carbon (EC) number index, which can predict its environmental fate. Here, we systematically and objectively re-evaluate the assignment of TPH to specific fractions using comparative molecular field analysis and hierarchical clustering. The approach is transparent and reproducible, reducing inherent reliance on judgment when toxicity information is limited. Our evaluation of membership in these fractions is highly consistent (˜80% on average across various fractions) with the empirical approach of MADEP and TPHCWG. Furthermore, the results support the general methodology of mixture risk assessment to assess both cancer and noncancer risk values after the application of fractionation

    Sexual conflict maintains variation at an insecticide resistance locus

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    Background: The maintenance of genetic variation through sexually antagonistic selection is controversial, partly because specific sexually-antagonistic alleles have not been identified. The Drosophila DDT resistance allele (DDT-R) is an exception. This allele increases female fitness, but simultaneously decreases male fitness, and it has been suggested that this sexual antagonism could explain why polymorphism was maintained at the locus prior to DDT use. We tested this possibility using a genetic model and then used evolving fly populations to test model predictions. Results: Theory predicted that sexual antagonism is able to maintain genetic variation at this locus, hence explaining why DDT-R did not fix prior to DDT use despite increasing female fitness, and experimentally evolving fly populations verified theoretical predictions. Conclusions: This demonstrates that sexually antagonistic selection can maintain genetic variation and explains the DDT-R frequencies observed in nature

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

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    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

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    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

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    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

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    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

    Cloning whole bacterial genomes in yeast

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    Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional characterization. Here we report the cloning of whole bacterial genomes in the yeast Saccharomyces cerevisiae as single-DNA molecules. We cloned the genomes of Mycoplasma genitalium (0.6 Mb), M. pneumoniae (0.8 Mb) and M. mycoides subspecies capri (1.1 Mb) as yeast circular centromeric plasmids. These genomes appear to be stably maintained in a host that has efficient, well-established methods for DNA manipulation
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