TSVdb: a web-tool for TCGA splicing variants analysis.

PubMed

Sun, Wenjie; Duan, Ting; Ye, Panmeng; Chen, Kelie; Zhang, Guanling; Lai, Maode; Zhang, Honghe

2018-05-29

Collaborative projects such as The Cancer Genome Atlas (TCGA) have generated various -omics and clinical data on cancer. Many computational tools have been developed to facilitate the study of the molecular characterization of tumors using data from the TCGA. Alternative splicing of a gene produces splicing variants, and accumulating evidence has revealed its essential role in cancer-related processes, implying the urgent need to discover tumor-specific isoforms and uncover their potential functions in tumorigenesis. We developed TSVdb, a web-based tool, to explore alternative splicing based on TCGA samples with 30 clinical variables from 33 tumors. TSVdb has an integrated and well-proportioned interface for visualization of the clinical data, gene expression, usage of exons/junctions and splicing patterns. Researchers can interpret the isoform expression variations between or across clinical subgroups and estimate the relationships between isoforms and patient prognosis. TSVdb is available at http://www.tsvdb.com , and the source code is available at https://github.com/wenjie1991/TSVdb . TSVdb will inspire oncologists and accelerate isoform-level advances in cancer research.

Cancer Research by the Numbers - TCGA

Cancer.gov

Biostatistician Dr. Jill Barnholtz-Sloan strives to make a difference in the field of cancer research while inspiring her students at the same time. Learn more about how she uses TCGA data in her career in this TCGA in Action Researcher Profile.

TopFed: TCGA tailored federated query processing and linking to LOD.

PubMed

Saleem, Muhammad; Padmanabhuni, Shanmukha S; Ngomo, Axel-Cyrille Ngonga; Iqbal, Aftab; Almeida, Jonas S; Decker, Stefan; Deus, Helena F

2014-01-01

The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to catalogue genetic mutations responsible for cancer using genome analysis techniques. One of the aims of this project is to create a comprehensive and open repository of cancer related molecular analysis, to be exploited by bioinformaticians towards advancing cancer knowledge. However, devising bioinformatics applications to analyse such large dataset is still challenging, as it often requires downloading large archives and parsing the relevant text files. Therefore, it is making it difficult to enable virtual data integration in order to collect the critical co-variates necessary for analysis. We address these issues by transforming the TCGA data into the Semantic Web standard Resource Description Format (RDF), link it to relevant datasets in the Linked Open Data (LOD) cloud and further propose an efficient data distribution strategy to host the resulting 20.4 billion triples data via several SPARQL endpoints. Having the TCGA data distributed across multiple SPARQL endpoints, we enable biomedical scientists to query and retrieve information from these SPARQL endpoints by proposing a TCGA tailored federated SPARQL query processing engine named TopFed. We compare TopFed with a well established federation engine FedX in terms of source selection and query execution time by using 10 different federated SPARQL queries with varying requirements. Our evaluation results show that TopFed selects on average less than half of the sources (with 100% recall) with query execution time equal to one third to that of FedX. With TopFed, we aim to offer biomedical scientists a single-point-of-access through which distributed TCGA data can be accessed in unison. We believe the proposed system can greatly help researchers in the biomedical domain to carry out their research effectively with TCGA as the amount and diversity of data exceeds the ability of local resources to handle its retrieval and

TCGA head Neck

Cancer.gov

Investigators with The Cancer Genome Atlas (TCGA) Research Network have discovered genomic differences – with potentially important clinical implications – in head and neck cancers caused by infection with the human papillomavirus (HPV).

Using Forensics to Untangle Batch Effects in TCGA Data - TCGA

Cancer.gov

Rehan Akbani, Ph.D., and colleagues at the University of Texas MD Anderson Cancer Center developed a tool called MBatch to detect, diagnose, and correct batch effects in TCGA data. Read more about batch effects in this Case Study.

Identification of druggable cancer driver genes amplified across TCGA datasets.

PubMed

Chen, Ying; McGee, Jeremy; Chen, Xianming; Doman, Thompson N; Gong, Xueqian; Zhang, Youyan; Hamm, Nicole; Ma, Xiwen; Higgs, Richard E; Bhagwat, Shripad V; Buchanan, Sean; Peng, Sheng-Bin; Staschke, Kirk A; Yadav, Vipin; Yue, Yong; Kouros-Mehr, Hosein

2014-01-01

The Cancer Genome Atlas (TCGA) projects have advanced our understanding of the driver mutations, genetic backgrounds, and key pathways activated across cancer types. Analysis of TCGA datasets have mostly focused on somatic mutations and translocations, with less emphasis placed on gene amplifications. Here we describe a bioinformatics screening strategy to identify putative cancer driver genes amplified across TCGA datasets. We carried out GISTIC2 analysis of TCGA datasets spanning 16 cancer subtypes and identified 486 genes that were amplified in two or more datasets. The list was narrowed to 75 cancer-associated genes with potential "druggable" properties. The majority of the genes were localized to 14 amplicons spread across the genome. To identify potential cancer driver genes, we analyzed gene copy number and mRNA expression data from individual patient samples and identified 42 putative cancer driver genes linked to diverse oncogenic processes. Oncogenic activity was further validated by siRNA/shRNA knockdown and by referencing the Project Achilles datasets. The amplified genes represented a number of gene families, including epigenetic regulators, cell cycle-associated genes, DNA damage response/repair genes, metabolic regulators, and genes linked to the Wnt, Notch, Hedgehog, JAK/STAT, NF-KB and MAPK signaling pathways. Among the 42 putative driver genes were known driver genes, such as EGFR, ERBB2 and PIK3CA. Wild-type KRAS was amplified in several cancer types, and KRAS-amplified cancer cell lines were most sensitive to KRAS shRNA, suggesting that KRAS amplification was an independent oncogenic event. A number of MAP kinase adapters were co-amplified with their receptor tyrosine kinases, such as the FGFR adapter FRS2 and the EGFR family adapters GRB2 and GRB7. The ubiquitin-like ligase DCUN1D1 and the histone methyltransferase NSD3 were also identified as novel putative cancer driver genes. We discuss the patient tailoring implications for existing cancer

Identification of Druggable Cancer Driver Genes Amplified across TCGA Datasets

PubMed Central

Chen, Ying; McGee, Jeremy; Chen, Xianming; Doman, Thompson N.; Gong, Xueqian; Zhang, Youyan; Hamm, Nicole; Ma, Xiwen; Higgs, Richard E.; Bhagwat, Shripad V.; Buchanan, Sean; Peng, Sheng-Bin; Staschke, Kirk A.; Yadav, Vipin; Yue, Yong; Kouros-Mehr, Hosein

2014-01-01

The Cancer Genome Atlas (TCGA) projects have advanced our understanding of the driver mutations, genetic backgrounds, and key pathways activated across cancer types. Analysis of TCGA datasets have mostly focused on somatic mutations and translocations, with less emphasis placed on gene amplifications. Here we describe a bioinformatics screening strategy to identify putative cancer driver genes amplified across TCGA datasets. We carried out GISTIC2 analysis of TCGA datasets spanning 14 cancer subtypes and identified 461 genes that were amplified in two or more datasets. The list was narrowed to 73 cancer-associated genes with potential “druggable” properties. The majority of the genes were localized to 14 amplicons spread across the genome. To identify potential cancer driver genes, we analyzed gene copy number and mRNA expression data from individual patient samples and identified 40 putative cancer driver genes linked to diverse oncogenic processes. Oncogenic activity was further validated by siRNA/shRNA knockdown and by referencing the Project Achilles datasets. The amplified genes represented a number of gene families, including epigenetic regulators, cell cycle-associated genes, DNA damage response/repair genes, metabolic regulators, and genes linked to the Wnt, Notch, Hedgehog, JAK/STAT, NF-KB and MAPK signaling pathways. Among the 40 putative driver genes were known driver genes, such as EGFR, ERBB2 and PIK3CA. Wild-type KRAS was amplified in several cancer types, and KRAS-amplified cancer cell lines were most sensitive to KRAS shRNA, suggesting that KRAS amplification was an independent oncogenic event. A number of MAP kinase adapters were co-amplified with their receptor tyrosine kinases, such as the FGFR adapter FRS2 and the EGFR family adapter GRB7. The ubiquitin-like ligase DCUN1D1 and the histone methyltransferase NSD3 were also identified as novel putative cancer driver genes. We discuss the patient tailoring implications for existing cancer drug

Using New Maps to Navigate Cancer Treatment - TCGA

Cancer.gov

Drs.Scott Hwang and Chad Holder of Emory University discuss the development of VARSARI and The Cancer Imaging Program's TCGA Radiology Initiative. Learn more about their and Dr. Carl Jaffe's work in this TCGA In Action Case Study.

TCGA_LowerGradeGliomas

Cancer.gov

TCGA researchers analyzed nearly 300 cases of diffuse low- and intermediate-grade gliomas, which together comprise lower-grade gliomas. LGGs occur mainly in adults and include astrocytomas, oligodendrogliomas and oligoastrocytomas.

Proteome Characterization Centers - TCGA

Cancer.gov

The centers, a component of NCI’s Clinical Proteomic Tumor Analysis Consortium, will analyze a subset of TCGA samples to define proteins translated from cancer genomes and their related biological processes.

David Haussler, Ph.D., Lectures on Cancer Genomics - TCGA

Cancer.gov

In this lecture, Dr. David Haussler provides a historical overview of the field of genomics leading up to TCGA, including the Cancer Genomics Hub at the University of California, Santa Cruz, and the TCGA Pan-Cancer initiative.

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

PubMed Central

Colaprico, Antonio; Silva, Tiago C.; Olsen, Catharina; Garofano, Luciano; Cava, Claudia; Garolini, Davide; Sabedot, Thais S.; Malta, Tathiane M.; Pagnotta, Stefano M.; Castiglioni, Isabella; Ceccarelli, Michele; Bontempi, Gianluca; Noushmehr, Houtan

2016-01-01

The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many important discoveries have been made by TCGA's research network, opportunities still exist to implement novel methods, thereby elucidating new biological pathways and diagnostic markers. However, mining the TCGA data presents several bioinformatics challenges, such as data retrieval and integration with clinical data and other molecular data types (e.g. RNA and DNA methylation). We developed an R/Bioconductor package called TCGAbiolinks to address these challenges and offer bioinformatics solutions by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data. We combined methods from computer science and statistics into the pipeline and incorporated methodologies developed in previous TCGA marker studies and in our own group. Using four different TCGA tumor types (Kidney, Brain, Breast and Colon) as examples, we provide case studies to illustrate examples of reproducibility, integrative analysis and utilization of different Bioconductor packages to advance and accelerate novel discoveries. PMID:26704973

TCGA and Its Vital Role in Understanding the Landscape of Somatic Alterations in Cancer - TCGA

Cancer.gov

Dr. Stephen Chanock, M.D., Director of the Division of Cancer Epidemiology & Genetics at the NCI, discusses how TCGA provides a strong foundation for understanding key biological alterations in cancer.

Exploring cancer genomic data from the cancer genome atlas project.

PubMed

Lee, Ju-Seog

2016-11-01

The Cancer Genome Atlas (TCGA) has compiled genomic, epigenomic, and proteomic data from more than 10,000 samples derived from 33 types of cancer, aiming to improve our understanding of the molecular basis of cancer development. Availability of these genome-wide information provides an unprecedented opportunity for uncovering new key regulators of signaling pathways or new roles of pre-existing members in pathways. To take advantage of the advancement, it will be necessary to learn systematic approaches that can help to uncover novel genes reflecting genetic alterations, prognosis, or response to treatments. This minireview describes the updated status of TCGA project and explains how to use TCGA data. [BMB Reports 2016; 49(11): 607-611].

Web-TCGA: an online platform for integrated analysis of molecular cancer data sets.

PubMed

Deng, Mario; Brägelmann, Johannes; Schultze, Joachim L; Perner, Sven

2016-02-06

The Cancer Genome Atlas (TCGA) is a pool of molecular data sets publicly accessible and freely available to cancer researchers anywhere around the world. However, wide spread use is limited since an advanced knowledge of statistics and statistical software is required. In order to improve accessibility we created Web-TCGA, a web based, freely accessible online tool, which can also be run in a private instance, for integrated analysis of molecular cancer data sets provided by TCGA. In contrast to already available tools, Web-TCGA utilizes different methods for analysis and visualization of TCGA data, allowing users to generate global molecular profiles across different cancer entities simultaneously. In addition to global molecular profiles, Web-TCGA offers highly detailed gene and tumor entity centric analysis by providing interactive tables and views. As a supplement to other already available tools, such as cBioPortal (Sci Signal 6:pl1, 2013, Cancer Discov 2:401-4, 2012), Web-TCGA is offering an analysis service, which does not require any installation or configuration, for molecular data sets available at the TCGA. Individual processing requests (queries) are generated by the user for mutation, methylation, expression and copy number variation (CNV) analyses. The user can focus analyses on results from single genes and cancer entities or perform a global analysis (multiple cancer entities and genes simultaneously).

Genomic underpinnings of brain tumors - TCGA

Cancer.gov

TCGA researchers analyzed nearly 300 cases of diffuse low- and intermediate-grade gliomas, which together comprise lower-grade gliomas. LGGs occur mainly in adults and include astrocytomas, oligodendrogliomas and oligoastrocytomas.

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

PubMed Central

Bontempi, Gianluca; Ceccarelli, Michele; Noushmehr, Houtan

2016-01-01

Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as The Cancer Genome Atlas (TCGA), The Encyclopedia of DNA Elements (ENCODE), and The NIH Roadmap Epigenomics Mapping Consortium (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, most packages are designed for specific data types (e.g. expression, epigenetics, genomics) and there is no one comprehensive tool that provides a complete integrative analysis of the resources and data provided by all three public projects. A need to create an integration of these different analyses was recently proposed. In this workflow, we provide a series of biologically focused integrative analyses of different molecular data. We describe how to download, process and prepare TCGA data and by harnessing several key Bioconductor packages, we describe how to extract biologically meaningful genomic and epigenomic data. Using Roadmap and ENCODE data, we provide a work plan to identify biologically relevant functional epigenomic elements associated with cancer. To illustrate our workflow, we analyzed two types of brain tumors: low-grade glioma (LGG) versus high-grade glioma (glioblastoma multiform or GBM). This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, MINET, RTCGAToolbox,  TCGAbiolinks. PMID:28232861

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages.

PubMed

Silva, Tiago C; Colaprico, Antonio; Olsen, Catharina; D'Angelo, Fulvio; Bontempi, Gianluca; Ceccarelli, Michele; Noushmehr, Houtan

2016-01-01

Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as The Cancer Genome Atlas (TCGA), The Encyclopedia of DNA Elements (ENCODE), and The NIH Roadmap Epigenomics Mapping Consortium (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, most packages are designed for specific data types (e.g. expression, epigenetics, genomics) and there is no one comprehensive tool that provides a complete integrative analysis of the resources and data provided by all three public projects. A need to create an integration of these different analyses was recently proposed. In this workflow, we provide a series of biologically focused integrative analyses of different molecular data. We describe how to download, process and prepare TCGA data and by harnessing several key Bioconductor packages, we describe how to extract biologically meaningful genomic and epigenomic data. Using Roadmap and ENCODE data, we provide a work plan to identify biologically relevant functional epigenomic elements associated with cancer. To illustrate our workflow, we analyzed two types of brain tumors: low-grade glioma (LGG) versus high-grade glioma (glioblastoma multiform or GBM). This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, MINET, RTCGAToolbox,  TCGAbiolinks.

TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas.

PubMed

Cumbo, Fabio; Fiscon, Giulia; Ceri, Stefano; Masseroli, Marco; Weitschek, Emanuel

2017-01-03

Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of high-throughout experiments, mainly Next Generation Sequencing, for more than 30 cancer types. We propose TCGA2BED a software tool to search and retrieve TCGA data, and convert them in the structured BED format for their seamless use and integration. Additionally, it supports the conversion in CSV, GTF, JSON, and XML standard formats. Furthermore, TCGA2BED extends TCGA data with information extracted from other genomic databases (i.e., NCBI Entrez Gene, HGNC, UCSC, and miRBase). We also provide and maintain an automatically updated data repository with publicly available Copy Number Variation, DNA-methylation, DNA-seq, miRNA-seq, and RNA-seq (V1,V2) experimental data of TCGA converted into the BED format, and their associated clinical and biospecimen meta data in attribute-value text format. The availability of the valuable TCGA data in BED format reduces the time spent in taking advantage of them: it is possible to efficiently and effectively deal with huge amounts of cancer genomic data integratively, and to search, retrieve and extend them with additional information. The BED format facilitates the investigators allowing several knowledge discovery analyses on all tumor types in TCGA with the final aim of understanding pathological mechanisms and aiding cancer treatments.

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

PubMed

Liu, Jianfang; Lichtenberg, Tara; Hoadley, Katherine A; Poisson, Laila M; Lazar, Alexander J; Cherniack, Andrew D; Kovatich, Albert J; Benz, Christopher C; Levine, Douglas A; Lee, Adrian V; Omberg, Larsson; Wolf, Denise M; Shriver, Craig D; Thorsson, Vesteinn; Hu, Hai

2018-04-05

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. Copyright © 2018 Elsevier Inc. All rights reserved.

The Cancer Digital Slide Archive - TCGA

Cancer.gov

Dr. David Gutman and Dr. Lee Cooper developed The Cancer Digital Slide Archive (CDSA), a web platform for accessing pathology slide images of TCGA samples. Find out how they did it and how to use the CDSA website in this Case Study.

Cloud Technology May Widen Genomic Bottleneck - TCGA

Cancer.gov

Computational biologist Dr. Ilya Shmulevich suggests that renting cloud computing power might widen the bottleneck for analyzing genomic data. Learn more about his experience with the Cloud in this TCGA in Action Case Study.

Genomic features of lobular breast carcinoma - TCGA

Cancer.gov

Investigators with The Cancer Genome Atlas (TCGA) Research Network have identified molecular characteristics of a type of breast cancer, invasive lobular carcinoma (ILC), that distinguishes it from invasive ductal carcinoma (IDC), the most common invasive breast cancer subtype.

Home - The Cancer Genome Atlas - Cancer Genome - TCGA

Cancer.gov

The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing.

Phlebotomy and the Amish Inspired this Geneticist - TCGA

Cancer.gov

Dr. Stacey Gabriel began her career in genetics while working on a rare disease in the Amish. Learn more about her experience witnessing the human element of genetics in this TCGA in Action Researcher Profile.

TCGA researchers identify 4 subtypes of stomach cancer

Cancer.gov

Stomach cancers fall into four distinct molecular subtypes, researchers with The Cancer Genome Atlas (TCGA) Network have found. Scientists report that this discovery could change how researchers think about developing treatments for stomach cancer, also c

TCGA study identifies genomic features of cervical cancer

Cancer.gov

Investigators with The Cancer Genome Atlas (TCGA) Research Network have identified novel genomic and molecular characteristics of cervical cancer that will aid in subclassification of the disease and may help target therapies that are most appropriate for each patient.

TCGA bladder cancer study reveals potential drug targets

Cancer.gov

Investigators with TCGA have identified new potential therapeutic targets for a major form of bladder cancer, including important genes and pathways that are disrupted in the disease. They also discovered that, at the molecular level, some subtypes of bla

Studying the Genetic Basis of Kidney Cancer - TCGA

Cancer.gov

Dr. Marston Linehan, NCI's Chief of Urologic Surgery, has spent the last several decades studying kidney cancer genes and treating kidney cancer patients. Learn more about his experience as a kidney cancer physician scientist and TCGA contributor in this

New study reveals relatively few mutations in AML genomes - TCGA

Cancer.gov

Investigators for The Cancer Genome Atlas (TCGA) Research Network have detailed and broadly classified the genomic alterations that frequently underlie the development of acute myeloid leukemia (AML).

AACR 2010: Strategy for Mapping of 20 Cancers - TCGA

Cancer.gov

TCGA held an NCI-sponsored session at the American Association for Cancer Research's (AACR) 101st Annual Meeting 2010 to address the program’s Phase II structure and strategies for sample acquisition, evolving technologies, data management and analysis.

Brad Ozenberger, Ph.D., Presents the Achievements of The Cancer Genome Atlas During its Early Years - TCGA

Cancer.gov

Dr. Brad Ozenberger, former TCGA Program Director for the National Human Genome Research Institute, describes the goals and achievements of TCGA during its pilot phase, which involved the genomic characterization of brain, ovarian, and lung cancers.

Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls.

PubMed

Buckley, Alexandra R; Standish, Kristopher A; Bhutani, Kunal; Ideker, Trey; Lasken, Roger S; Carter, Hannah; Harismendy, Olivier; Schork, Nicholas J

2017-06-12

Cancer research to date has largely focused on somatically acquired genetic aberrations. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibly due to a lack of accessible germline variant data. Here we called germline variants on 9618 cases from The Cancer Genome Atlas (TCGA) database representing 31 cancer types. We identified batch effects affecting loss of function (LOF) variant calls that can be traced back to differences in the way the sequence data were generated both within and across cancer types. Overall, LOF indel calls were more sensitive to technical artifacts than LOF Single Nucleotide Variant (SNV) calls. In particular, whole genome amplification of DNA prior to sequencing led to an artificially increased burden of LOF indel calls, which confounded association analyses relating germline variants to tumor type despite stringent indel filtering strategies. The samples affected by these technical artifacts include all acute myeloid leukemia and practically all ovarian cancer samples. We demonstrate how technical artifacts induced by whole genome amplification of DNA can lead to false positive germline-tumor type associations and suggest TCGA whole genome amplified samples be used with caution. This study draws attention to the need to be sensitive to problems associated with a lack of uniformity in data generation in TCGA data.

TCGA researchers identify potential drug targets, markers for leukemia risk

Cancer.gov

Investigators for The Cancer Genome Atlas (TCGA) Research Network have detailed and broadly classified the genomic alterations that frequently underlie the development of acute myeloid leukemia (AML), a deadly cancer of the blood and bone marrow. Their wo

Serum-based six-miRNA signature as a potential marker for EC diagnosis: Comparison with TCGA miRNAseq dataset and identification of miRNA-mRNA target pairs by integrated analysis of TCGA miRNAseq and RNAseq datasets.

PubMed

Sharma, Priyanka; Saraya, Anoop; Sharma, Rinu

2018-01-30

To evaluate the diagnostic potential of a six microRNAs (miRNAs) panel consisting of miR-21, miR-144, miR-107, miR-342, miR-93 and miR-152 for esophageal cancer (EC) detection. The expression of miRNAs was analyzed in EC sera samples using quantitative real-time PCR. Risk score analysis was performed and linear regression models were then fitted to generate the six-miRNA panel. In addition, we made an effort to identify significantly dysregulated miRNAs and mRNAs in EC using the Cancer Genome Atlas (TCGA) miRNAseq and RNAseq datasets, respectively. Further, we identified significantly correlated miRNA-mRNA target pairs by integrating TCGA EC miRNAseq dataset with RNAseq dataset. The panel of circulating miRNAs showed enhanced sensitivity (87.5%) and specificity (90.48%) in terms of discriminating EC patients from normal subjects (area under the curve [AUC] = 0.968). Pathway enrichment analysis for potential targets of six miRNAs revealed 48 significant (P < 0.05) pathways, viz. pathways in cancer, mRNA surveillance, MAPK, Wnt, mTOR signaling, and so on. The expression data for mRNAs and miRNAs, downloaded from TCGA database, lead to identification of 2309 differentially expressed genes and 189 miRNAs. Gene ontology and pathway enrichment analysis showed that cell-cycle processes were most significantly enriched for differentially expressed mRNA. Integrated analysis of TCGA miRNAseq and RNAseq datasets resulted in identification of 53 063 significantly and negatively correlated miRNA-mRNA pairs. In summary, a novel and highly sensitive signature of serum miRNAs was identified for EC detection. Moreover, this is the first report identifying miRNA-mRNA target pairs from EC TCGA dataset, thus providing a comprehensive resource for understanding the interactions existing between miRNA and their target mRNAs in EC. © 2018 John Wiley & Sons Australia, Ltd.

B-CAN: a resource sharing platform to improve the operation, visualization and integrated analysis of TCGA breast cancer data.

PubMed

Wen, Can-Hong; Ou, Shao-Min; Guo, Xiao-Bo; Liu, Chen-Feng; Shen, Yan-Bo; You, Na; Cai, Wei-Hong; Shen, Wen-Jun; Wang, Xue-Qin; Tan, Hai-Zhu

2017-12-12

Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA's complex data format and diverse files. For ease of use, we build the breast cancer (B-CAN) platform, which enables data customization, data visualization, and private data center. The B-CAN platform runs on Apache server and interacts with the backstage of MySQL database by PHP. Users can customize data based on their needs by combining tables from original TCGA database and selecting variables from each table. The private data center is applicable for private data and two types of customized data. A key feature of the B-CAN is that it provides single table display and multiple table display. Customized data with one barcode corresponding to many records and processed customized data are allowed in Multiple Tables Display. The B-CAN is an intuitive and high-efficient data-sharing platform.

Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data

PubMed Central

Gutman, David A; Cobb, Jake; Somanna, Dhananjaya; Park, Yuna; Wang, Fusheng; Kurc, Tahsin; Saltz, Joel H; Brat, Daniel J; Cooper, Lee A D

2013-01-01

Background The integration and visualization of multimodal datasets is a common challenge in biomedical informatics. Several recent studies of The Cancer Genome Atlas (TCGA) data have illustrated important relationships between morphology observed in whole-slide images, outcome, and genetic events. The pairing of genomics and rich clinical descriptions with whole-slide imaging provided by TCGA presents a unique opportunity to perform these correlative studies. However, better tools are needed to integrate the vast and disparate data types. Objective To build an integrated web-based platform supporting whole-slide pathology image visualization and data integration. Materials and methods All images and genomic data were directly obtained from the TCGA and National Cancer Institute (NCI) websites. Results The Cancer Digital Slide Archive (CDSA) produced is accessible to the public (http://cancer.digitalslidearchive.net) and currently hosts more than 20 000 whole-slide images from 22 cancer types. Discussion The capabilities of CDSA are demonstrated using TCGA datasets to integrate pathology imaging with associated clinical, genomic and MRI measurements in glioblastomas and can be extended to other tumor types. CDSA also allows URL-based sharing of whole-slide images, and has preliminary support for directly sharing regions of interest and other annotations. Images can also be selected on the basis of other metadata, such as mutational profile, patient age, and other relevant characteristics. Conclusions With the increasing availability of whole-slide scanners, analysis of digitized pathology images will become increasingly important in linking morphologic observations with genomic and clinical endpoints. PMID:23893318

TCGA divides gastric cancer into four molecular subtypes: implications for individualized therapeutics.

PubMed

Zhang, Wei

2014-10-01

Gastric cancer is a leading cause of cancer deaths in the world. The treatment of gastric cancer is challenging because of its highly heterogeneous etiology and clinical characteristics. Recent genomic and molecular characterization of gastric cancer, especially the findings reported by the Cancer Genome Atlas (TCGA), have shed light on the heterogeneity and potential targeted therapeutics for four different subtypes of gastric cancer.

B-CAN: a resource sharing platform to improve the operation, visualization and integrated analysis of TCGA breast cancer data

PubMed Central

Wen, Can-Hong; Ou, Shao-Min; Guo, Xiao-Bo; Liu, Chen-Feng; Shen, Yan-Bo; You, Na; Cai, Wei-Hong; Shen, Wen-Jun; Wang, Xue-Qin; Tan, Hai-Zhu

2017-01-01

Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA’s complex data format and diverse files. For ease of use, we build the breast cancer (B-CAN) platform, which enables data customization, data visualization, and private data center. The B-CAN platform runs on Apache server and interacts with the backstage of MySQL database by PHP. Users can customize data based on their needs by combining tables from original TCGA database and selecting variables from each table. The private data center is applicable for private data and two types of customized data. A key feature of the B-CAN is that it provides single table display and multiple table display. Customized data with one barcode corresponding to many records and processed customized data are allowed in Multiple Tables Display. The B-CAN is an intuitive and high-efficient data-sharing platform. PMID:29312567

Mining TCGA Data Using Boolean Implications

PubMed Central

Sinha, Subarna; Tsang, Emily K.; Zeng, Haoyang; Meister, Michela; Dill, David L.

2014-01-01

Boolean implications (if-then rules) provide a conceptually simple, uniform and highly scalable way to find associations between pairs of random variables. In this paper, we propose to use Boolean implications to find relationships between variables of different data types (mutation, copy number alteration, DNA methylation and gene expression) from the glioblastoma (GBM) and ovarian serous cystadenoma (OV) data sets from The Cancer Genome Atlas (TCGA). We find hundreds of thousands of Boolean implications from these data sets. A direct comparison of the relationships found by Boolean implications and those found by commonly used methods for mining associations show that existing methods would miss relationships found by Boolean implications. Furthermore, many relationships exposed by Boolean implications reflect important aspects of cancer biology. Examples of our findings include cis relationships between copy number alteration, DNA methylation and expression of genes, a new hierarchy of mutations and recurrent copy number alterations, loss-of-heterozygosity of well-known tumor suppressors, and the hypermethylation phenotype associated with IDH1 mutations in GBM. The Boolean implication results used in the paper can be accessed at http://crookneck.stanford.edu/microarray/TCGANetworks/. PMID:25054200

Investigation of miR-136-5p key target genes and pathways in lung squamous cell cancer based on TCGA database and bioinformatics analysis.

PubMed

Xie, Zu-Cheng; Li, Tian-Tian; Gan, Bin-Liang; Gao, Xiang; Gao, Li; Chen, Gang; Hu, Xiao-Hua

2018-05-01

Lung squamous cell cancer (LUSC) is a common but challenging malignancy. It is important to illuminate the molecular mechanism of LUSC. Thus, we aim to explore the molecular mechanism of miR-136-5p in relation to LUSC. We used the Cancer Genome Atlas (TCGA) database to investigate the expression of miR-136-5p in relation to LUSC. Then, we identified the possible miR-136-5p target genes through intersection of the predicted miR-136-5p target genes and LUSC upregulated genes from TCGA. Bioinformatics analysis was performed to determine the key miR-136-5p targets and pathways associated with LUSC. Finally, the expression of hub genes, correlation between miR-136-5p and hub genes, and expected significance of hub genes were evaluated via the TCGA and Genotype-Tissue Expression (GTEx) project. MiR-136-5p was significantly downregulated in LUSC patients. Glucuronidation, glucuronosyltransferase, and the retinoic acid metabolic process were the most enriched metabolic interactions in LUSC patients. Ascorbate and aldarate metabolism, pentose and glucuronate interconversions, and retinol metabolism were identified as crucial pathways. Seven hub genes (UGT1A1, UGT1A3, UGT1A6, UGT1A7, UGT1A10, SRD5A1, and ADH7) were found to be upregulated, and UGT1A1, UGT1A3, UGT1A6, UGT1A7, and ADH7 were negatively correlated with miR-136-5p. UGT1A7 and ADH7 were the most significantly involved miR-136-5p target genes, and high expression of these genes was correlated with better overall survival and disease-free survival of LUSC patients. Downregulated miR-136-5p may target UGT1A7 and ADH7 and participate in ascorbate and aldarate metabolism, pentose and glucuronate interconversions, and retinol metabolism. High expression of UGT1A7 and ADH7 may indicate better prognosis of LUSC patients. Copyright © 2018. Published by Elsevier GmbH.

Neil Hayes, M.D., M.P.H., Explains TCGA Findings on GBM Subtypes - TCGA

Cancer.gov

New findings by researchers at UNC Lineberger Comprehensive Cancer Center suggest that the most common form of malignant brain cancer in adults, glioblastoma multiforme (GBM), is probably not a single disease but a set of diseases, each with a distinct underlying molecular disease process. The study was published by Cell Press in the January issue of the journal Cancer Cell and the researchers are part of the The Cancer Genome Atlas.

[Implications of TCGA Network Data on 2nd Generation Immunotherapy Concepts Based on PD-L1 and PD-1 Target Structures].

PubMed

Peters, I; Tezval, H; Kramer, M W; Wolters, M; Grünwald, V; Kuczyk, M A; Serth, J

2015-11-01

The era of cytokines, given to patients with metastatic renal cell carcinoma (mRCC) as part of an unspecific immunomodulatory treatment concept, seems to have ended with the introduction of targeted therapies. However, preliminary data from studies on treatment with checkpoint inhibitors (e. g. anti-PD-1 and anti-PD-L1) may point the way to second-generation immunotherapy. The rationale of such immunomodulatory treatment is to stop or interrupt the tumour from "escaping" the body's immune defence. Thompson et al. report that increased protein expression of PD-L1 (CD274/ B7-H1) in tumour cells and tumour-infiltrating immune cells (TILs; lymphocytes and histiocytes) is associated with unfavourable clinical pathological parameters as well as poor survival. In small pilot groups of mRCC patients it was found that increased PD-L1 protein expression in tumours and TILs may be correlated with the objective response to anti-PD-1 treatment. Sometimes, however, a very wide variety of response rates was observed, which raises the question if this can be explained by individual expression levels of PD-L1 (CD 274) or PD-1 (PDCD1).Recently published data from the Cancer Genome Atlas (TCGA) Kidney Renal Clear Cell Carcinoma (KIRC) Network now provide a genome-wide data base that allows us to review or validate the molecular results obtained in clear cell renal cell carcinomas (ccRCC) to date.In this study, we analysed the TCGA KIRC mRNA expression data for PD-L1 and PD-1 for a possible association with clinical pathological parameters and the survival of 417 ccRCC patients.The mRNA expression of PD-L1 in primary nephrectomy specimens revealed no significant association with unfavourable clinical parameters. Interestingly, though, a positive correlation with patient survival was found (HR=0,59, p=0,006).These results, which partly contradict the concept applied to date, point out the necessity to ascertain the characteristics of PD-L1 and PD-1 expression at mRNA and protein

TU-CD-BRB-07: Identification of Associations Between Radiologist-Annotated Imaging Features and Genomic Alterations in Breast Invasive Carcinoma, a TCGA Phenotype Research Group Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, A; Net, J; Brandt, K

2015-06-15

Purpose: To determine associations between radiologist-annotated MRI features and genomic measurements in breast invasive carcinoma (BRCA) from the Cancer Genome Atlas (TCGA). Methods: 98 TCGA patients with BRCA were assessed by a panel of radiologists (TCGA Breast Phenotype Research Group) based on a variety of mass and non-mass features according to the Breast Imaging Reporting and Data System (BI-RADS). Batch corrected gene expression data was obtained from the TCGA Data Portal. The Kruskal-Wallis test was used to assess correlations between categorical image features and tumor-derived genomic features (such as gene pathway activity, copy number and mutation characteristics). Image-derived features weremore » also correlated with estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2/neu) status. Multiple hypothesis correction was done using Benjamini-Hochberg FDR. Associations at an FDR of 0.1 were selected for interpretation. Results: ER status was associated with rim enhancement and peritumoral edema. PR status was associated with internal enhancement. Several components of the PI3K/Akt pathway were associated with rim enhancement as well as heterogeneity. In addition, several components of cell cycle regulation and cell division were associated with imaging characteristics.TP53 and GATA3 mutations were associated with lesion size. MRI features associated with TP53 mutation status were rim enhancement and peritumoral edema. Rim enhancement was associated with activity of RB1, PIK3R1, MAP3K1, AKT1,PI3K, and PIK3CA. Margin status was associated with HIF1A/ARNT, Ras/ GTP/PI3K, KRAS, and GADD45A. Axillary lymphadenopathy was associated with RB1 and BCL2L1. Peritumoral edema was associated with Aurora A/GADD45A, BCL2L1, CCNE1, and FOXA1. Heterogeneous internal nonmass enhancement was associated with EGFR, PI3K, AKT1, HF/MET, and EGFR/Erbb4/neuregulin 1. Diffuse nonmass enhancement was associated with HGF/MET/MUC20

Clinical value of miR-182-5p in lung squamous cell carcinoma: a study combining data from TCGA, GEO, and RT-qPCR validation.

PubMed

Luo, Jie; Shi, Ke; Yin, Shu-Ya; Tang, Rui-Xue; Chen, Wen-Jie; Huang, Lin-Zhen; Gan, Ting-Qing; Cai, Zheng-Wen; Chen, Gang

2018-04-10

MiR-182-5p, as a member of miRNA family, can be detected in lung cancer and plays an important role in lung cancer. To explore the clinical value of miR-182-5p in lung squamous cell carcinoma (LUSC) and to unveil the molecular mechanism of LUSC. The clinical value of miR-182-5p in LUSC was investigated by collecting and calculating data from The Cancer Genome Atlas (TCGA) database, the Gene Expression Omnibus (GEO) database, and real-time quantitative polymerase chain reaction (RT-qPCR). Twelve prediction platforms were used to predict the target genes of miR-182-5p. Protein-protein interaction (PPI) networks and gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to explore the molecular mechanism of LUSC. The expression of miR-182-5p was significantly over-expressed in LUSC than in non-cancerous tissues, as evidenced by various approaches, including the TCGA database, GEO microarrays, RT-qPCR, and a comprehensive meta-analysis of 501 LUSC cases and 148 non-cancerous cases. Furthermore, a total of 81 potential target genes were chosen from the union of predicted genes and the TCGA database. GO and KEGG analyses demonstrated that the target genes are involved in pathways related to biological processes. PPIs revealed the relationships between these genes, with EPAS1, PRKCE, NR3C1, and RHOB being located in the center of the PPI network. MiR-182-5p upregulation greatly contributes to LUSC and may serve as a biomarker in LUSC.

Stephen Baylin, M.D., Explains Genetics and Epigenetics - TCGA

Cancer.gov

Stephen Baylin, M.D., at the Johns Hopkins Kimmel Cancer Center discusses the how alterations in the DNA code are deciphered in a combined effort with The Cancer Genome Atlas at the National Cancer Institute to decode the brain cancer genome.

Utility of miR‑133a‑3p as a diagnostic indicator for hepatocellular carcinoma: An investigation combined with GEO, TCGA, meta‑analysis and bioinformatics.

PubMed

Liang, Hai-Wei; Yang, Xia; Wen, Dong-Yue; Gao, Li; Zhang, Xiang-Yu; Ye, Zhi-Hua; Luo, Jie; Li, Zu-Yun; He, Yun; Pang, Yu-Yan; Chen, Gang

2018-01-01

Increasing evidence has demonstrated that microRNA (miR)‑133a‑3p is an important regulator of hepatocellular carcinoma (HCC). In the present study, the diagnostic role of miR‑133a‑3p in HCC, and the potential functional pathways, were both explored based on publicly available data. Eligible microarray datasets were collected from NCBI Gene Expression Omnibus (GEO) database and ArrayExpress database. The data related to HCC and matched adjacent normal tissues were also downloaded from The Cancer Genome Atlas (TCGA). Published studies reporting the association between miR‑133a‑3p expression and HCC were reviewed from multiple databases. By combining the data derived from three sources (GEO, TCGA and published studies), the authors analyzed the comprehensive relationship between miR‑133a‑3p expression and clinicopathological features of HCC. Eventually, putative targets of miR‑133a‑3p in HCC were selected for further bioinformatics prediction. A total of eight published microarray datasets were gathered, and the pooled results demonstrated that the expression of miR‑133a‑3p in the tumor group was lower than that in normal groups [standardized mean difference (SMD)=‑0.54; 95% confidence interval (CI), ‑0.74 to ‑0.35; P<0.001]. Consistently, the level of miR‑133a‑1 in HCC was reduced markedly compared to normal tissues (P<0.001) based on TCGA data, and the AUC value of low miR‑133a‑1 expression for HCC diagnosis was 0.670 (P<0.001). Furthermore, the combined SMD of all datasets (GEO, TCGA and literature) suggested that significant difference was observed between the HCC group and the normal control group, and lower miR‑133a‑3p expression in HCC group was noted (SMD=‑0.69; 95% CI, ‑1.10 to ‑0.29; P=0.001). In addition, the authors discovered five key genes of the calcium signaling pathway (NOS1, ADRA1A, ADRA1B, ADRA1D and TBXA2R) that may probably be targeted by miR‑133a‑3p in HCC. The study reveals that miR‑133a‑3p

Evaluating the Prognostic Value of microRNA-203 in Solid Tumors Based on a Meta-Analysis and the Cancer Genome Atlas (TCGA) Datasets.

PubMed

Shao, Yingjie; Gu, Wendong; Ning, Zhonghua; Song, Xing; Pei, Honglei; Jiang, Jingting

2017-01-01

It has been reported that miR-203 expression was aberrant in various types of cancers, and it could be used as a prognostic biomarker. Therefore, in this study, we aimed to evaluate the prognostic value of miR-203 expression in solid tumors by using meta-analysis and The Cancer Genome Atlas (TCGA) datasets. By doing a literature research in PubMed, Embase and the Cochrane Library (last update by December 2016), we were able to identify the studies assessing the prognostic role of miR-203 in various tumors. We then used TCGA datasets to validate the results of meta-analysis. 33 studies from 26 articles were qualified and enrolled in this meta-analysis. Pooled analyses showed that higher expression of miR-203 in tissues couldn't predict poor overall survival (OS) and progression-free survival (PFS) in solid tumors. However, the results of subgroup analyses revealed that the upregulation of tissue miR-203 expression was associated with poor OS in colorectal cancer (hazard ratio (HR)=1.81, 95% confidence intervals (CI) 1.31-2.49; P<0.001), pancreatic cancer (HR=1.19, 95% CI 1.09-1.31; P<0.001) and ovarian cancer (HR=1.85, 95% CI 1.45-2.37; P<0.001); but it had opposite association in liver cancer (HR=0.52, 95% CI 0.28-0.97; P=0.040) and esophageal cancer (HR=0.41, 95% CI 0.25-0.66; P<0.001). Based on TCGA datasets, we found the same results for pancreatic cancer and esophageal cancer, but not for colorectal cancer and liver cancer. Moreover, patients with high circulating miR-203 in blood had significantly poor OS and PFS in colorectal cancer and breast cancer. Our study showed that the prognostic values of tissue miR-203 varied in different tumor types. In addition, the upregulation of circulating miR-203 in blood was associated with poor prognosis in colorectal cancer and breast cancer. © 2017 The Author(s)Published by S. Karger AG, Basel.

Long noncoding RNA CYTOR in cancer: A TCGA data review.

PubMed

Liang, Jiayu; Wei, Xin; Liu, Zhihong; Cao, Dehong; Tang, Yongquan; Zou, Zijun; Zhou, Chuan; Lu, Yiping

2018-08-01

Increasing evidence has shown the critical role of long non-coding RNA cytoskeleton regulator (CYTOR) in cancers. The expression of CYTOR is reported to be up-regulated in many kinds of cancers, such as gastric cancer, hepatocellular carcinoma, colon cancer, lung adenocarcinoma, oesophageal squamous cell carcinoma and renal cell carcinoma. Here, we summarized related studies and performed a meta-analysis to investigate the prognostic value of CYTOR in multiple cancers. Eligible studies were retrieved from PubMed, Embase and Cochrane Library databases, and the role of CYTOR in cancers was evaluated by pooled odds ratios (ORs) and hazard ratios (HRs) with 95% confidence intervals (CIs). The results were further validated using The Cancer Genome Atlas (TCGA) dataset. Our results showed that elevated CYTOR expression was significantly associated with poor prognosis in cancer patients (overall survival, HR = 2.03, 95% CI = 1.73-2.38, P < 0.00001). In addition, increased CYTOR expression is associated with lymph node metastasis (OR = 2.76, 95% CI = 1.28-5.95, P = 0.01), advanced TNM stage (OR = 2.23, 95% CI = 1.48-3.38, P = 0.001) and higher tumour grade (OR = 1.54, 95% CI = 1.03-2.29, P = 0.04). Overall, this study indicates that CYTOR may serve as a prognostic biomarker for cancer patients during the follow-up. Copyright © 2018 Elsevier B.V. All rights reserved.

Role of miR-1 expression in clear cell renal cell carcinoma (ccRCC): A bioinformatics study based on GEO, ArrayExpress microarrays and TCGA database.

PubMed

Yan, Hai-Biao; Huang, Jia-Cheng; Chen, You-Rong; Yao, Jian-Ni; Cen, Wei-Ning; Li, Jia-Yi; Jiang, Yi-Fan; Chen, Gang; Li, Sheng-Hua

2018-02-01

To investigate the clinical value and potential molecular mechanisms of miR-1 in clear cell renal cell carcinoma (ccRCC). We searched the Gene Expression Omnibus (GEO), ArrayExpress, several online publication databases and the Cancer Genome Atlas (TCGA). Continuous variable meta-analysis and diagnostic meta-analysis were conducted, both in Stata 14, to show the expression of miR-1 in ccRCC. Furthermore, we acquired the potential targets of miR-1 from datasets that transfected miR-1 into ccRCC cells, online prediction databases, differentially expressed genes from TCGA and literature. Subsequently bioinformatics analysis based on aforementioned selected target genes was conducted. The combined effect was -0.92 with the 95% confidence interval (CI) of -1.08 to -0.77 based on fixed effect model (I 2  = 81.3%, P < 0.001). No publication bias was found in our investigation. Sensitivity analysis showed that GSE47582 and 2 TCGA studies might cause heterogeneity. After eliminating them, the combined effect was -0.47 (95%CI: -0.78, -0.16) with I 2  = 18.3%. As for the diagnostic meta-analysis, the combined sensitivity and specificity were 0.90 (95%CI: 0.61, 0.98) and 0.63 (95%CI: 0.39, 0.82). The area under the curve (AUC) in the summarized receiver operating characteristic (SROC) curve was 0.83 (95%CI: 0.80, 0.86). No publication bias was found (P = 0.15). We finally got 67 genes which were defined the promising target genes of miR-1 in ccRCC. The most three significant KEGG pathways based on the aforementioned genes were Complement and coagulation cascades, ECM-receptor interaction and Focal adhesion. The downregulation of miR-1 might play an important role in ccRCC by targeting its target genes. Copyright © 2017 Elsevier GmbH. All rights reserved.

Evaluation of hierarchical models for integrative genomic analyses.

PubMed

Denis, Marie; Tadesse, Mahlet G

2016-03-01

Advances in high-throughput technologies have led to the acquisition of various types of -omic data on the same biological samples. Each data type gives independent and complementary information that can explain the biological mechanisms of interest. While several studies performing independent analyses of each dataset have led to significant results, a better understanding of complex biological mechanisms requires an integrative analysis of different sources of data. Flexible modeling approaches, based on penalized likelihood methods and expectation-maximization (EM) algorithms, are studied and tested under various biological relationship scenarios between the different molecular features and their effects on a clinical outcome. The models are applied to genomic datasets from two cancer types in the Cancer Genome Atlas project: glioblastoma multiforme and ovarian serous cystadenocarcinoma. The integrative models lead to improved model fit and predictive performance. They also provide a better understanding of the biological mechanisms underlying patients' survival. Source code implementing the integrative models is freely available at https://github.com/mgt000/IntegrativeAnalysis along with example datasets and sample R script applying the models to these data. The TCGA datasets used for analysis are publicly available at https://tcga-data.nci.nih.gov/tcga/tcgaDownload.jsp marie.denis@cirad.fr or mgt26@georgetown.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

JOINT AND INDIVIDUAL VARIATION EXPLAINED (JIVE) FOR INTEGRATED ANALYSIS OF MULTIPLE DATA TYPES.

PubMed

Lock, Eric F; Hoadley, Katherine A; Marron, J S; Nobel, Andrew B

2013-03-01

Research in several fields now requires the analysis of datasets in which multiple high-dimensional types of data are available for a common set of objects. In particular, The Cancer Genome Atlas (TCGA) includes data from several diverse genomic technologies on the same cancerous tumor samples. In this paper we introduce Joint and Individual Variation Explained (JIVE), a general decomposition of variation for the integrated analysis of such datasets. The decomposition consists of three terms: a low-rank approximation capturing joint variation across data types, low-rank approximations for structured variation individual to each data type, and residual noise. JIVE quantifies the amount of joint variation between data types, reduces the dimensionality of the data, and provides new directions for the visual exploration of joint and individual structure. The proposed method represents an extension of Principal Component Analysis and has clear advantages over popular two-block methods such as Canonical Correlation Analysis and Partial Least Squares. A JIVE analysis of gene expression and miRNA data on Glioblastoma Multiforme tumor samples reveals gene-miRNA associations and provides better characterization of tumor types.

The Cancer Genome Atlas Pan-Cancer analysis project.

PubMed

Weinstein, John N; Collisson, Eric A; Mills, Gordon B; Shaw, Kenna R Mills; Ozenberger, Brad A; Ellrott, Kyle; Shmulevich, Ilya; Sander, Chris; Stuart, Joshua M

2013-10-01

The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.

Overexpression of LncRNA HOTAIR is Associated with Poor Prognosis in Thyroid Carcinoma: A Study Based on TCGA and GEO Data.

PubMed

Li, Hong-Mei; Yang, Hong; Wen, Dong-Yue; Luo, Yi-Huan; Liang, Chun-Yan; Pan, Deng-Hua; Ma, Wei; Chen, Gang; He, Yun; Chen, Jun-Qiang

2017-05-01

The role of long non-coding RNA (lncRNA) HOX transcript antisense RNA (HOTAIR) in thyroid carcinoma (TC) remains unclear. The current study was aimed to assess the clinical value of HOTAIR expression levels in TC based on publically available data and to evaluate its potential signaling pathways. The expression data of HOTAIR and clinical information concerning TC were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), respectively. Furthermore, 3 online biological databases, Starbase, Cbioportal, and Multi Experiment Matrix, were used to identify HOTAIR-related genes in TC. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Panther pathway analyses were then undertaken to study the most enriched signaling pathways in TC (EASE score<0.1, Bonferroni<0.05). The TCGA results demonstrated that the expression level of HOTAIR in TC tissues was significantly increased compared with non-cancerous tissues (p<0.001). HOTAIR over-expression was significantly associated with poor survival in TC patients (p=0.03). Meta-analyses of GEO datasets revealed a trend consistent with the above results on HOTAIR expression levels in TC (SMD=0.23; 95%CI, 0.00-0.45; p=0.047). Finally, the results of functional analysis for HOTAIR-related genes indicated that HOTAIR might participate in tumorigenesis via the Wnt signaling pathway. In conclusion, our study demonstrates that HOTAIR may be involved in thyroid carcinogenesis, and the over-expression of HOTAIR could act as a biomarker associated with a poor outcome in TC patients. Moreover, the Wnt signaling pathway may be the key pathway regulated by HOTAIR in TC. © Georg Thieme Verlag KG Stuttgart · New York.

The Best Question: Explaining the Projection Behavior of Factives

ERIC Educational Resources Information Center

Simons, Mandy; Beaver, David; Roberts, Craige; Tonhauser, Judith

2017-01-01

This article deals with projection in factive sentences. The article first challenges standard assumptions by presenting a series of detailed observations about the interpretations of factive sentences in context, showing that what implication projects, if any, is quite variable and that projection is tightly constrained by prosodic and contextual…

Down-regulation of miR-146a-5p and its potential targets in hepatocellular carcinoma validated by a TCGA- and GEO-based study.

PubMed

Zhang, Xin; Ye, Zhi-Hua; Liang, Hai-Wei; Ren, Fang-Hui; Li, Ping; Dang, Yi-Wu; Chen, Gang

2017-04-01

Our previous research has demonstrated that miR-146a-5p is down-regulated in hepatocellular carcinoma (HCC) and might play a tumor-suppressive role. In this study, we sought to validate the decreased expression with a larger cohort and to explore potential molecular mechanisms. GEO and TCGA databases were used to gather miR-146a-5p expression data in HCC, which included 762 HCC and 454 noncancerous liver tissues. A meta-analysis of the GEO-based microarrays, TCGA-based RNA-seq data, and additional qRT-PCR data validated the down-regulation of miR-146a-5p in HCC and no publication bias was observed. Integrated genes were generated by overlapping miR-146a-5p-related genes from predicted and formerly reported HCC-related genes using natural language processing. The overlaps were comprehensively analyzed to discover the potential gene signatures, regulatory pathways, and networks of miR-146a-5p in HCC. A total of 251 miR-146a-5p potential target genes were predicted by bioinformatics platforms and 104 genes were considered as both HCC- and miR-146a-5p-related overlaps. RAC1 was the most connected hub gene for miR-146a-5p and four pathways with high enrichment (VEGF signaling pathway, adherens junction, toll-like receptor signaling pathway, and neurotrophin signaling pathway) were denoted for the overlapped genes. The down-regulation of miR-146a-5p in HCC has been validated with the most complete data possible. The potential gene signatures, regulatory pathways, and networks identified for miR-146a-5p in HCC could prove useful for molecular-targeted diagnostics and therapeutics.

Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study.

PubMed

Städler, Nicolas; Dondelinger, Frank; Hill, Steven M; Akbani, Rehan; Lu, Yiling; Mills, Gordon B; Mukherjee, Sach

2017-09-15

Molecular pathways and networks play a key role in basic and disease biology. An emerging notion is that networks encoding patterns of molecular interplay may themselves differ between contexts, such as cell type, tissue or disease (sub)type. However, while statistical testing of differences in mean expression levels has been extensively studied, testing of network differences remains challenging. Furthermore, since network differences could provide important and biologically interpretable information to identify molecular subgroups, there is a need to consider the unsupervised task of learning subgroups and networks that define them. This is a nontrivial clustering problem, with neither subgroups nor subgroup-specific networks known at the outset. We leverage recent ideas from high-dimensional statistics for testing and clustering in the network biology setting. The methods we describe can be applied directly to most continuous molecular measurements and networks do not need to be specified beforehand. We illustrate the ideas and methods in a case study using protein data from The Cancer Genome Atlas (TCGA). This provides evidence that patterns of interplay between signalling proteins differ significantly between cancer types. Furthermore, we show how the proposed approaches can be used to learn subtypes and the molecular networks that define them. As the Bioconductor package nethet. staedler.n@gmail.com or sach.mukherjee@dzne.de. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Cost Avoidance vs. Utility Bill Accounting - Explaining theDiscrepancy Between Guaranteed Savings in ESPC Projects and UtilityBills

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, S.; Sartor, D.

2005-08-15

Federal agencies often ask if Energy Savings PerformanceContracts (ESPCs) result in the energy and cost savings projected duringthe project development phase. After investing in ESPCs, federal agenciesexpect a reduction in the total energy use and energy cost at the agencylevel. Such questions about the program are common when implementing anESPC project. But is this a fair or accurate perception? Moreimportantly, should the federal agencies evaluate the success or failureof ESPCs by comparing the utility costs before and after projectimplementation?In fact, ESPC contracts employ measurement andverification (M&V) protocols to measure and ensure kilowatt-hour orBTU savings at the project level. In mostmore » cases, the translation toenergy cost savings is not based on actual utility rate structure, but acontracted utility rate that takes the existing utility rate at the timethe contract is signed with a clause to escalate the utility rate by afixed percentage for the duration of the contract. Reporting mechanisms,which advertise these savings in dollars, may imply an impact to budgetsat a much higher level depending on actual utility rate structure. FEMPhas prepared the following analysis to explain why the utility billreduction may not materialize, demonstrate its larger implication onagency s energy reduction goals, and advocate setting the rightexpectations at the outset to preempt the often asked question why I amnot seeing the savings in my utility bill?« less

Fully automatic GBM segmentation in the TCGA-GBM dataset: Prognosis and correlation with VASARI features.

PubMed

Rios Velazquez, Emmanuel; Meier, Raphael; Dunn, William D; Alexander, Brian; Wiest, Roland; Bauer, Stefan; Gutman, David A; Reyes, Mauricio; Aerts, Hugo J W L

2015-11-18

Reproducible definition and quantification of imaging biomarkers is essential. We evaluated a fully automatic MR-based segmentation method by comparing it to manually defined sub-volumes by experienced radiologists in the TCGA-GBM dataset, in terms of sub-volume prognosis and association with VASARI features. MRI sets of 109 GBM patients were downloaded from the Cancer Imaging archive. GBM sub-compartments were defined manually and automatically using the Brain Tumor Image Analysis (BraTumIA). Spearman's correlation was used to evaluate the agreement with VASARI features. Prognostic significance was assessed using the C-index. Auto-segmented sub-volumes showed moderate to high agreement with manually delineated volumes (range (r): 0.4 - 0.86). Also, the auto and manual volumes showed similar correlation with VASARI features (auto r = 0.35, 0.43 and 0.36; manual r = 0.17, 0.67, 0.41, for contrast-enhancing, necrosis and edema, respectively). The auto-segmented contrast-enhancing volume and post-contrast abnormal volume showed the highest AUC (0.66, CI: 0.55-0.77 and 0.65, CI: 0.54-0.76), comparable to manually defined volumes (0.64, CI: 0.53-0.75 and 0.63, CI: 0.52-0.74, respectively). BraTumIA and manual tumor sub-compartments showed comparable performance in terms of prognosis and correlation with VASARI features. This method can enable more reproducible definition and quantification of imaging based biomarkers and has potential in high-throughput medical imaging research.

The Cancer Genome Atlas Pan-Cancer Analysis Project

PubMed Central

Weinstein, John N.; Collisson, Eric A.; Mills, Gordon B.; Shaw, Kenna M.; Ozenberger, Brad A.; Ellrott, Kyle; Shmulevich, Ilya; Sander, Chris; Stuart, Joshua M.

2014-01-01

Cancer can take hundreds of different forms depending on the location, cell of origin and spectrum of genomic alterations that promote oncogenesis and affect therapeutic response. Although many genomic events with direct phenotypic impact have been identified, much of the complex molecular landscape remains incompletely charted for most cancer lineages. For that reason, The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumours to discover molecular aberrations at the DNA, RNA, protein, and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences, and emergent themes across tumour lineages. The Pan-Cancer initiative compares the first twelve tumour types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumour types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. PMID:24071849

Differentiated Success: Combining Theories to Explain Learning

ERIC Educational Resources Information Center

Jorgensen, Robyn; Larkin, Kevin

2015-01-01

This paper explores the value of different paradigms to explain dispositions towards mathematics among primary school students from different social backgrounds. As part of a larger project designed to elicit students' thinking and attitudes towards mathematics, we seek to develop an explanatory model for the socially-differentiated outcomes in…

Explaining the VET Applied Research Developmental Framework

ERIC Educational Resources Information Center

Simon, Linda; Beddie, Francesca M.

2017-01-01

This document explains the VET Applied Research Developmental Framework, created as part of a project that explored how the vocational education and training (VET) sector could broaden its engagement in Australia's research and development (R&D) and innovation systems. Achieving this engagement will rely significantly on building the…

Viral expression associated with gastrointestinal adenocarcinomas in TCGA high-throughput sequencing data

PubMed Central

2013-01-01

Background Up to 20% of cancers worldwide are thought to be associated with microbial pathogens, including bacteria and viruses. The widely used methods of viral infection detection are usually limited to a few a priori suspected viruses in one cancer type. To our knowledge, there have not been many broad screening approaches to address this problem more comprehensively. Methods In this study, we performed a comprehensive screening for viruses in nine common cancers using a multistep computational approach. Tumor transcriptome and genome sequencing data were available from The Cancer Genome Atlas (TCGA). Nine hundred fifty eight primary tumors in nine common cancers with poor prognosis were screened against a non-redundant database of virus sequences. DNA sequences from normal matched tissue specimens were used as controls to test whether each virus is associated with tumors. Results We identified human papilloma virus type 18 (HPV-18) and four human herpes viruses (HHV) types 4, 5, 6B, and 8, also known as EBV, CMV, roseola virus, and KSHV, in colon, rectal, and stomach adenocarcinomas. In total, 59% of screened gastrointestinal adenocarcinomas (GIA) were positive for at least one virus: 26% for EBV, 21% for CMV, 7% for HHV-6B, and 20% for HPV-18. Over 20% of tumors were co-infected with multiple viruses. Two viruses (EBV and CMV) were statistically significantly associated with colorectal cancers when compared to the matched healthy tissues from the same individuals (p = 0.02 and 0.03, respectively). HPV-18 was not detected in DNA, and thus, no association testing was possible. Nevertheless, HPV-18 expression patterns suggest viral integration in the host genome, consistent with the potentially oncogenic nature of HPV-18 in colorectal adenocarcinomas. The estimated counts of viral copies were below one per cell for all identified viruses and approached the detection limit. Conclusions Our comprehensive screening for viruses in multiple cancer types using next

CAS-viewer: web-based tool for splicing-guided integrative analysis of multi-omics cancer data.

PubMed

Han, Seonggyun; Kim, Dongwook; Kim, Youngjun; Choi, Kanghoon; Miller, Jason E; Kim, Dokyoon; Lee, Younghee

2018-04-20

The Cancer Genome Atlas (TCGA) project is a public resource that provides transcriptomic, DNA sequence, methylation, and clinical data for 33 cancer types. Transforming the large size and high complexity of TCGA cancer genome data into integrated knowledge can be useful to promote cancer research. Alternative splicing (AS) is a key regulatory mechanism of genes in human cancer development and in the interaction with epigenetic factors. Therefore, AS-guided integration of existing TCGA data sets will make it easier to gain insight into the genetic architecture of cancer risk and related outcomes. There are already existing tools analyzing and visualizing alternative mRNA splicing patterns for large-scale RNA-seq experiments. However, these existing web-based tools are limited to the analysis of individual TCGA data sets at a time, such as only transcriptomic information. We implemented CAS-viewer (integrative analysis of Cancer genome data based on Alternative Splicing), a web-based tool leveraging multi-cancer omics data from TCGA. It illustrates alternative mRNA splicing patterns along with methylation, miRNAs, and SNPs, and then provides an analysis tool to link differential transcript expression ratio to methylation, miRNA, and splicing regulatory elements for 33 cancer types. Moreover, one can analyze AS patterns with clinical data to identify potential transcripts associated with different survival outcome for each cancer. CAS-viewer is a web-based application for transcript isoform-driven integration of multi-omics data in multiple cancer types and will aid in the visualization and possible discovery of biomarkers for cancer by integrating multi-omics data from TCGA.

TCGA analysis of adrenocortical carcinoma - TCGA

Cancer.gov

In the most comprehensive molecular characterization to date of adrenocortical carcinoma, a rare cancer of the adrenal cortex, researchers extensively analyzed 91 cases for alterations in the tumor genomes.

TCGA Third Annual Scientific Symposium - TCGA

Cancer.gov

Monday, May 12 - Tuesday, May 13, 2014 National Institutes of Health, Bethesda, Md. This open scientific meeting will consist of collaborative workshops, poster sessions, and plenary sessions. Registration is now open.

Further Confirmation of Germline Glioma Risk Variant rs78378222 in TP53 and Its Implication in Tumor Tissues via Integrative Analysis of TCGA Data

PubMed Central

Wang, Zhaoming; Rajaraman, Preetha; Melin, Beatrice S.; Chung, Charles C.; Zhang, Weijia; McKean-Cowdin, Roberta; Michaud, Dominique; Yeager, Meredith; Ahlbom, Anders; Albanes, Demetrius; Andersson, Ulrika; Beane Freeman, Laura E.; Buring, Julie E.; Butler, Mary Ann; Carreón, Tania; Feychting, Maria; Gapstur, Susan M.; Gaziano, J. Michael; Giles, Graham G.; Hallmans, Goran; Henriksson, Roger; Hoffman-Bolton, Judith; Inskip, Peter D.; Kitahara, Cari M.; Le Marchand, Loic; Linet, Martha S.; Li, Shengchao; Peters, Ulrike; Purdue, Mark P.; Rothman, Nathaniel; Ruder, Avima M.; Sesso, Howard D.; Severi, Gianluca; Stampfer, Meir; Stevens, Victoria L.; Visvanathan, Kala; Wang, Sophia S.; White, Emily; Zeleniuch-Jacquotte, Anne; Hoover, Robert; Fraumeni, Joseph F.; Chatterjee, Nilanjan; Hartge, Patricia; Chanock, Stephen J.

2016-01-01

We confirmed strong association of rs78378222:A>C (per allele odds ratio [OR] = 3.14; P = 6.48 × 10−11), a germline rare single-nucleotide polymorphism (SNP) in TP53, via imputation of a genome-wide association study of glioma (1,856 cases and 4,955 controls). We subsequently performed integrative analyses on the Cancer Genome Atlas (TCGA) data for GBM (glioblastoma multiforme) and LUAD (lung adenocarcinoma). Based on SNP data, we imputed genotypes for rs78378222 and selected individuals carrying rare risk allele (C). Using RNA sequencing data, we observed aberrant transcripts with ~3 kb longer than normal for those individuals. Using exome sequencing data, we further showed that loss of haplotype carrying common protective allele (A) occurred somatically in GBM but not in LUAD. Our bioinformatic analysis suggests rare risk allele (C) disrupts mRNA termination, and an allelic loss of a genomic region harboring common protective allele (A) occurs during tumor initiation or progression for glioma. PMID:25907361

Clinical Value of miR-101-3p and Biological Analysis of its Prospective Targets in Breast Cancer: A Study Based on The Cancer Genome Atlas (TCGA) and Bioinformatics.

PubMed

Li, Chun-Yao; Xiong, Dan-Dan; Huang, Chun-Qin; He, Rong-Quan; Liang, Hai-Wei; Pan, Deng-Hua; Wang, Han-Lin; Wang, Yi-Wen; Zhu, Hua-Wei; Chen, Gang

2017-04-18

BACKGROUND MiR-101-3p can promote apoptosis and inhibit proliferation, invasion, and metastasis in breast cancer (BC) cells. However, its mechanisms in BC are not fully understood. Therefore, a comprehensive analysis of the target genes, pathways, and networks of miR-101-3p in BC is necessary. MATERIAL AND METHODS The miR-101 profiles for 781 patients with BC from The Cancer Genome Atlas (TCGA) were analyzed. Gene expression profiling of GSE31397 with miR-101-3p transfected MCF-7 cells and scramble control cells was downloaded from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified. The potential genes targeted by miR-101-3p were also predicted. Gene Ontology (GO) and pathway and network analyses were constructed for the DEGs and predicted genes. RESULTS In the TCGA data, a low level of miR-101-2 expression might represent a diagnostic (AUC: 0.63) marker, and the miR-101-1 was a prognostic (HR=1.79) marker. MiR-101-1 was linked to the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2), and miR-101-2 was associated with the tumor (T), lymph node (N), and metastasis (M) stages of BC. Moreover, 427 genes were selected from the 921 DEGs in GEO and the 7924 potential target genes from the prediction databases. These genes were related to transcription, metabolism, biosynthesis, and proliferation. The results were also significantly enriched in the VEGF, mTOR, focal adhesion, Wnt, and chemokine signaling pathways. CONCLUSIONS MiR-101-1 and miR-101-2 may be prospective biomarkers for the prognosis and diagnosis of BC, respectively, and are associated with diverse clinical parameters. The target genes of miR-101-3p regulate the development and progression of BC. These results provide insight into the pathogenic mechanism and potential therapies for BC.

Integrative Genome-Wide Gene Expression Profiling of Clear Cell Renal Cell Carcinoma in Czech Republic and in the United States

PubMed Central

Wozniak, Magdalena B.; Le Calvez-Kelm, Florence; Abedi-Ardekani, Behnoush; Byrnes, Graham; Durand, Geoffroy; Carreira, Christine; Michelon, Jocelyne; Janout, Vladimir; Holcatova, Ivana; Foretova, Lenka; Brisuda, Antonin; Lesueur, Fabienne; McKay, James; Brennan, Paul; Scelo, Ghislaine

2013-01-01

Gene expression microarray and next generation sequencing efforts on conventional, clear cell renal cell carcinoma (ccRCC) have been mostly performed in North American and Western European populations, while the highest incidence rates are found in Central/Eastern Europe. We conducted whole-genome expression profiling on 101 pairs of ccRCC tumours and adjacent non-tumour renal tissue from Czech patients recruited within the “K2 Study”, using the Illumina HumanHT-12 v4 Expression BeadChips to explore the molecular variations underlying the biological and clinical heterogeneity of this cancer. Differential expression analysis identified 1650 significant probes (fold change ≥2 and false discovery rate <0.05) mapping to 630 up- and 720 down-regulated unique genes. We performed similar statistical analysis on the RNA sequencing data of 65 ccRCC cases from the Cancer Genome Atlas (TCGA) project and identified 60% (402) of the downregulated and 74% (469) of the upregulated genes found in the K2 series. The biological characterization of the significantly deregulated genes demonstrated involvement of downregulated genes in metabolic and catabolic processes, excretion, oxidation reduction, ion transport and response to chemical stimulus, while simultaneously upregulated genes were associated with immune and inflammatory responses, response to hypoxia, stress, wounding, vasculature development and cell activation. Furthermore, genome-wide DNA methylation analysis of 317 TCGA ccRCC/adjacent non-tumour renal tissue pairs indicated that deregulation of approximately 7% of genes could be explained by epigenetic changes. Finally, survival analysis conducted on 89 K2 and 464 TCGA cases identified 8 genes associated with differential prognostic outcomes. In conclusion, a large proportion of ccRCC molecular characteristics were common to the two populations and several may have clinical implications when validated further through large clinical cohorts. PMID:23526956

The Cancer Genome Atlas Clinical Explorer: a web and mobile interface for identifying clinical-genomic driver associations.

PubMed

Lee, HoJoon; Palm, Jennifer; Grimes, Susan M; Ji, Hanlee P

2015-10-27

The Cancer Genome Atlas (TCGA) project has generated genomic data sets covering over 20 malignancies. These data provide valuable insights into the underlying genetic and genomic basis of cancer. However, exploring the relationship among TCGA genomic results and clinical phenotype remains a challenge, particularly for individuals lacking formal bioinformatics training. Overcoming this hurdle is an important step toward the wider clinical translation of cancer genomic/proteomic data and implementation of precision cancer medicine. Several websites such as the cBio portal or University of California Santa Cruz genome browser make TCGA data accessible but lack interactive features for querying clinically relevant phenotypic associations with cancer drivers. To enable exploration of the clinical-genomic driver associations from TCGA data, we developed the Cancer Genome Atlas Clinical Explorer. The Cancer Genome Atlas Clinical Explorer interface provides a straightforward platform to query TCGA data using one of the following methods: (1) searching for clinically relevant genes, micro RNAs, and proteins by name, cancer types, or clinical parameters; (2) searching for genomic/proteomic profile changes by clinical parameters in a cancer type; or (3) testing two-hit hypotheses. SQL queries run in the background and results are displayed on our portal in an easy-to-navigate interface according to user's input. To derive these associations, we relied on elastic-net estimates of optimal multiple linear regularized regression and clinical parameters in the space of multiple genomic/proteomic features provided by TCGA data. Moreover, we identified and ranked gene/micro RNA/protein predictors of each clinical parameter for each cancer. The robustness of the results was estimated by bootstrapping. Overall, we identify associations of potential clinical relevance among genes/micro RNAs/proteins using our statistical analysis from 25 cancer types and 18 clinical parameters that

Life-Saving Space Technology Explained

NASA Technical Reports Server (NTRS)

2000-01-01

Dr. Harry Whelan, a pediatric Neurologist at the Medical Hospital of Wisconsin in Milwaukee and professor of Neurology at the Medical College of Wisconsin, explains the operation of light-emitting diodes (LEDs) developed for use in space plant growth experiments and now adapted for use in photodynamic therapy, a technique in which light from the LEDs activates light-sensitive, tumor-treating drugs. The technique has been used in at least two surgeries on brain tumors. The LED project was one of several NASA exhibits at AirVenture 2000 sponsored by the Experimental Aircraft Association in Oshkosh, WI.

Elective Program Projects

ERIC Educational Resources Information Center

Estrada, Christelle

1976-01-01

Outlined is an interdisciplinary program in Ecology and Oceanography for grades six through eight. Numerous student projects are suggested in the outline and the course requirements and the project system are explained. (MA)

Project development process.

DOT National Transportation Integrated Search

2007-08-01

The following chapter explains the purpose of this document, outlines the essential elements involved in : the Project Development Process, describes the differences in the three main project classifications, and : provides the necessary background i...

Toward a Comprehensive Genomic Analysis of Cancer - TCGA

Cancer.gov

The National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI) convened a "Toward a Comprehensive Genomic Analysis of Cancer" workshop in Washington, D.C. This workshop brought together physicians, basic scientists and other members of the U.S. and international cancer communities to assist in outlining the most effective strategies for the development of a successful project. Information about this workshop is reported in the Executive Summary.

The benefits of looking across many cancer genomes

Cancer.gov

Cancer is not a single entity, but rather, it is more than one hundred complex and distinct diseases, with most cancer types demanding a unique treatment strategy. TCGA researchers have developed a formal project for a cross tumor analysis, called Pan-Can

TCGA study of genetic drivers of melanoma - TCGA

Cancer.gov

A comprehensive analysis of the genome of cutaneous melanoma has provided new insights into the roles of frequently mutated cancer genes and other genomic alterations that drive the development of this disease.

Unifying cancer and normal RNA sequencing data from different sources

PubMed Central

Wang, Qingguo; Armenia, Joshua; Zhang, Chao; Penson, Alexander V.; Reznik, Ed; Zhang, Liguo; Minet, Thais; Ochoa, Angelica; Gross, Benjamin E.; Iacobuzio-Donahue, Christine A.; Betel, Doron; Taylor, Barry S.; Gao, Jianjiong; Schultz, Nikolaus

2018-01-01

Driven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude of large-scale studies were conducted recently that have resulted in an unprecedented volume of whole transcriptome sequencing (RNA-seq) data, such as the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA). While these data offer new opportunities to identify the mechanisms underlying disease, the comparison of data from different sources remains challenging, due to differences in sample and data processing. Here, we developed a pipeline that processes and unifies RNA-seq data from different studies, which includes uniform realignment, gene expression quantification, and batch effect removal. We find that uniform alignment and quantification is not sufficient when combining RNA-seq data from different sources and that the removal of other batch effects is essential to facilitate data comparison. We have processed data from GTEx and TCGA and successfully corrected for study-specific biases, enabling comparative analysis between TCGA and GTEx. The normalized datasets are available for download on figshare. PMID:29664468

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.

PubMed

Ellrott, Kyle; Bailey, Matthew H; Saksena, Gordon; Covington, Kyle R; Kandoth, Cyriac; Stewart, Chip; Hess, Julian; Ma, Singer; Chiotti, Kami E; McLellan, Michael; Sofia, Heidi J; Hutter, Carolyn; Getz, Gad; Wheeler, David; Ding, Li

2018-03-28

The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a comprehensive encyclopedia of somatic mutation calls for the TCGA data to enable robust cross-tumor-type analyses. Our approach accounts for variance and batch effects introduced by the rapid advancement of DNA extraction, hybridization-capture, sequencing, and analysis methods over time. We present best practices for applying an ensemble of seven mutation-calling algorithms with scoring and artifact filtering. The dataset created by this analysis includes 3.5 million somatic variants and forms the basis for PanCan Atlas papers. The results have been made available to the research community along with the methods used to generate them. This project is the result of collaboration from a number of institutes and demonstrates how team science drives extremely large genomics projects. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Khalid Alshibli explains MGM to Sean O'Keefe

NASA Technical Reports Server (NTRS)

2002-01-01

Khalid Alshibli of Louisiana State University, project scientist for the Mechanics of Granular Materials (MGM-III) experiment, uses a jar of sand as he explains MGM to NASA Administrator Sean O'Keefe. A training model of an MGM test cell is in the foreground. The activity was part of the Space Research and You education event held by NASA's Office of Biological and Physical Research on June 25, 2002, in Arlington, VA, to highlight the research that will be conducted on STS-107.

Defense styles explain psychiatric symptoms: an empirical study.

PubMed

Holi, M M; Sammallahti, P R; Aalberg, V A

1999-11-01

To examine the relation between psychiatric symptoms and defense mechanisms, we administered two questionnaires, the Symptom Check-list 90 (SCL-90) and the Defense Style Questionnaire (DSQ) to 122 psychiatric out-patients and to a community sample of 337 subjects. Using regression analysis, we found that 51.8% of the variation in subject's Global Severity Index value could be explained by his defense style. Of the three defense styles, the immature style explained most of the variation in the symptoms. We found little overall evidence for specific connections between particular defenses and symptoms. Projection and dissociation were central in most of the symptom dimensions. We compared patients and controls with the same level of general symptom severity and found that patients used significantly more devaluation and splitting, and controls used significantly more altruism and idealization. Whether defenses predispose to certain symptomatology or are one of its aspects is discussed.

Projecting technological change

Treesearch

Kenneth E. Skog

2007-01-01

Improving efficiency in the use of both wood and nonwood inputs has characterized the US forest sector over the last 50 years. This chapter explores methods used to reflect this pattern of technological change and others in the Timber Assessment Projection System models. The development and use of three types of technology projection methods are explained: (1)...

Integrative Bioinformatics and Functional Analyses of GEO, ENCODE, and TCGA Reveal FADD as a Direct Target of the Tumor Suppressor BRCA1.

PubMed

Nguyen, Dinh-Duc; Lee, Dong Gyu; Kim, Sinae; Kang, Keunsoo; Rhee, Je-Keun; Chang, Suhwan

2018-05-14

BRCA1 is a multifunctional tumor suppressor involved in several essential cellular processes. Although many of these functions are driven by or related to its transcriptional/epigenetic regulator activity, there has been no genome-wide study to reveal the transcriptional/epigenetic targets of BRCA1. Therefore, we conducted a comprehensive analysis of genomics/transcriptomics data to identify novel BRCA1 target genes. We first analyzed ENCODE data with BRCA1 chromatin immunoprecipitation (ChIP)-sequencing results and identified a set of genes with a promoter occupied by BRCA1. We collected 3085 loci with a BRCA1 ChIP signal from four cell lines and calculated the distance between the loci and the nearest gene transcription start site (TSS). Overall, 66.5% of the BRCA1-bound loci fell into a 2-kb region around the TSS, suggesting a role in transcriptional regulation. We selected 45 candidate genes based on gene expression correlation data, obtained from two GEO (Gene Expression Omnibus) datasets and TCGA data of human breast cancer, compared to BRCA1 expression levels. Among them, we further tested three genes ( MEIS2 , CKS1B and FADD ) and verified FADD as a novel direct target of BRCA1 by ChIP, RT-PCR, and a luciferase reporter assay. Collectively, our data demonstrate genome-wide transcriptional regulation by BRCA1 and suggest target genes as biomarker candidates for BRCA1-associated breast cancer.

TCGA study improves understanding of thyroid cancer genetics - TCGA

Cancer.gov

A comprehensive analysis of the genomes of nearly 500 papillary thyroid carcinomas has provided new insights into the roles of frequently mutated cancer genes and other genomic alterations that drive disease development.

First Large-Scale Proteogenomic Study of Breast Cancer Provides Insight into Potential Therapeutic Targets | Office of Cancer Clinical Proteomics Research

Cancer.gov

News Release: May 25, 2016 — Building on data from The Cancer Genome Atlas (TCGA) project, a multi-institutional team of scientists has completed the first large-scale “proteogenomic” study of breast cancer, linking DNA mutations to protein signaling and helping pinpoint the genes that drive cancer.

GASB's Basis of Accounting Project.

ERIC Educational Resources Information Center

Kovlak, Daniel L.

1986-01-01

In July 1984, the Governmental Accounting Standards Board began its "Measurement Focus/Basis of Accounting" project, which addresses measurement issues and revenue and expenditure recognition problems involving governmental funds. This article explains the project's background, alternatives discussed by the board, and tentative…

Reflections on the Gall-Peters Projection.

ERIC Educational Resources Information Center

Robinson, Arthur H.

1987-01-01

Explains the cartographic qualities of rectangular world maps and compares the merits of various projections such as the Mercator and the recently-created Gall-Peters. States that the Gall-Peters projection does not provide a reasonable base for a general world map; that no rectangular projection does. (JDH)

TU-CD-BRB-04: Automated Radiomic Features Complement the Prognostic Value of VASARI in the TCGA-GBM Dataset

DOE Office of Scientific and Technical Information (OSTI.GOV)

Velazquez, E Rios; Narayan, V; Grossmann, P

2015-06-15

Purpose: To compare the complementary prognostic value of automated Radiomic features to that of radiologist-annotated VASARI features in TCGA-GBM MRI dataset. Methods: For 96 GBM patients, pre-operative MRI images were obtained from The Cancer Imaging Archive. The abnormal tumor bulks were manually defined on post-contrast T1w images. The contrast-enhancing and necrotic regions were segmented using FAST. From these sub-volumes and the total abnormal tumor bulk, a set of Radiomic features quantifying phenotypic differences based on the tumor intensity, shape and texture, were extracted from the post-contrast T1w images. Minimum-redundancy-maximum-relevance (MRMR) was used to identify the most informative Radiomic, VASARI andmore » combined Radiomic-VASARI features in 70% of the dataset (training-set). Multivariate Cox-proportional hazards models were evaluated in 30% of the dataset (validation-set) using the C-index for OS. A bootstrap procedure was used to assess significance while comparing the C-Indices of the different models. Results: Overall, the Radiomic features showed a moderate correlation with the radiologist-annotated VASARI features (r = −0.37 – 0.49); however that correlation was stronger for the Tumor Diameter and Proportion of Necrosis VASARI features (r = −0.71 – 0.69). After MRMR feature selection, the best-performing Radiomic, VASARI, and Radiomic-VASARI Cox-PH models showed a validation C-index of 0.56 (p = NS), 0.58 (p = NS) and 0.65 (p = 0.01), respectively. The combined Radiomic-VASARI model C-index was significantly higher than that obtained from either the Radiomic or VASARI model alone (p = <0.001). Conclusion: Quantitative volumetric and textural Radiomic features complement the qualitative and semi-quantitative annotated VASARI feature set. The prognostic value of informative qualitative VASARI features such as Eloquent Brain and Multifocality is increased with the addition of quantitative volumetric and textural features from

Association between differential gene expression and body mass index among endometrial cancers from The Cancer Genome Atlas Project.

PubMed

Roque, Dario R; Makowski, Liza; Chen, Ting-Huei; Rashid, Naim; Hayes, D Neil; Bae-Jump, Victoria

2016-08-01

The Cancer Genome Atlas (TCGA) identified four integrated clusters for endometrial cancer (EC): POLE, MSI, CNL and CNH. We evaluated differences in gene expression profiles of obese and non-obese women with EC and examined the association of body mass index (BMI) within the clusters identified in TCGA. TCGA RNAseq data was used to identify genes related to increasing BMI among ECs. The POLE, MSI and CNL clusters were composed mostly of endometrioid EC. Patient BMI was compared between these three clusters with one-way ANOVA. Association between gene expression and BMI was also assessed while adjusting for confounding effects of potential confounding factors. p-Values testing the association between gene expression and BMI were adjusted for multiple hypothesis testing over the 20,531 genes considered. Mean BMI was statistically different between the ECs in the CNL (35.8) versus POLE (29.8) cluster (p=0.006) and approached significance for the MSI (33.0) versus CNL (35.8) cluster (p=0.05). 181 genes were significantly up- or down-regulated with increasing BMI in endometrioid EC (q-value<0.01), including LPL, IRS-1, IGFBP4, IGFBP7 and the progesterone receptor. DAVID functional annotation analysis revealed significant enrichment in "cell cycle" (adjusted p-value=1.5E-5) and "DNA metabolic processes" (adjusted p-value=1E-3) for the identified genes. Obesity related genes were found to be upregulated with increasing BMI among endometrioid ECs. Patients with POLE tumors have the lowest median BMI when compared to MSI and CNL. Given the heterogeneity among endometrioid EC, consideration should be given to abandoning the Type I and II classification of EC tumors. Copyright © 2016 Elsevier Inc. All rights reserved.

A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms

ERIC Educational Resources Information Center

Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.

2015-01-01

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do…

Molecular Pathology of Patient Tumors, Patient-Derived Xenografts, and Cancer Cell Lines.

PubMed

Guo, Sheng; Qian, Wubin; Cai, Jie; Zhang, Likun; Wery, Jean-Pierre; Li, Qi-Xiang

2016-08-15

The Cancer Genome Atlas (TCGA) project has generated abundant genomic data for human cancers of various histopathology types and enabled exploring cancer molecular pathology per big data approach. We developed a new algorithm based on most differentially expressed genes (DEG) per pairwise comparisons to calculate correlation coefficients to be used to quantify similarity within and between cancer types. We systematically compared TCGA cancers, demonstrating high correlation within types and low correlation between types, thus establishing molecular specificity of cancer types and an alternative diagnostic method largely equivalent to histopathology. Different coefficients for different cancers in study may reveal that the degree of the within-type homogeneity varies by cancer types. We also performed the same calculation using the TCGA-derived DEGs on patient-derived xenografts (PDX) of different histopathology types corresponding to the TCGA types, as well as on cancer cell lines. We, for the first time, demonstrated highly similar patterns for within- and between-type correlation between PDXs and patient samples in a systematic study, confirming the high relevance of PDXs as surrogate experimental models for human diseases. In contrast, cancer cell lines have drastically reduced expression similarity to both PDXs and patient samples. The studies also revealed high similarity between some types, for example, LUSC and HNSCC, but low similarity between certain subtypes, for example, LUAD and LUSC. Our newly developed algorithm seems to be a practical diagnostic method to classify and reclassify a disease, either human or xenograft, with better accuracy than traditional histopathology. Cancer Res; 76(16); 4619-26. ©2016 AACR. ©2016 American Association for Cancer Research.

Occupational Outlook and Projections: Bureau of Labor Statistics Explains Which Jobs Show Promise for 1985

ERIC Educational Resources Information Center

La Luz, 1977

1977-01-01

The Bureau of Labor Statistics examines job prospects in hundreds of occupations and publishes many books and pamphlets that explain which jobs will and will not be promising between now and 1985, i.e., the Occupational Outlook Handbook and the Occupational Outlook for College Graduates. (NQ)

Validation of Early Detection Ovarian Cancer Biomarkers (Team Project) — EDRN Public Portal

Cancer.gov

Early detection of Ovarian Cancer (OC) is one of the key clinical problems in this disease. We propose a team EDRN project to address the issue of early detection of OC by performing a validation study on candidate protein markers already identified in previous EDRN research or in the literature (e.g. protein products of TCGA identified mutations specific to ovarian cancer). (See appendix for full listing) Biospecimen sources have been identified which include samples obtained at diagnosis and matched controls (Urban, Godwin, Marks, Skates), and longitudinal samples obtained prior to diagnosis (Urban, Skates, Godwin). Bioinformatic filters will be applied to rank the candidates (Diamandis). In order of ranking, candidate proteins for which high quality antibodies are available will be measured by development of ELISAs at JHU (Chan/Zhang) or through NAPPA at DFCI (Anderson/LaBaer), while for other candidates mass spectrometry based selective reaction monitoring (SRM) assays will be developed at PNNL (Rodland). Three milestones are defined. The first two milestones are to assemble the necessary specimens and to develop the qualifying assay(s). The final milestone is to estimate the markers’ sensitivity one year prior to diagnosis at a given high specificity.

Integration of Multi-Modal Biomedical Data to Predict Cancer Grade and Patient Survival.

PubMed

Phan, John H; Hoffman, Ryan; Kothari, Sonal; Wu, Po-Yen; Wang, May D

2016-02-01

The Big Data era in Biomedical research has resulted in large-cohort data repositories such as The Cancer Genome Atlas (TCGA). These repositories routinely contain hundreds of matched patient samples for genomic, proteomic, imaging, and clinical data modalities, enabling holistic and multi-modal integrative analysis of human disease. Using TCGA renal and ovarian cancer data, we conducted a novel investigation of multi-modal data integration by combining histopathological image and RNA-seq data. We compared the performances of two integrative prediction methods: majority vote and stacked generalization. Results indicate that integration of multiple data modalities improves prediction of cancer grade and outcome. Specifically, stacked generalization, a method that integrates multiple data modalities to produce a single prediction result, outperforms both single-data-modality prediction and majority vote. Moreover, stacked generalization reveals the contribution of each data modality (and specific features within each data modality) to the final prediction result and may provide biological insights to explain prediction performance.

A Gene Expression Profile of BRCAness that Predicts for Responsiveness to Platinum and PARP Inhibitors

DTIC Science & Technology

2013-08-01

like ( NBL ) corresponding to tumors predicted to have a BRCAness phenotype (BL tumors) or not ( NBL tumors). In the previous years we performed a...TCGA EOC project that have been characterized as BL or NBL by our profile to identify 3 candidate miRNAs (let-7f-2*, miR-744*, miR-342-5p) that may be

Student Support using Project Adventure

NASA Astrophysics Data System (ADS)

Kawanishi, Toshimasa

University students become maladjustment at the time of entrance to school not to have friends. Project adventure is effective in the making of friend and brings up confidence with persons. General concepts of project adventure make from experimental learning cycle, full value contract and challenge by choice. This paper explains purpose of PA, practice, ice breaking, trust and initiative.

TU-AB-BRA-11: Evaluation of Fully Automatic Volumetric GBM Segmentation in the TCGA-GBM Dataset: Prognosis and Correlation with VASARI Features

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rios Velazquez, E; Meier, R; Dunn, W

Purpose: Reproducible definition and quantification of imaging biomarkers is essential. We evaluated a fully automatic MR-based segmentation method by comparing it to manually defined sub-volumes by experienced radiologists in the TCGA-GBM dataset, in terms of sub-volume prognosis and association with VASARI features. Methods: MRI sets of 67 GBM patients were downloaded from the Cancer Imaging archive. GBM sub-compartments were defined manually and automatically using the Brain Tumor Image Analysis (BraTumIA), including necrosis, edema, contrast enhancing and non-enhancing tumor. Spearman’s correlation was used to evaluate the agreement with VASARI features. Prognostic significance was assessed using the C-index. Results: Auto-segmented sub-volumes showedmore » high agreement with manually delineated volumes (range (r): 0.65 – 0.91). Also showed higher correlation with VASARI features (auto r = 0.35, 0.60 and 0.59; manual r = 0.29, 0.50, 0.43, for contrast-enhancing, necrosis and edema, respectively). The contrast-enhancing volume and post-contrast abnormal volume showed the highest C-index (0.73 and 0.72), comparable to manually defined volumes (p = 0.22 and p = 0.07, respectively). The non-enhancing region defined by BraTumIA showed a significantly higher prognostic value (CI = 0.71) than the edema (CI = 0.60), both of which could not be distinguished by manual delineation. Conclusion: BraTumIA tumor sub-compartments showed higher correlation with VASARI data, and equivalent performance in terms of prognosis compared to manual sub-volumes. This method can enable more reproducible definition and quantification of imaging based biomarkers and has a large potential in high-throughput medical imaging research.« less

Student-Generated Multimedia Projects in the Classroom.

ERIC Educational Resources Information Center

Green, Tim; Brown, Abbie H.

2002-01-01

Explains how student-generated, computer-based multimedia projects can be meaningful learning activities to integrate into the K-12 curriculum. Describes three phases: design, including goals and objectives of the project and use of the finished product; production, including choosing multimedia software, prototyping, and usability testing; and…

Constructing a Stereographic Projection Model

ERIC Educational Resources Information Center

Lovett, D. R.; King, G. D.

1978-01-01

Explains how to construct a three dimensional model for stereographic projection. It will be suitable for presenting the symmetry of crystal systems, and will help physics students understand the nature of crystallography. (GA)

Cancer Bulletin Profile: In Their Own Words: Raju Kucherlapati, Ph.D. - TCGA

Cancer.gov

Dr. Raju Kucherlapati, the Paul C. Cabot Professor of Genetics at Harvard Medical School, speaks about cancer genetics and genomics, specifically the Cancer Genome Atlas project and the tools that personalized medicine may provide to detect, treat, and prevent cancer.

What Are Scientists Really Like? The Acclaim Project.

ERIC Educational Resources Information Center

Fenton, Sharon; Jordan, Julie

2001-01-01

Introduces the Acclaim Project which aims to familiarize school children and the public with today's scientists. Focuses on scientists' activities in daily life and laboratories as well as participant scientists' comments. Explains how this project can be implemented at the elementary education level. (YDS)

ART/Ada design project, phase 1

NASA Technical Reports Server (NTRS)

1989-01-01

An Ada-Based Expert System Building Tool Design Research Project was conducted. The goal was to investigate various issues in the context of the design of an Ada-based expert system building tool. An attempt was made to achieve a comprehensive understanding of the potential for embedding expert systems in Ada systems for eventual application in future projects. The current status of the project is described by introducing an operational prototype, ART/Ada. How the project was conducted is explained. The performance of the prototype is analyzed and compared with other related works. Future research directions are suggested.

Learning by Doing: the Progressive Novella Project.

ERIC Educational Resources Information Center

Conroy, Michael G.

1996-01-01

States that the Progressive Novella Project for high school students involves the collaborative writing of a 35-50 page novella. Explains that prior to the actual writing process, students are educated in the basic elements of fiction writing. Describes the division of labor into groups. Comments that the results of the project are invariably…

Priority programming for highway project selections.

DOT National Transportation Integrated Search

1981-01-01

This report provides an introduction to the methodologies of priority programming as developed by state transportation departments in their highway and transportation project selection processes. It explains the interrelationships between needs studi...

GenomeVIP: a cloud platform for genomic variant discovery and interpretation

PubMed Central

Mashl, R. Jay; Scott, Adam D.; Huang, Kuan-lin; Wyczalkowski, Matthew A.; Yoon, Christopher J.; Niu, Beifang; DeNardo, Erin; Yellapantula, Venkata D.; Handsaker, Robert E.; Chen, Ken; Koboldt, Daniel C.; Ye, Kai; Fenyö, David; Raphael, Benjamin J.; Wendl, Michael C.; Ding, Li

2017-01-01

Identifying genomic variants is a fundamental first step toward the understanding of the role of inherited and acquired variation in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional “download and analyze” paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis. Here, we introduce the Genome Variant Investigation Platform (GenomeVIP), an open-source framework for performing genomics variant discovery and annotation using cloud- or local high-performance computing infrastructure. GenomeVIP orchestrates the analysis of whole-genome and exome sequence data using a set of robust and popular task-specific tools, including VarScan, GATK, Pindel, BreakDancer, Strelka, and Genome STRiP, through a web interface. GenomeVIP has been used for genomic analysis in large-data projects such as the TCGA PanCanAtlas and in other projects, such as the ICGC Pilots, CPTAC, ICGC-TCGA DREAM Challenges, and the 1000 Genomes SV Project. Here, we demonstrate GenomeVIP's ability to provide high-confidence annotated somatic, germline, and de novo variants of potential biological significance using publicly available data sets. PMID:28522612

Using the Project Method in Distributive Education. Teacher's Manual.

ERIC Educational Resources Information Center

Maletta, Edwin

The document explains how to integrate the project training methods into a distributive education curriculum for grades 10 or 11. The purpose of this teacher's manual is to give an overall picture of the project method in use. Ten sample projects are included which could apply to any distributive education student concentrating on the major areas…

Two Project Methods: Preliminary Observations on the Similarities and Differences between William Heard Kilpatrick's Project Method and John Dewey's Problem-Solving Method

ERIC Educational Resources Information Center

Sutinen, Ari

2013-01-01

The project method became a famous teaching method when William Heard Kilpatrick published his article "Project Method" in 1918. The key idea in Kilpatrick's project method is to try to explain how pupils learn things when they work in projects toward different common objects. The same idea of pupils learning by work or action in an…

Chapter 4 - The LANDFIRE Prototype Project reference database

Treesearch

John F. Caratti

2006-01-01

This chapter describes the data compilation process for the Landscape Fire and Resource Management Planning Tools Prototype Project (LANDFIRE Prototype Project) reference database (LFRDB) and explains the reference data applications for LANDFIRE Prototype maps and models. The reference database formed the foundation for all LANDFIRE tasks. All products generated by the...

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.

PubMed

Ding, Li; Bailey, Matthew H; Porta-Pardo, Eduard; Thorsson, Vesteinn; Colaprico, Antonio; Bertrand, Denis; Gibbs, David L; Weerasinghe, Amila; Huang, Kuan-Lin; Tokheim, Collin; Cortés-Ciriano, Isidro; Jayasinghe, Reyka; Chen, Feng; Yu, Lihua; Sun, Sam; Olsen, Catharina; Kim, Jaegil; Taylor, Alison M; Cherniack, Andrew D; Akbani, Rehan; Suphavilai, Chayaporn; Nagarajan, Niranjan; Stuart, Joshua M; Mills, Gordon B; Wyczalkowski, Matthew A; Vincent, Benjamin G; Hutter, Carolyn M; Zenklusen, Jean Claude; Hoadley, Katherine A; Wendl, Michael C; Shmulevich, Llya; Lazar, Alexander J; Wheeler, David A; Getz, Gad

2018-04-05

The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we present our current understanding of the molecular processes governing oncogenesis. We illustrate our insights into cancer through synthesis of the findings of the TCGA PanCancer Atlas project on three facets of oncogenesis: (1) somatic driver mutations, germline pathogenic variants, and their interactions in the tumor; (2) the influence of the tumor genome and epigenome on transcriptome and proteome; and (3) the relationship between tumor and the microenvironment, including implications for drugs targeting driver events and immunotherapies. These results will anchor future characterization of rare and common tumor types, primary and relapsed tumors, and cancers across ancestry groups and will guide the deployment of clinical genomic sequencing. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Explaining the Growth in US Health Care Spending Using State-Level Variation in Income, Insurance, and Provider Market Dynamics

PubMed Central

Herring, Bradley; Trish, Erin

2015-01-01

The slowed growth in national health care spending over the past decade has led analysts to question the extent to which this recent slowdown can be explained by predictable factors such as the Great Recession or must be driven by some unpredictable structural change in the health care sector. To help address this question, we first estimate a regression model for state personal health care spending for 1991-2009, with an emphasis on the explanatory power of income, insurance, and provider market characteristics. We then use the results from this simple predictive model to produce state-level projections of health care spending for 2010-2013 to subsequently compare those average projected state values with actual national spending for 2010-2013, finding that at least 70% of the recent slowdown in health care spending can likely be explained by long-standing patterns. We also use the results from this predictive model to both examine the Great Recession’s likely reduction in health care spending and project the Affordable Care Act’s insurance expansion’s likely increase in health care spending. PMID:26655685

Elementary Education: What Is Project Omega?

ERIC Educational Resources Information Center

Kirman, Joseph M.

1980-01-01

Describes Project Omega for Research in Remote Sensing Education, a program in space education designed for inservice training of elementary social studies teachers. Explains a few research areas dealing with the classroom applications of Landsat imagery. (CS)

How to Select a Project Delivery Method for School Facilities

ERIC Educational Resources Information Center

Kalina, David

2007-01-01

In this article, the author discusses and explains three project delivery methods that are commonly used today in the United States. The first project delivery method mentioned is the design-bid-build, which is still the predominant method of project delivery for public works and school construction in the United States. The second is the…

What Climate Sensitivity Index Is Most Useful for Projections?

NASA Astrophysics Data System (ADS)

Grose, Michael R.; Gregory, Jonathan; Colman, Robert; Andrews, Timothy

2018-02-01

Transient climate response (TCR), transient response at 140 years (T140), and equilibrium climate sensitivity (ECS) indices are intended as benchmarks for comparing the magnitude of climate response projected by climate models. It is generally assumed that TCR or T140 would explain more variability between models than ECS for temperature change over the 21st century, since this timescale is the realm of transient climate change. Here we find that TCR explains more variability across Coupled Model Intercomparison Project phase 5 than ECS for global temperature change since preindustrial, for 50 or 100 year global trends up to the present, and for projected change under representative concentration pathways in regions of delayed warming such as the Southern Ocean. However, unexpectedly, we find that ECS correlates higher than TCR for projected change from the present in the global mean and in most regions. This higher correlation does not relate to aerosol forcing, and the physical cause requires further investigation.

Digging into Archaeology Projects.

ERIC Educational Resources Information Center

Grambo, Greg

1996-01-01

Suggestions are offered for a classroom project of planning and conducting an archaeological dig on or near school property. Principles of archaeological practice such as making drawings of the site and using a grid frame to record locations are explained. Also suggested is a simulation activity in which students pick imbedded "findings" out of…

A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms

PubMed Central

Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.

2015-01-01

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do explanations made by experts from different biology subdisciplines at a university support the validity of this model? Guided by the modeling framework of R. S. Justi and J. K. Gilbert, the validity of an initial model was tested by asking seven biologists to explain a molecular mechanism of their choice. Data were collected from interviews, artifacts, and drawings, and then subjected to thematic analysis. We found that biologists explained the specific activities and organization of entities of the mechanism. In addition, they contextualized explanations according to their biological and social significance; integrated explanations with methods, instruments, and measurements; and used analogies and narrated stories. The derived methods, analogies, context, and how themes informed the development of our final MACH model of mechanistic explanations. Future research will test the potential of the MACH model as a guiding framework for instruction to enhance the quality of student explanations. PMID:25999313

Clinical applications of The Cancer Genome Atlas project (TCGA) for squamous cell lung carcinoma.

PubMed

Devarakonda, Siddhartha; Morgensztern, Daniel; Govindan, Ramaswamy

2013-09-01

Very little progress has been made in the treatment of patients with metastatic squamous cell lung cancer over the past 2 decades. Identification of novel molecular alterations for targeted therapies is necessary to improve outcomes. Advances in genomic technology have now made it possible to analyze the genomic landscape of tumor tissues comprehensively. We summarize here key findings from the comprehensive analysis of squamous cell lung cancer by The Cancer Genome Atlas group and discuss the clinical implications of these findings.

Explaining Disparities in Youth Aerobic Fitness and Body Mass Index: Relative Impact of Socioeconomic and Minority Status

ERIC Educational Resources Information Center

Bai, Yang; Saint-Maurice, Pedro F.; Welk, Gregory J.; Allums-Featherston, Kelly; Candelaria, Norma

2016-01-01

Background: To advance research on youth fitness promotion it is important to understand factors that may explain the disparities in fitness. Methods: We evaluated data from the FitnessGram NFL PLAY60 Partnership Project to examine school factors influencing aerobic capacity (AC) and body mass index (BMI) in schoolchildren. Individual observations…

Explaining mortality rate plateaus

PubMed Central

Weitz, Joshua S.; Fraser, Hunter B.

2001-01-01

We propose a stochastic model of aging to explain deviations from exponential growth in mortality rates commonly observed in empirical studies. Mortality rate plateaus are explained as a generic consequence of considering death in terms of first passage times for processes undergoing a random walk with drift. Simulations of populations with age-dependent distributions of viabilities agree with a wide array of experimental results. The influence of cohort size is well accounted for by the stochastic nature of the model. PMID:11752476

Japanese Teabowls: A Historical Look and a Class Project.

ERIC Educational Resources Information Center

Macaulay, Sara Grove

2003-01-01

Provides background information about tea in Japan and a description of the tea ceremony used in Japan. Explains that the teabowls of Sasaki Chojiro inspired the project in which students created their own teabowls. States that this project can be used with a study about Japanese history. (CMK)

Project Work in Social Biology at GCE Advanced Level

ERIC Educational Resources Information Center

Gadd, P.; Smith, S. Tyrell

1977-01-01

The system by which projects are submitted, modified, and approved is outlined and an indication is given of the standards and quantity of work expected. Criteria on which assessment is based are explained, the range of individual studies is summarized, and cases for and against project work are given. (Author/AJ)

Instructional System Design for Executive Orientation and Project Management Training Packages, Technical Memorandum No. 3. Interim Report. RF Project No. 3131-A1.

ERIC Educational Resources Information Center

Cook, Desmond L.; And Others

This memorandum reports on the third phase, the design, of a four-phase project to design project management training materials for local educational agencies. The first section of the memorandum explains some considerations regarding management education and the organization of the report. Section 2 presents the design specifications for the…

Projection of Teachers' Salaries for Contract Negotiations.

ERIC Educational Resources Information Center

Ott, Jack P.

1982-01-01

Lists and explains a computer program written in BASIC which calculates teacher salaries using a salary index. Modification of this payroll program is suggested as a student project in schools which teach computer programing. (JJD)

Genomic understanding of glioblastoma expanded

Cancer.gov

Glioblastoma multiforme (GBM) was the first cancer type to be systematically studied by TCGA in 2008. In a new, complementary report, TCGA experts examined more than 590 GBM samples--the largest to date utilizing genomic characterization techniques and ne

Northwestern Pennsylvania Cooperative Demonstration Project (High Technology). Process Manual.

ERIC Educational Resources Information Center

Indiana Univ. of Pennsylvania. Center for Vocational Personnel Preparation.

This process manual explains the procedures followed by a project that provided training for employees of manufacturing industries. It also focuses on the project's attainment of two other objectives: (1) helping industry in the target area become more competitive with foreign rivals; and (2) building a network between industry and education. A…

Humans Do It Better: Inside the Open Directory Project.

ERIC Educational Resources Information Center

Sherman, Chris

2000-01-01

Explains the Open Directory Project (ODP), an attempt to catalog the World Wide Web by creating a human-compiled Web directory. Discusses the history of the project; open source models; the use of volunteer editors; quality control; problems and complaints; and use of ODP data by commercial services such as Google. (LRW)

Explaining Algorithms: A New Perspective

ERIC Educational Resources Information Center

Müldner, Tomasz; Shakshuki, Elhadi

2006-01-01

This article presents a novel approach for explaining algorithms that aims to overcome various pedagogical limitations of the current visualization systems. The main idea is that at any given time, a learner is able to focus on a single problem. This problem can be explained, studied, understood, and tested, before the learner moves on to study…

The Intrinsic Temperature Sensitivity of Ecosystem Respiration as Explained by Thermodynamics

NASA Astrophysics Data System (ADS)

Woods, K. D.; Arcus, V. L.; Schipper, L. A.; Schwalm, C.

2016-12-01

Biological processes exhibit thermal optima; a range within which processes such as photosynthesis and respiration reach a maximum rate. The response of these processes to temperature is well observed in the field and lab experiments, but is poorly captured or explained by widely used Arrhenius equations and Q10 constants. Both Arrhenius and Q10-based explanations of respiration misleadingly project an exponential increase in rate with temperature and rely on concepts such as enzyme denaturation to explain decreases at higher temperatures. This explanation is problematic in that it ignores observed declines which are far below experimental observations of enzyme denaturation. Here, we present a novel theory which explains the intrinsic temperature dependence of plant, soil, and ecosystem respiration based on the thermodynamics of enzyme-catalysed reactions. MacroMolecular Rate Theory (MMRT) allows for the calculation of thermal optima for respiration and photosynthesis (an important input substrate for respiration), as well as for the calculation of the curvature of response which defines temperatures where changes in rates are maximal. To test this theory, we used the recently released FLUXNET2015 dataset which is comprised of 165 sites and 23 years of data. We accounted for the effect of water through partial correlation analysis and extracted the temperature signal of respiration and photosynthesis to fit MacroMolecular Rate Theory. Across ecosystems and biomes, photosynthesis and respiration rates maximized at 7-18oC and 15-27oC respectively. At 16-25oC, and 26-36oC rates photosynthesis and respiration declined. These points, and this method for explaining changes in these processes are important for understanding and predicting net ecosystem carbon gain or loss. They demonstrate temperatures where the sign and magnitude of carbon exchange undergoes important shifts, holding important implications for future carbon cycling.

Systemic analysis of different colorectal cancer cell lines and TCGA datasets identified IGF-1R/EGFR-PPAR-CASPASE axis as important indicator for radiotherapy sensitivity.

PubMed

Chen, Lin; Zhu, Zhe; Gao, Wei; Jiang, Qixin; Yu, Jiangming; Fu, Chuangang

2017-09-05

Insulin-like growth factor 1 receptor (IGF-1R) is proved to contribute the development of many types of cancers. But, little is known about its roles in radio-resistance of colorectal cancer (CRC). Here, we demonstrated that low IGF-1R expression value was associated with the better radiotherapy sensitivity of CRC. Besides, through Quantitative Real-time PCR (qRT-PCR), the elevated expression value of epidermal growth factor receptor (EGFR) was observed in CRC cell lines (HT29, RKO) with high radio-sensitivity compared with those with low sensitivity (SW480, LOVO). The irradiation induced apoptosis rates of wild type and EGFR agonist (EGF) or IGF-1R inhibitor (NVP-ADW742) treated HT29 and SW480 cells were quantified by flow cytometry. As a result, the apoptosis rate of EGF and NVP-ADW742 treated HT29 cells was significantly higher than that of those wild type ones, which indicated that high EGFR and low IGF-1R expression level in CRC was associated with the high sensitivity to radiotherapy. We next conducted systemic bioinformatics analysis of genome-wide expression profiles of CRC samples from the Cancer Genome Atlas (TCGA). Differential expression analysis between IGF-1R and EGFR abnormal CRC samples, i.e. CRC samples with higher IGF-1R and lower EGFR expression levels based on their median expression values, and the rest of CRC samples identified potential genes contribute to radiotherapy sensitivity. Functional enrichment of analysis of those differential expression genes (DEGs) in the Database for Annotation, Visualization and Integrated Discovery (DAVID) indicated PPAR signaling pathway as an important pathway for the radio-resistance of CRC. Our study identified the potential biomarkers for the rational selection of radiotherapy for CRC patients. Copyright © 2017 Elsevier B.V. All rights reserved.

[Application of the technique of analytical structure of project for the sub-project of websites catalog of the Virtual Health Library-Nursing].

PubMed

dos, Santos Luís Augusto; Marin, Heimar de Fátima; Marques, Isaac Rosa; Cunha, Isabel Cristina Kowal Olm

2007-01-01

This work intents, in a didactic form, to explain the benefits of use of a technique of project management, named Work Breakdown Structure: a graphical tool to identify the main results to be developed in a project. The real examples are applied to a sub-project of the Virtual Library in Health in Nursing (BVS-Enfermagem) to development of the Sites Catalogs. The benefits of graphical visualization for a major agreement between professionals of different expertise are presented.

Impact of aging on host immune response and survival in melanoma: an analysis of 3 patient cohorts.

PubMed

Weiss, Sarah A; Han, Joseph; Darvishian, Farbod; Tchack, Jeremy; Han, Sung Won; Malecek, Karolina; Krogsgaard, Michelle; Osman, Iman; Zhong, Judy

2016-10-19

Age has been reported as an independent prognostic factor for melanoma-specific survival (MSS). We tested the hypothesis that age impacts the host anti-tumor immune response, accounting for age-specific survival outcomes in three unique melanoma patient cohorts. We queried the U.S. population-based Surveillance, Epidemiology, and End Results Program (SEER), the prospective tertiary care hospital-based Interdisciplinary Melanoma Cooperative Group (IMCG) biorepository, and the Cancer Genome Atlas (TCGA) biospecimen database to test the association of patient age at time of melanoma diagnosis with clinicopathologic features and survival outcomes. Age groups were defined as ≤45 (young), 46-65 (intermediate), and >65 (older). Each age group in the IMCG and TCGA cohorts was stratified by tumor infiltrating lymphocyte (TIL) measurements and tested for association with MSS. Differential expression of 594 immunoregulatory genes was assessed in a subset of primary melanomas in the IMCG and TCGA cohorts using an integrative pathway analysis. We analyzed 304, 476 (SEER), 1241 (IMCG), and 292 (TCGA) patients. Increasing age at melanoma diagnosis in both the SEER and IMCG cohorts demonstrated a positive correlation with tumor thickness, ulceration, stage, and mortality, however age in the TCGA cohort did not correlate with mortality. Older age was associated with shorter MSS in all three cohorts. When the young age group in both the IMCG and TCGA cohorts was stratified by TIL status, there were no differences in MSS. However, older IMCG patients with brisk TILs and intermediate aged TCGA patients with high lymphocyte scores (3-6) had improved MSS. Gene expression analysis revealed top pathways (T cell trafficking, communication, and differentiation) and top upstream regulators (CD3, CD28, IFNG, and STAT3) that significantly changed with age in 84 IMCG and 43 TCGA primary melanomas. Older age at time of melanoma diagnosis is associated with shorter MSS, however age

Risk management integration into complex project organizations

NASA Technical Reports Server (NTRS)

Fisher, K.; Greanias, G.; Rose, J.; Dumas, R.

2002-01-01

This paper describes the approach used in designing and adapting the SIRTF prototype, discusses some of the lessons learned in developing the SIRTF prototype, and explains the adaptability of the risk management database to varying levels project complexity.

Compassion and Curiosity - TCGA

Cancer.gov

William Kim, M.D., is motivated by two things: compassion and curiosity. Dr. Kim has taken these dual motivations and created a career in which he cares directly for patients and spearheads research that may lead to improved treatment options.

2010 ESMD Faculty Fellowship Project

NASA Technical Reports Server (NTRS)

Carmen, Christina L.; Morris, Tommy; Schmidt, Peter; van Susante, Paul; Zalewski, Janusz; Murphy, Gloria

2010-01-01

This slide presentation reviews is composed of 6 individual sections. The first is a introductory section that explains the Exploration Systems Mission Directorate (ESMD) Faculty Fellowship Project, the purpose of which is to prepare selected university faculty to work with senior design students to complete projects that have potential to contribute to NASA objectives. The following university presentations represent the chosen projects: (1) the use of Exploration Toolset for the Optimization of Launch and Space Systems (X-TOOLSS) to optimize the Lunar Wormbot design; (2) development of Hardware Definition Language (HDL) realization of ITU G.729 for FGPA; (3) cryogenic fluid and electrical quick connect system and a lunar regolith design; (4) Lunar Landing Pad development; and (5) Prognostics for complex systems.

Cancer in silico drug discovery: a systems biology tool for identifying candidate drugs to target specific molecular tumor subtypes.

PubMed

San Lucas, F Anthony; Fowler, Jerry; Chang, Kyle; Kopetz, Scott; Vilar, Eduardo; Scheet, Paul

2014-12-01

Large-scale cancer datasets such as The Cancer Genome Atlas (TCGA) allow researchers to profile tumors based on a wide range of clinical and molecular characteristics. Subsequently, TCGA-derived gene expression profiles can be analyzed with the Connectivity Map (CMap) to find candidate drugs to target tumors with specific clinical phenotypes or molecular characteristics. This represents a powerful computational approach for candidate drug identification, but due to the complexity of TCGA and technology differences between CMap and TCGA experiments, such analyses are challenging to conduct and reproduce. We present Cancer in silico Drug Discovery (CiDD; scheet.org/software), a computational drug discovery platform that addresses these challenges. CiDD integrates data from TCGA, CMap, and Cancer Cell Line Encyclopedia (CCLE) to perform computational drug discovery experiments, generating hypotheses for the following three general problems: (i) determining whether specific clinical phenotypes or molecular characteristics are associated with unique gene expression signatures; (ii) finding candidate drugs to repress these expression signatures; and (iii) identifying cell lines that resemble the tumors being studied for subsequent in vitro experiments. The primary input to CiDD is a clinical or molecular characteristic. The output is a biologically annotated list of candidate drugs and a list of cell lines for in vitro experimentation. We applied CiDD to identify candidate drugs to treat colorectal cancers harboring mutations in BRAF. CiDD identified EGFR and proteasome inhibitors, while proposing five cell lines for in vitro testing. CiDD facilitates phenotype-driven, systematic drug discovery based on clinical and molecular data from TCGA. ©2014 American Association for Cancer Research.

Using Computer Conferencing and Electronic Mail to Facilitate Group Projects.

ERIC Educational Resources Information Center

Anderson, Margaret D.

1996-01-01

Reports on the use of electronic mail and an electronic conferencing system to conduct group projects in three educational psychology courses at the State University of New York College at Cortland. Course design is explained and group project design is described, including assignments and oral presentations during regular class sessions.…

An Email Exchange Project between Non-Native Speakers of English.

ERIC Educational Resources Information Center

Fedderholdt, Karen

2001-01-01

Describes a recent email writing project between nonnative speakers of English. The project was carried out by a group of Japanese university students, and a group of Danish students preparing for university entrance examinations. Explains the reasons for choosing to use email in writing classes and why nonnative speakers were chosen. (Author/VWL)

Experiential Learning through Integrated Project Work: An Example from Soil Science.

ERIC Educational Resources Information Center

Mellor, Antony

1991-01-01

Describes the planning, implementation, and evaluation of an integrated student soil science project. Reports that the course was designed to develop student-centered approaches to learning and to develop transferable skills and personal qualities at the same time. Explains that the project included fieldwork, laboratory analysis, data…

A multilevel study of the impact of project manager's leadership on extra-role performance of project team members

NASA Astrophysics Data System (ADS)

Shokory, Suzyanty Mohd; Suradi, Nur Riza Mohd

2018-04-01

The current study examines the impact of transformational and transactional leadership of project manager on the extra-role performance of project team members. In addition, this study also identifies factor dominant to extra-role performance of project team members when the transformational and transactional leadership of project managers are analyzed simultaneously. The study involved 175 of project team members from 35 project teams (each project team consists of different contracting companies registered in the Selangor (N = 175 from 35 contractors company). A multilevel analysis with hierarchical linear modeling (HLM) approach was used in this study. The analysis showed that transformational and transactional leadership of the project manager is a positive significant with extra-role performance project team members when analyzed separately. However when the two constructs (transformational leadership and transactional leadership of project manager) were analyzed simultaneously, transformational leadership was found to have more impact on extra-role performance project team members compared to transactional leadership. These findings explained that although transformational and transactional leadership of project managers can improve extra-role performance project team members, but this study has proved that transformational leadership of project managers affect extra-role performance project team members more as compared to transactional leadership.

The UCLA Young Autism Project: A Reply to Gresham and Macmillan.

ERIC Educational Resources Information Center

Smith, Tristam; Lovass, O. Ivar

1997-01-01

Responds to "Autistic Recovery? An Analysis and Critique of the Empirical Evidence on the Early Intervention Project" (Gresham and MacMillan), which criticizes research showing the effectiveness of the UCLA Youth Autism Project program for children with autism. The article's misunderstandings are discussed and the program is explained. (CR)

Supporting Digital Literacy across the Curriculum through Blended Support: A Pilot Project Report

ERIC Educational Resources Information Center

Smith, Samara

2014-01-01

This article describes the Collaborative Media Center pilot at SUNY Old Westbury, a digital literacy project with the aim of narrowing the digital divide at the College by embedding digital projects across the curriculum. The article explains how the Center supported students in four linked courses to create digital projects. Assessment data and…

Natural gas projects in the developing world: An empirical evaluation of merits, obstacles, and risks

NASA Astrophysics Data System (ADS)

Mor, Amit

Significant amounts of natural gas have been discovered in developing countries throughout the years during the course of oil exploration. The vast majority of these resources have not been utilized. Some developing countries may benefit from a carefully planned utilization of their indigenous resources, which can either be exported or used domestically to substitute imported or exportable fuels or feedstock. Governments, potential private sector investors, and financiers have been searching for strategies to promote natural gas schemes, some of which have been in the pipeline for more than two decades. The purpose of this thesis is to identify the crucial factors determining the success or failure of launching natural gas projects in the developing world. The methodology used to evaluate these questions included: (1) establishing a representative sample of natural gas projects in developing countries that were either implemented or failed to materialize during the 1980-1995 period, (2) utilizing a Probit limited dependent variable econometric model in which the explained variable is project success or failure, and (3) choosing representing indicators to reflect the assumed factors affecting project success. The study identified two conditions for project success: (1) the economic viability of the project and (2) securing financing for the investment. The factors that explain the ability or inability of the sponsors to secure financing were: (1) the volume of investment that represented the large capital costs of gas transportation, distribution, and storage, (2) the level of foreign exchange constraint in the host country, and (3) the level of development of the country. The conditions for private sector participation in natural gas projects in developing countries were identified in the study by a Probit model in which the explained variable was private sector participation. The results showed that a critical condition for private sector participation is the

Middlesex Community College Geothermal Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klein, Jessie; Spaziani, Gina

The purpose of the project was to install a geothermal system in the trustees house on the Bedford campus of Middlesex Community College. In partnership with the environmental science faculty, learning activities for environmental science courses were developed to explain geothermal energy and more specifically the newly installed system to Middlesex students. A real-time monitoring system highlights the energy use and generation.

The Harvard Project Physics Film Program

ERIC Educational Resources Information Center

Bork, Alfred M.

1970-01-01

States the philosophy behind the Harvard Project Physics (HPP) film program. Describes the three long HPP films. Lists the 48 color film loops covering six broad topics, primarily motion and energy. The 8-mm silent loops are synchronized with the text materials. Explains some of the pedagogical possibilities of these film loops. (RR)

Theoretical Perspectives Guiding QOL Indicator Projects

ERIC Educational Resources Information Center

Sirgy, M. Joseph

2011-01-01

Most of the theoretically based QOL indicators projects can be classified in terms of six major theoretical concepts: (a) socio-economic development (b) personal utility, (c) just society, (d) human development, (e) sustainability, and (f) functioning. I explain the core aspects of these six theoretical paradigms and show how they help guide QOL…

Explaining Constrains Causal Learning in Childhood

ERIC Educational Resources Information Center

Walker, Caren M.; Lombrozo, Tania; Williams, Joseph J.; Rafferty, Anna N.; Gopnik, Alison

2017-01-01

Three experiments investigate how self-generated explanation influences children's causal learning. Five-year-olds (N = 114) observed data consistent with two hypotheses and were prompted to explain or to report each observation. In Study 1, when making novel generalizations, explainers were more likely to favor the hypothesis that accounted for…

Explaining the Gender Wealth Gap

PubMed Central

Ruel, Erin; Hauser, Robert M.

2013-01-01

To assess and explain the United States’ gender wealth gap, we use the Wisconsin Longitudinal Study to examine wealth accumulated by a single cohort over 50 years by gender, by marital status, and limited to the respondents who are their family’s best financial reporters. We find large gender wealth gaps between currently married men and women, and never-married men and women. The never-married accumulate less wealth than the currently married, and there is a marital disruption cost to wealth accumulation. The status-attainment model shows the most power in explaining gender wealth gaps between these groups explaining about one-third to one-half of the gap, followed by the human-capital explanation. In other words, a lifetime of lower earnings for women translates into greatly reduced wealth accumulation. A gender wealth gap remains between married men and women after controlling for the full model that we speculate may be related to gender differences in investment strategies and selection effects. PMID:23264038

Knowledge Wisdom and Networks: A Project Management Centre of Excellence Example

ERIC Educational Resources Information Center

Walker, Derek H. T.; Christenson, Dale

2005-01-01

Purpose: This conceptual paper aims to explain how "project management centres of excellence (CoEs)", a particular class of knowledge network, can be viewed as providing great potential for assisting project management (PM) teams to make wise decisions. Design/methodology/approach: The paper presents a range of knowledge network types and…

Explaining Human Behavior.

ERIC Educational Resources Information Center

Olson, Alton T.; And Others

The Deductive-Nomological (D-N) model of human behavior is useful and provides the most objective explanation when it is appropriate but it is not necessarily an all-inclusive statement. For instance, explaining human behavior is always an act that entails languages and theories that are value laden and reveal human choices; however the D-N model…

Regulatory interactions between long noncoding RNA LINC00968 and miR-9-3p in non-small cell lung cancer: A bioinformatic analysis based on miRNA microarray, GEO and TCGA.

PubMed

Li, Dong-Yao; Chen, Wen-Jie; Shang, Jun; Chen, Gang; Li, Shi-Kang

2018-06-01

Long non-coding RNAs (lncRNAs) have been demonstrated to mediate carcinogenesis in various types of cancer. However, the regulatory role of lncRNA LINC00968 in lung adenocarcinoma remains unclear. The microRNA (miRNA) expression in LINC00968-overexpressing human lung adenocarcinoma A549 cells was detected using miRNA microarray analysis. miR-9-3p was selected for further analysis, and its expression was verified in the Gene Expression Omnibus (GEO) database. In addition, the regulatory axis of LINC00968 was validated using The Cancer Genome Atlas (TCGA) database. Results of the GEO database indicated miR-9-3p expression in lung adenocarcinoma was significantly higher compared with normal tissues. Functional enrichment analyses of the target genes of miR-9-3p indicated protein binding and the AMP-activated protein kinase pathway were the most enriched Gene Ontology and KEGG terms, respectively. Combining target genes with the correlated genes of LINC00968 and miR-9-3p, 120 objective genes were obtained, which were used to construct a protein-protein interaction (PPI) network. Cyclin A2 (CCNA2) was identified to have a vital role in the PPI network. Significant correlations were detected between LINC00968, miR-9-3p and CCNA2 in lung adenocarcinoma. The LINC00968/miR-9-3p/CCNA2 regulatory axis provides a new foundation for further evaluating the regulatory mechanisms of LINC00968 in lung adenocarcinoma.

High/Scope Outreach Project. Final Report. October 1, 1983-September 30, 1984.

ERIC Educational Resources Information Center

High/Scope Educational Research Foundation, Ypsilanti, MI.

The final report reviews accomplishments of an outreach project designed to provide technical assistance and training to early childhood programs for handicapped children. The project features the Cognitively Oriented Preschool Curriculum, a developmental approach based on Piagetian theory and explained to build on the child's accomplishments. A…

An Interview with Mark Ahlness and Jean Carmody about the Earth Day Groceries Project.

ERIC Educational Resources Information Center

Strangman, Nicole

2002-01-01

Outlines an interview with Mark Ahlness, a third-grade teacher at Arbor Heights Elementary School in Seattle, Washington, and Jean Carmody, an art teacher at two elementary schools in Cranston, Rhode Island. Describes their collaborative project called the Earth Day Groceries Project. Explains that in this Internet project, students decorate…

Using Web-Based Peer Benchmarking to Manage the Client-Based Project

ERIC Educational Resources Information Center

Raska, David; Keller, Eileen Weisenbach; Shaw, Doris

2013-01-01

The complexities of integrating client-based projects into marketing courses provide challenges for the instructor but produce richness of context and active learning for the student. This paper explains the integration of Web-based peer benchmarking as a means of improving student performance on client-based projects within a single semester in…

Clinical value of survivin and its underlying mechanism in ovarian cancer: A bioinformatics study based on GEO and TCGA data mining.

PubMed

Li, Xiao-Jiao; Pang, Jin-Shu; Li, Yao-Mei; Ahmed, Farah Abdirahman; He, Rong-Quan; Ma, Jie; Ma, Fu-Chao; Chen, Gang

2018-03-01

An increasing number of studies have confirmed that survivin (BIRC5) plays essential roles in ovarian cancer. Nevertheless, inconsistent or controversial results exist in some studies. In the present study, we sought to determine the clinical significance of survivin and its potential molecular pathways. The correlation between survivin (BIRC5) expression and diagnostic value, prognostic value and clinicopathological features was assessed by meta-analysis with more than 4000 patients from literature, GEO and TCGA. In addition, the potential molecular mechanism of survivin in ovarian cancer was also determined. The pooled sensitivity and specificity were 0.71 (95%CI: 0.68-0.74) and 0.97 (95%CI: 0.94-0.98), respectively. The AUC of sROC was 0.8765. The results showed that there was also a significant relationship between survivin expression and poor overall survival (HR: 1.24, 95%CI: 1.14-1.35, p < 0.001), disease-free survival (HR: 1.53, 95%CI: 0.57-4.09, p < 0.001), as well as higher recurrence rate (HR: 1.11, 95%CI: 0.97-1.27). Moreover, survivin expression was also associated with tumor progression (cancerous vs. benign, OR: 11.29, 95%CI: 8.96-14.24, p < 0.001), TNM stage (III + IV vs. I + II, OR: 5.38, 95%CI: 4.16-6.97, p < 0.001), histological grades (G3 vs. G1 ∼ G2, OR: 4.36, 95%CI: 3.29-5.77, p < 0.001), and lymphatic metastasis (metastasis vs. non-metastasis, 3.35, 95%CI 2.36-4.75, p < 0.001). Bioinformatics analysis revealed the 50 most frequently altered neighboring genes of survivin in OC, and then Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted. GO analysis showed that these genes were related to signal conduction, cell cycle, apoptosis, and metabolism. KEGG pathways analysis indicated that these genes were primarily enriched in mitotic prometaphase, PLK1 signaling events and the regulation of glucokinase by the glucokinase regulatory protein. Survivin (BIRC5) expression

ISIS and META projects

NASA Technical Reports Server (NTRS)

Birman, Kenneth; Cooper, Robert; Marzullo, Keith

1990-01-01

ISIS and META are two distributed systems projects at Cornell University. The ISIS project, has developed a new methodology, virtual synchrony, for writing robust distributed software. This approach is directly supported by the ISIS Toolkit, a programming system that is distributed to over 300 academic and industrial sites. Several interesting applications that exploit the strengths of ISIS, including an NFS-compatible replicated file system, are being developed. The META project, is about distributed control in a soft real time environment incorporating feedback. This domain encompasses examples as diverse as monitoring inventory and consumption on a factory floor and performing load-balancing on a distributed computing system. One of the first uses of META is for distributed application management: the tasks of configuring a distributed program, dynamically adapting to failures, and monitoring its performance. Recent progress and current plans are presented. This approach to distributed computing, a philosophy that is believed to significantly distinguish the work from that of others in the field, is explained.

A model of how different biology experts explain molecular and cellular mechanisms.

PubMed

Trujillo, Caleb M; Anderson, Trevor R; Pelaez, Nancy J

2015-01-01

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do explanations made by experts from different biology subdisciplines at a university support the validity of this model? Guided by the modeling framework of R. S. Justi and J. K. Gilbert, the validity of an initial model was tested by asking seven biologists to explain a molecular mechanism of their choice. Data were collected from interviews, artifacts, and drawings, and then subjected to thematic analysis. We found that biologists explained the specific activities and organization of entities of the mechanism. In addition, they contextualized explanations according to their biological and social significance; integrated explanations with methods, instruments, and measurements; and used analogies and narrated stories. The derived methods, analogies, context, and how themes informed the development of our final MACH model of mechanistic explanations. Future research will test the potential of the MACH model as a guiding framework for instruction to enhance the quality of student explanations. © 2015 C. M. Trujillo et al. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Network Meta-Analysis on the Effects of DNA Damage Response-Related Gene Mutations on Overall Survival of Breast Cancer Based on TCGA Database.

PubMed

Liu, Chang; Chang, Hong; Li, Xiao-Han; Qi, Ya-Fei; Wang, Jin-Ou; Zhang, Ying; Yang, Xiang-Hong

2017-12-01

The study was conducted for comparing the effects of 12 DNA damage response gene mutations (CHEK1, CHEK2, RAD51, BRCA1, BRCA2, MLH1, MSH2, ATM, ATR, MDC1, PARP1, and FANCF) on the overall survival (OS) of breast cancer (BC) patients. We searched the Cancer Genome Atlas (TCGA) database from inception to September 2016. Studies that investigated the association between 12 DNA damage responses related genes and BC consolidated into this Network meta-analysis, by comparing directly or indirectly to evaluate the hazard rate (HR) value and the surface under the cumulative sequence ranking curves (SUCRA). In total four articles were involved. Our results demonstrated 12 DNA damage response gene mutations were associated to the poor prognosis of BC patients (CHEK1: HR = 9.9, 95%CI = 3.6-26.0; CHEK2: HR = 6.9, 95%CI = 3.1-15.0; RAD51: HR = 5.8, 95%CI = 2.2-15.0; BRCA1: HR = 2.8, 95%CI = 1.3-6.1; BRCA2: HR = 3.9, 95%CI = 2.0-7.7; MLH1: HR = 11.0, 95%CI = 3.4-33.0; MSH2: HR = 6.5, 95%CI = 2.1-20.0; ATM: HR = 5.6, 95%CI = 2.6-12.0; ATR: HR = 2.9, 95%CI = 1.3-6.9; MDC1: HR = 15.0, 95%CI = 5.0-45.0; PARP1: HR = 3.4, 95%CI = 1.8-6.6; FANCF: HR = 6.0, 95%CI = 1.8-20.0). SUCRA results revealed that the mutation of MDC1 gene was related to the worst prognosis in patients with BC (SUCRA = 17.32%). DNA damage response gene mutations were associated to the poor prognosis in patients with BC and the BC patients with MDC1 gene mutation had the worst prognosis. J. Cell. Biochem. 118: 4728-4734, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Robotic Form-Finding and Construction Based on the Architectural Projection Logic

NASA Astrophysics Data System (ADS)

Zexin, Sun; Mei, Hongyuan

2017-06-01

In this article we analyze the relationship between the architectural drawings and form-finding, indicate that architects should reuse and redefine the traditional architectural drawings as a from-finding tool. Explain the projection systems and analyze how these systems affected the architectural design. Use robotic arm to do the experiment and establish a cylindrical projection form-finding system.

Nabisco Foods Division--"New Indy" Workplace Literacy Project. Final Performance Report.

ERIC Educational Resources Information Center

Ivy Tech State Coll., Indianapolis, IN.

This document contains a final report, evaluation, and curriculum materials from a project conducted at the RJR Nabisco plant in Indianapolis to upgrade the literacy and numeracy skills of the workers to facilitate technological changes to production lines. As the final report explains, although the goal of the project was to recruit and test 150…

The Project-Approach to GIS as an Integrative Classroom Technology: An Environmental Case Study.

ERIC Educational Resources Information Center

Gatrell, Jay D.; Oshiro, Kenji K.

2001-01-01

Explains how Geographic Information Systems (GIS) influences geography curricula and how project-based learning can be applied to GIS experiences. Introduces a project investigating non-geography college students' design and implementation of a environmental GIS application. (Contains 16 references.) (YDS)

A Prominence Puzzle Explained?

NASA Astrophysics Data System (ADS)

Yeates, A. R.; Mackay, D. H.; van Ballegooijen, A. A.

2009-02-01

Long-standing observations reveal a global organisation of the magnetic field direction in solar prominences (aka filaments), large clouds of cool dense plasma suspended in the Sun's hot corona. However, theorists have thus far been unable to explain the origin of this hemispheric pattern. In particular, simple shearing by large-scale surface motions would appear to lead to the wrong magnetic field direction. To explain the observations, we have developed a new model of the global magnetic field evolution in the solar corona over six months. For the first time our model can follow the build-up of magnetic helicity and shear on a global scale, driven by flux emergence and surface motions. The model is successful in predicting the correct magnetic field direction in the vast majority of prominences tested, and has enabled us to determine the key physical mechanisms behind the mysterious hemispheric pattern.

Next-generation sequencing of translocation renal cell carcinoma reveals novel RNA splicing partners and frequent mutations of chromatin-remodeling genes.

PubMed

Malouf, Gabriel G; Su, Xiaoping; Yao, Hui; Gao, Jianjun; Xiong, Liangwen; He, Qiuming; Compérat, Eva; Couturier, Jérôme; Molinié, Vincent; Escudier, Bernard; Camparo, Philippe; Doss, Denaha J; Thompson, Erika J; Khayat, David; Wood, Christopher G; Yu, Willie; Teh, Bin T; Weinstein, John; Tannir, Nizar M

2014-08-01

MITF/TFE translocation renal cell carcinoma (TRCC) is a rare subtype of kidney cancer. Its incidence and the genome-wide characterization of its genetic origin have not been fully elucidated. We performed RNA and exome sequencing on an exploratory set of TRCC (n = 7), and validated our findings using The Cancer Genome Atlas (TCGA) clear-cell RCC (ccRCC) dataset (n = 460). Using the TCGA dataset, we identified seven TRCC (1.5%) cases and determined their genomic profile. We discovered three novel partners of MITF/TFE (LUC7L3, KHSRP, and KHDRBS2) that are involved in RNA splicing. TRCC displayed a unique gene expression signature as compared with other RCC types, and showed activation of MITF, the transforming growth factor β1 and the PI3K complex targets. Genes differentially spliced between TRCC and other RCC types were enriched for MITF and ID2 targets. Exome sequencing of TRCC revealed a distinct mutational spectrum as compared with ccRCC, with frequent mutations in chromatin-remodeling genes (six of eight cases, three of which were from the TCGA). In two cases, we identified mutations in INO80D, an ATP-dependent chromatin-remodeling gene, previously shown to control the amplitude of the S phase. Knockdown of INO80D decreased cell proliferation in a novel cell line bearing LUC7L3-TFE3 translocation. This genome-wide study defines the incidence of TRCC within a ccRCC-directed project and expands the genomic spectrum of TRCC by identifying novel MITF/TFE partners involved in RNA splicing and frequent mutations in chromatin-remodeling genes. ©2014 American Association for Cancer Research.

Heavy fermion behavior explained by bosons

NASA Technical Reports Server (NTRS)

Kallio, A.; Poykko, S.; Apaja, V.

1995-01-01

Conventional heavy fermion (HF) theories require existence of massive fermions. We show that heavy fermion phenomena can also be simply explained by existence of bosons with moderate mass but temperature dependent concentration below the formation temperature T(sub B), which in turn is close to room temperature. The bosons B(++) are proposed to be in chemical equilibrium with a system of holes h(+): B(++) = h(+) + h(+). This equilibrium is governed by a boson breaking function f(T), which determines the decreasing boson density and the increasing fermion density with increasing temperature. Since HF-compounds are hybridized from minimum two elements, we assume in addition existence of another fermion component h(sub s)(+) with temperature independent density. This spectator component is thought to be the main agent in binding the bosons in analogy with electronic or muonic molecules. Using a linear boson breaking function we can explain temperature dependence of the giant linear specific heat coefficient gamma(T) coming essentially from bosons. The maxima in resistivity, Hall coefficient, and susceptibility are explained by boson localization effects due to the Wigner crystallization. The antiferromagnetic transitions in turn are explained by similar localization of the pairing fermion system when their density n(sub h)(T(sub FL)) becomes lower than n(sub WC), the critical density of Wigner crystallization. The model applies irrespective whether a compound is superconducting or not. The same model explains the occurrence of low temperature antiferromagnetism also in high-T(sub c) superconductors. The double transition in UPt3 is proposed to be due to the transition of the pairing fermion liquid from spin polarized to unpolarized state.

NASA Project Planning and Control Handbook

NASA Technical Reports Server (NTRS)

Moreland, Robert; Claunch, Cathy L.

2016-01-01

This handbook provides an overview of the fundamental principles and explains the functions and products that go into project planning and control. The 2010 Interim Results of the NASA Program Planning and Control (PPC) Study identified seven categories of activities for PPC, and those provide the basis for the seven functions described in this handbook. This handbook maps out the interfaces and interactions between PPC functions, as well as their external interfaces. This integration of information and products within and between functions is necessary to form the whole picture of how a project is progressing. The handbook descriptions are meant to facilitate consistent, common, and comprehensive approaches for providing valued analysis, assessment, and evaluation focused on the project level at NASA. The handbook also describes activities in terms of function rather than the job title or the specific person or organization responsible for the activity, which could differ by Center or size of a project. This handbook is primarily guidance for project planning and control: however, the same principles apply to programs and generally apply to institutional planning and control.

Project Success for the SLD Child, Curriculum Modification.

ERIC Educational Resources Information Center

Owens, Jean

The curriculum modification guide, developed by project success (Nebraska) through a Title III grant for language disabled elementary level students, contains suggested activities and instructional materials to be used in units of art, health, mathematics, music, science, and social studies. Explained are program planning, criteria for selecting…

Use of safety management practices for improving project performance.

PubMed

Cheng, Eddie W L; Kelly, Stephen; Ryan, Neal

2015-01-01

Although site safety has long been a key research topic in the construction field, there is a lack of literature studying safety management practices (SMPs). The current research, therefore, aims to test the effect of SMPs on project performance. An empirical study was conducted in Hong Kong and the data collected were analysed with multiple regression analysis. Results suggest that 3 of the 15 SMPs, which were 'safety committee at project/site level', 'written safety policy', and 'safety training scheme' explained the variance in project performance significantly. Discussion about the impact of these three SMPs on construction was provided. Assuring safe construction should be an integral part of a construction project plan.

Project T.E.A.M. (Technical Education Advancement Modules). Introduction to Industrial Physics.

ERIC Educational Resources Information Center

Whisenhunt, James E.

This instructional guide, one of a series developed by the Technical Education Advancement Modules (TEAM) project, is a 20-hour introduction to industrial physics that explains and demonstrates to industrial maintenance mechanics the direct relationship of physics to machinery. Project TEAM is intended to upgrade basic technical competencies of…

Building Bridges: A Study of Coordination in Projects

ERIC Educational Resources Information Center

Hemphill, Libby Marie

2009-01-01

In our efforts to understand how collaborative work can be accomplished, we often turn to discussions of "coordination" for help. However, the concept of coordination is inadequate for explaining the many interdependent processes at work within successful collaborations. In this dissertation, I examined a collaborative construction project--the…

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.

PubMed

Cole, Charles; Krampis, Konstantinos; Karagiannis, Konstantinos; Almeida, Jonas S; Faison, William J; Motwani, Mona; Wan, Quan; Golikov, Anton; Pan, Yang; Simonyan, Vahan; Mazumder, Raja

2014-01-27

Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data

PubMed Central

2014-01-01

Background Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. Results To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire

Explaining Ramps with Models

ERIC Educational Resources Information Center

Campbell, Todd; Neilson, Drew

2016-01-01

In this article Campbell and Neilson discuss several design strategies developed or adopted that were found particularly helpful when sequencing a unit that focused on learning about motion and acceleration. Students were expected to predict, observe, and explain why a ball traveled down one ramp faster than the other. Before engaging students,…

Thermally-assisted Magma Emplacement Explains Restless Calderas.

PubMed

Amoruso, Antonella; Crescentini, Luca; D'Antonio, Massimo; Acocella, Valerio

2017-08-11

Many calderas show repeated unrest over centuries. Though probably induced by magma, this unique behaviour is not understood and its dynamics remains elusive. To better understand these restless calderas, we interpret deformation data and build thermal models of Campi Flegrei caldera, Italy. Campi Flegrei experienced at least 4 major unrest episodes in the last decades. Our results indicate that the inflation and deflation of magmatic sources at the same location explain most deformation, at least since the build-up of the last 1538 AD eruption. However, such a repeated magma emplacement requires a persistently hot crust. Our thermal models show that this repeated emplacement was assisted by the thermal anomaly created by magma that was intruded at shallow depth ~3 ka before the last eruption. This may explain the persistence of the magmatic sources promoting the restless behaviour of the Campi Flegrei caldera; moreover, it explains the crystallization, re-melting and mixing among compositionally distinct magmas recorded in young volcanic rocks. Our model of thermally-assisted unrest may have a wider applicability, possibly explaining also the dynamics of other restless calderas.

Cancers Selected for Study - TCGA

Cancer.gov

The Cancer Genome Atlas researchers are mapping the genetic changes in 33 cancers. Find out which cancers have been selected for study, the criteria for selection and the scientific questions being asked about each cancer.

Which Genes Drive Cancers? - TCGA

Cancer.gov

Associate Professor of Medicine at the Dana-Farber Cancer Institute, William Hahn, describes the method his lab has developed to tease apart the crucial driver mutations from passenger mutations in ovarian cancer.

Genomic Data Commons launches - TCGA

Cancer.gov

The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features

PubMed Central

Bakas, Spyridon; Akbari, Hamed; Sotiras, Aristeidis; Bilello, Michel; Rozycki, Martin; Kirby, Justin S.; Freymann, John B.; Farahani, Keyvan; Davatzikos, Christos

2017-01-01

Gliomas belong to a group of central nervous system tumors, and consist of various sub-regions. Gold standard labeling of these sub-regions in radiographic imaging is essential for both clinical and computational studies, including radiomic and radiogenomic analyses. Towards this end, we release segmentation labels and radiomic features for all pre-operative multimodal magnetic resonance imaging (MRI) (n=243) of the multi-institutional glioma collections of The Cancer Genome Atlas (TCGA), publicly available in The Cancer Imaging Archive (TCIA). Pre-operative scans were identified in both glioblastoma (TCGA-GBM, n=135) and low-grade-glioma (TCGA-LGG, n=108) collections via radiological assessment. The glioma sub-region labels were produced by an automated state-of-the-art method and manually revised by an expert board-certified neuroradiologist. An extensive panel of radiomic features was extracted based on the manually-revised labels. This set of labels and features should enable i) direct utilization of the TCGA/TCIA glioma collections towards repeatable, reproducible and comparative quantitative studies leading to new predictive, prognostic, and diagnostic assessments, as well as ii) performance evaluation of computer-aided segmentation methods, and comparison to our state-of-the-art method. PMID:28872634

Explaining drug policy: Towards an historical sociology of policy change.

PubMed

Seddon, Toby

2011-11-01

The goal of seeking to understand the development over time of drug policies is a specific version of the more general intellectual project of finding ways of explaining social change. The latter has been a preoccupation of some of the greatest thinkers within the social sciences of the last 200 years, from Foucault all the way back to the three nineteenth-century pioneers, Marx, Durkheim and Weber. I describe this body of work as 'historical sociology'. In this paper, I outline how a particular approach to historical sociology can be fruitfully drawn upon to understand the development of drug policy, using by way of illustration the example of the analysis of a recent transformation in British drug policy: the rise of the criminal justice agenda. I conclude by arguing that by looking at developments in drug policy in this way, some new insights are opened up. Copyright © 2011 Elsevier B.V. All rights reserved.

[The human variome project and its progress].

PubMed

Gao, Shan; Zhang, Ning; Zhang, Lei; Duan, Guang-You; Zhang, Tao

2010-11-01

The main goal of post genomics is to explain how the genome, the map of which has been constructed in the Human Genome Project, affacts activities of life. This leads to generate multiple "omics": structural genomics, functional genomics, proteomics, metabonomics, et al. In Jun. 2006, Melbourne, Australia, Human Genome Variation Society (HGVS) initiated the Human Variome Project (HVP) to collect all the sequence variation and polymorphism data worldwidely. HVP is to search and determine those mutations related with human diseases by association study between genetype and phenotype on the scale of genome level and other methods. Those results will be translated into clinical application. Considering the potential effects of this project on human health, this paper introduced its origin and main content in detail and discussed its meaning and prospect.

Chapter 1: An Introduction to the Saber-Tooth Project.

ERIC Educational Resources Information Center

Ward, Phillip

1999-01-01

Introduces a theme issue on the Saber-Tooth Project, an ongoing reform effort involving a university and school district that collaborate to improve middle school physical education by improving teaching conditions and engaging teachers in professional development emphasizing curriculum improvement. The monograph explains the nature of…

Exposing the cancer genome atlas as a SPARQL endpoint.

PubMed

Deus, Helena F; Veiga, Diogo F; Freire, Pablo R; Weinstein, John N; Mills, Gordon B; Almeida, Jonas S

2010-12-01

The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to characterize several types of cancer. Datasets from biomedical domains such as TCGA present a particularly challenging task for those interested in dynamically aggregating its results because the data sources are typically both heterogeneous and distributed. The Linked Data best practices offer a solution to integrate and discover data with those characteristics, namely through exposure of data as Web services supporting SPARQL, the Resource Description Framework query language. Most SPARQL endpoints, however, cannot easily be queried by data experts. Furthermore, exposing experimental data as SPARQL endpoints remains a challenging task because, in most cases, data must first be converted to Resource Description Framework triples. In line with those requirements, we have developed an infrastructure to expose clinical, demographic and molecular data elements generated by TCGA as a SPARQL endpoint by assigning elements to entities of the Simple Sloppy Semantic Database (S3DB) management model. All components of the infrastructure are available as independent Representational State Transfer (REST) Web services to encourage reusability, and a simple interface was developed to automatically assemble SPARQL queries by navigating a representation of the TCGA domain. A key feature of the proposed solution that greatly facilitates assembly of SPARQL queries is the distinction between the TCGA domain descriptors and data elements. Furthermore, the use of the S3DB management model as a mediator enables queries to both public and protected data without the need for prior submission to a single data source. Copyright © 2010 Elsevier Inc. All rights reserved.

Exposing the cancer genome atlas as a SPARQL endpoint

PubMed Central

Deus, Helena F.; Veiga, Diogo F.; Freire, Pablo R.; Weinstein, John N.; Mills, Gordon B.; Almeida, Jonas S.

2011-01-01

The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to characterize several types of cancer. Datasets from biomedical domains such as TCGA present a particularly challenging task for those interested in dynamically aggregating its results because the data sources are typically both heterogeneous and distributed. The Linked Data best practices offer a solution to integrate and discover data with those characteristics, namely through exposure of data as Web services supporting SPARQL, the Resource Description Framework query language. Most SPARQL endpoints, however, cannot easily be queried by data experts. Furthermore, exposing experimental data as SPARQL endpoints remains a challenging task because, in most cases, data must first be converted to Resource Description Framework triples. In line with those requirements, we have developed an infrastructure to expose clinical, demographic and molecular data elements generated by TCGA as a SPARQL endpoint by assigning elements to entities of the Simple Sloppy Semantic Database (S3DB) management model. All components of the infrastructure are available as independent Representational State Transfer (REST) Web services to encourage reusability, and a simple interface was developed to automatically assemble SPARQL queries by navigating a representation of the TCGA domain. A key feature of the proposed solution that greatly facilitates assembly of SPARQL queries is the distinction between the TCGA domain descriptors and data elements. Furthermore, the use of the S3DB management model as a mediator enables queries to both public and protected data without the need for prior submission to a single data source. PMID:20851208

When Twitter Meets Advocacy: A Multicultural Undergraduate Research Project from a First-Year Seminar

ERIC Educational Resources Information Center

Maben, Sarah; Helvie-Mason, Lora

2017-01-01

Two professors share how they combined Web 2.0, multicultural themes, and undergraduate research in a first-year seminar. The professors explain the "perfect storm" of a project in which undergraduate students collected and analyzed tweets from advocates for various multicultural causes to produce their first collegiate research project.…

Exploring the explaining quality of physics online explanatory videos

NASA Astrophysics Data System (ADS)

Kulgemeyer, Christoph; Peters, Cord H.

2016-11-01

Explaining skills are among the most important skills educators possess. Those skills have also been researched in recent years. During the same period, another medium has additionally emerged and become a popular source of information for learners: online explanatory videos, chiefly from the online video sharing website YouTube. Their content and explaining quality remain to this day mostly unmonitored, as well is their educational impact in formal contexts such as schools or universities. In this study, a framework for explaining quality, which has emerged from surveying explaining skills in expert-novice face-to-face dialogues, was used to explore the explaining quality of such videos (36 YouTube explanatory videos on Kepler’s laws and 15 videos on Newton’s third law). The framework consists of 45 categories derived from physics education research that deal with explanation techniques. YouTube provides its own ‘quality measures’ based on surface features including ‘likes’, views, and comments for each video. The question is whether or not these measures provide valid information for educators and students if they have to decide which video to use. We compared the explaining quality with those measures. Our results suggest that there is a correlation between explaining quality and only one of these measures: the number of content-related comments.

The Effect of Coexistence of a Pair of Mutated Oncogenes on the Survival Rate of Invasive Breast Carcinoma Patients

NASA Astrophysics Data System (ADS)

Nair, D. R.

2017-12-01

The purpose of this project was to determine the effect of two mutated oncogenes on the survival rate from invasive breast carcinoma when in comparison to the mutation of a single oncogene on the survival rate. An oncogene is defined as a gene, that when mutated, can lead to cancer. The two oncogenes used in this project were human epidermal growth factor receptor 2 (HER2) and c-myc (MYC). HER2 and MYC are both oncogenes that contribute to the formation of cancer. HER2 proteins are receptors on breast cells, and when the HER2 gene is mutated, there is an overexpression of HER2 protein on the breast cell. This makes the breast cells proliferate uncontrollably. MYC is a gene that codes for a transcription factor that plays a role in cell cycle progression. The overexpression of MYC also leads to the proliferation of cells. I hypothesized that if there is a mutation in both the MYC and HER2 genes, then the survival rate of invasive breast carcinoma patients will be lower compared to patients with the mutations of only MYC or HER2. To test this hypothesis, we conducted individual gene searches in CBioPortal for HER2 in the datasets from the studies titled TCGA Nature 2012, TCGA Cell 2015, and TCGA Provisional. We conducted individual gene searches in CBioPortal for MYC in the same datasets. The survival rate data was then exported and analyzed for patients with mutations of either HER2 or MYC and with mutations of both genes. To determine the cases that had both HER2 and MYC mutations, we found the overlapping cases in both HER2 and MYC groups for all three datasets. We calculated the median of the survival data for cases where either HER2 or MYC was mutated and cases where both MYC and HER2 were mutated. From the first dataset, the median of MYC data was 95.53, HER2 data was 95.83, and both HER2 and MYC data was 91.24. In the second dataset, the median of MYC data was 92.17 , HER2 data was 93.5, and both HER2 and MYC data was 87.95 . In the third dataset, the median

Using endemic road features to create self-explaining roads and reduce vehicle speeds.

PubMed

Charlton, Samuel G; Mackie, Hamish W; Baas, Peter H; Hay, Karen; Menezes, Miguel; Dixon, Claire

2010-11-01

This paper describes a project undertaken to establish a self-explaining roads (SER) design programme on existing streets in an urban area. The methodology focussed on developing a process to identify functional road categories and designs based on endemic road characteristics taken from functional exemplars in the study area. The study area was divided into two sections, one to receive SER treatments designed to maximise visual differences between road categories, and a matched control area to remain untreated for purposes of comparison. The SER design for local roads included increased landscaping and community islands to limit forward visibility, and removal of road markings to create a visually distinct road environment. In comparison, roads categorised as collectors received increased delineation, addition of cycle lanes, and improved amenity for pedestrians. Speed data collected 3 months after implementation showed a significant reduction in vehicle speeds on local roads and increased homogeneity of speeds on both local and collector roads. The objective speed data, combined with residents' speed choice ratings, indicated that the project was successful in creating two discriminably different road categories. 2010 Elsevier Ltd. All rights reserved.

A radiosensitivity gene signature and PD-L1 status predict clinical outcome of patients with invasive breast carcinoma in The Cancer Genome Atlas (TCGA) dataset.

PubMed

Jang, Bum-Sup; Kim, In Ah

2017-09-01

We investigated the link between the radiosensitivity gene signature and programmed cell death ligand 1 (PD-L1) status and clinical outcome in order to identify a group of patients that would possibly receive clinical benefit of radiotherapy (RT) combined with anti-PD1/PD-L1 therapy. We validated the identified gene signature related to radiosensitivity and analyzed the PD-L1 status of invasive breast cancer in The Cancer Genome Atlas (TCGA) dataset. To validate the gene signature, 1045 patients were selected and divided into two clusters using a consensus clustering algorithm based on their radiosensitive (RS) or radioresistant (RR) designation according to their prognosis. Patients were also stratified as PD-L1-high or PD-L1-low based on the median value of CD274 mRNA expression level as surrogates of PD-L1. Patents assigned to the RS group had decreased risk of recurrence-free survival (RFS) rate than patients in the RR group by univariate analysis (HR 0.45, 95% CI 0.25-0.81, p=0.008) only when treated with RT. The RS group was independently associated with the PD-L1-high group, and CD274 mRNA expression was significantly higher in the RS group (p<0.001) than the RR group. In the PD-L1-high group, the RS group was associated with better RFS compared to the RR group (HR 0.37, 95% CI 0.16-0.87, p=0.022) in multivariate analysis. The level of PD-L1 expression may represent the immunogenicity of tumors, and thus, we speculated that the PD-L1-high group had more immunogenic tumors, which could be more sensitive to radiation-induced immunologic cell death. We first evaluated the predictive value of the radiosensitivity gene signature and described a relationship with this radiosensitivity gene signature and PD-L1. The radiosensitivity gene signature and PD-L1 status were important factors for prediction of the clinical outcome of RT in patients with invasive breast cancer and may be used for selecting patients who will benefit from RT combined with anti-PD1/PDL1

The Azimuth Project: an Open-Access Educational Resource

NASA Astrophysics Data System (ADS)

Baez, J. C.

2012-12-01

The Azimuth Project is an online collaboration of scientists, engineers and programmers who are volunteering their time to do something about a wide range of environmental problems. The project has several aspects: 1) a wiki designed to make reliable, sourced information easy to find and accessible to a technically literate nonexperts, 2) a blog featuring expository articles and news items, 3) a project to write programs that explain basic concepts of climate physics and illustrate principles of good open-source software design, and 4) a project to develop mathematical tools for studying complex networked systems. We discuss the progress so far and some preliminary lessons. For example, enlisting the help of experts outside academia highlights the problems with pay-walled journals and the benefits of open access, as well as differences between how software development is done commercially, in the free software community, and in academe.

Overestimation of the Projected Size of Objects on the Surface of Mirrors and Windows

ERIC Educational Resources Information Center

Lawson, Rebecca; Bertamini, Marco; Liu, Dan

2007-01-01

Four experiments investigated judgments of the size of projections of objects on the glass surface of mirrors and windows. The authors tested different ways of explaining the task to overcome the difficulty that people had in understanding what the projection was, and they varied the distance of the observer and the object to the mirror or window…

Evaluation of the Field Test of Project Information Packages: Volume III--Resource Cost Analysis.

ERIC Educational Resources Information Center

Al-Salam, Nabeel; And Others

The third of three volumes evaluating the first year field test of the Project Information Packages (PIPs) provides a cost analysis study as a key element in the total evaluation. The resource approach to cost analysis is explained and the specific resource methodology used in the main cost analysis of the 19 PIP field-test projects detailed. The…

Project Scheduling Based on Risk of Gas Transmission Pipe

NASA Astrophysics Data System (ADS)

Silvianita; Nurbaity, A.; Mulyadi, Y.; Suntoyo; Chamelia, D. M.

2018-03-01

The planning of a project has a time limit on which must be completed before or right at a predetermined time. Thus, in a project planning, it is necessary to have scheduling management that is useful for completing a project to achieve maximum results by considering the constraints that will exists. Scheduling management is undertaken to deal with uncertainties and negative impacts of time and cost in project completion. This paper explains about scheduling management in gas transmission pipeline project Gresik-Semarang to find out which scheduling plan is most effectively used in accordance with its risk value. Scheduling management in this paper is assissted by Microsoft Project software to find the critical path of existing project scheduling planning data. Critical path is the longest scheduling path with the fastest completion time. The result is found a critical path on project scheduling with completion time is 152 days. Furthermore, the calculation of risk is done by using House of Risk (HOR) method and it is found that the critical path has a share of 40.98 percent of all causes of the occurence of risk events that will be experienced.

Astronomy Explained

NASA Astrophysics Data System (ADS)

North, Gerald

Every year large numbers of people take up the study of astronomy, mostly at amateur level. There are plenty of elementary books on the market, full of colourful photographs, but lacking in proper explanations of how and why things are as they are. Many people eventually wish to go beyond the 'coffee-table book' stage and study this fascinating subject in greater depth. This book is written for them. In addition, many people sit for public examinations in this subject each year and this book is also intended to be of use to them. All the topics from the GCSE syllabus are covered here, with sample questions at the end of each chapter. Astronomy Explained provides a comprehensive treatment of the subject in more depth than is usually found in elementary works, and will be of interest to both amateur astronomers and students of astronomy.

Regulation of Breast Cancer Stem Cell by Tissue Rigidity

DTIC Science & Technology

2015-06-01

analysis. The TCGA breast cancer gene expression data set (TCGA BRCA G4502A_07_3) was downloaded from the UCSC Cancer Genome Browser (https:// genome ...Public Release; Distribution Unlimited The views, opinions and/or findings contained in this report are those of the author(s) and should not be...construed as an official Department of the Army position, policy or decision unless so designated by other documentation. Report Documentation Page Form

Systematic Evaluation of the "Forests in Schools" (SIS) Project.

ERIC Educational Resources Information Center

School Research Newsletter, 1985

1985-01-01

The purpose of an inquiry was to study the feasibility, content, mediation, and results of the Swedish "Forests in Schools" (SIS) project, an example of a link between schools and working life (the latter represented by forest enterprise in general). It also sought to describe and, if possible, explain the effects of the activities…

Green Schools Energy Project: A Step-by-Step Manual.

ERIC Educational Resources Information Center

Quigley, Gwen

This publication contains a step-by-step guide for implementing an energy-saving project in local school districts: the installation of newer, more energy-efficient "T-8" fluorescent tube lights in place of "T-12" lights. Eleven steps are explained in detail: (1) find out what kind of lights the school district currently uses;…

Explaining Infinite Series--An Exploration of Students' Images

ERIC Educational Resources Information Center

Champney, Danielle Dawn

2013-01-01

This study uses self-generated representations (SGR)--images produced in the act of explaining--as a means of uncovering what university calculus students understand about infinite series convergence. It makes use of student teaching episodes, in which students were asked to explain to a peer what that student might have missed had they been…

Teachers mathematical communication profile in explaining subject matter

NASA Astrophysics Data System (ADS)

Umami, Rohmatul; Budayasa, I. Ketut; Suwarsono, St.

2017-12-01

This study aimed to see a teachers mathematical communication profile in explaining a subject matter. It is a qualitative research. A high-school junior teacher (i.e., a teacher with 1- to 5-year experience) teaching mathematics at X-Social Class was selected as the subject of this study. The data was collected by observing the teachers mathematical communication in explaining a given material (i.e., the rule of sine) in class and an in-depth interview would be organized respectively. The result showed that the junior teacher explained the subject matter in systematic, complete, fluent, and centered manner. In this case, she began with reminding students on the previous material related to the current material to be learned, informing the current learning objectives, and finally delivering the subject matter. To support her explanation, the teacher also provided some related information, led the students attention into the given material by asking them particular related questions, and did not use any confusing terms. However, the study found that some of high-school teachers still used less appropriate language in explaining materials.

Explaining errors in children's questions.

PubMed

Rowland, Caroline F

2007-07-01

The ability to explain the occurrence of errors in children's speech is an essential component of successful theories of language acquisition. The present study tested some generativist and constructivist predictions about error on the questions produced by ten English-learning children between 2 and 5 years of age. The analyses demonstrated that, as predicted by some generativist theories [e.g. Santelmann, L., Berk, S., Austin, J., Somashekar, S. & Lust. B. (2002). Continuity and development in the acquisition of inversion in yes/no questions: dissociating movement and inflection, Journal of Child Language, 29, 813-842], questions with auxiliary DO attracted higher error rates than those with modal auxiliaries. However, in wh-questions, questions with modals and DO attracted equally high error rates, and these findings could not be explained in terms of problems forming questions with why or negated auxiliaries. It was concluded that the data might be better explained in terms of a constructivist account that suggests that entrenched item-based constructions may be protected from error in children's speech, and that errors occur when children resort to other operations to produce questions [e.g. Dabrowska, E. (2000). From formula to schema: the acquisition of English questions. Cognitive Liguistics, 11, 83-102; Rowland, C. F. & Pine, J. M. (2000). Subject-auxiliary inversion errors and wh-question acquisition: What children do know? Journal of Child Language, 27, 157-181; Tomasello, M. (2003). Constructing a language: A usage-based theory of language acquisition. Cambridge, MA: Harvard University Press]. However, further work on constructivist theory development is required to allow researchers to make predictions about the nature of these operations.

Integrative, multimodal analysis of glioblastoma using TCGA molecular data, pathology images, and clinical outcomes.

PubMed

Kong, Jun; Cooper, Lee A D; Wang, Fusheng; Gutman, David A; Gao, Jingjing; Chisolm, Candace; Sharma, Ashish; Pan, Tony; Van Meir, Erwin G; Kurc, Tahsin M; Moreno, Carlos S; Saltz, Joel H; Brat, Daniel J

2011-12-01

Multimodal, multiscale data synthesis is becoming increasingly critical for successful translational biomedical research. In this letter, we present a large-scale investigative initiative on glioblastoma, a high-grade brain tumor, with complementary data types using in silico approaches. We integrate and analyze data from The Cancer Genome Atlas Project on glioblastoma that includes novel nuclear phenotypic data derived from microscopic slides, genotypic signatures described by transcriptional class and genetic alterations, and clinical outcomes defined by response to therapy and patient survival. Our preliminary results demonstrate numerous clinically and biologically significant correlations across multiple data types, revealing the power of in silico multimodal data integration for cancer research.

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.

PubMed

Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

2017-01-04

Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Differential loss of striatal projection neurons in Huntington disease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reiner, A.; Albin, R.L.; Anderson, K.D.

1988-08-01

Huntington disease (HD) is characterized by the loss of striatal projection neurons, which constitute the vast majority of striatal neurons. To determine whether there is differential loss among different populations of striatal projection neurons, the integrity of the axon terminal plexuses arising from the different populations of substance P-containing and enkephalin-containing striatal projection neurons was studied in striatal target areas by immunohistochemistry. Analysis of 17 HD specimens indicated that in early and middle stages of HD, enkephalin-containing neurons projecting to the external segment of the globus pallidus were much more affected than substance P-containing neurons projecting to the internal pallidalmore » segment. Furthermore, substance P-containing neurons projecting to the substantia nigra pars reticulata were more affected than those projecting to the substantia nigra pars compacta. At the most advanced stages of the disease, projections to all striatal target areas were depleted, with the exception of some apparent sparing of the striatal projection to the substantia nigra pars compacta. These finding may explain some of the clinical manifestations and pharmacology of HD. They also may aid in identifying the neural defect underlying HD and provide additional data with which to evaluate current models of HD pathogenesis.« less

Does market competition explain fairness?

PubMed

Descioli, Peter

2013-02-01

The target article by Baumard et al. uses their previous model of bargaining with outside options to explain fairness and other features of human sociality. This theory implies that fairness judgments are determined by supply and demand but humans often perceive prices (divisions of surplus) in competitive markets to be unfair.

Success in large high-technology projects: What really works?

NASA Astrophysics Data System (ADS)

Crosby, P.

2014-08-01

Despite a plethora of tools, technologies and management systems, successful execution of big science and engineering projects remains problematic. The sheer scale of globally funded projects such as the Large Hadron Collider and the Square Kilometre Array telescope means that lack of project success can impact both on national budgets, and collaborative reputations. In this paper, I explore data from contemporary literature alongside field research from several current high-technology projects in Europe and Australia, and reveal common `pressure points' that are shown to be key influencers of project control and success. I discuss the how mega-science projects sit between being merely complicated, and chaotic, and explain the importance of understanding multiple dimensions of project complexity. Project manager/leader traits are briefly discussed, including capability to govern and control such enterprises. Project structures are examined, including the challenge of collaborations. I show that early attention to building project resilience, curbing optimism, and risk alertness can help prepare large high-tech projects against threats, and why project managers need to understand aspects of `the silent power of time'. Mission assurance is advanced as a critical success function, alongside the deployment of task forces and new combinations of contingency plans. I argue for increased project control through industrial-style project reviews, and show how post-project reviews are an under-used, yet invaluable avenue of personal and organisational improvement. Lastly, I discuss the avoidance of project amnesia through effective capture of project knowledge, and transfer of lessons-learned to subsequent programs and projects.

Building a Framework that Supports Project Teams: An Example from a University/Community Collaborative Initiative

ERIC Educational Resources Information Center

Kolb, Judith A.; Sandmeyer, Louise E.

2007-01-01

In the university initiative described in this article, a series of project teams were funded to work on a variety of collaborative projects. The focus of this piece is on the framework that was developed and executed to select, support, and evaluate these teams. The framework is explained and described using data gathered throughout the study and…

Using School Change States to Analyze Comprehensive School Reform Projects

ERIC Educational Resources Information Center

Wetherill, Karen S.; Applefield, James M.

2005-01-01

Comprehensive school reform (CSR) projects are being funded throughout the United States in a determined effort to improve the performance of public education. The multidimensional nature of comprehensive school reform presents unique challenges for explaining widely discrepant outcomes among schools. These challenges are addressed in a study of 8…

[Projective identification in human relations].

PubMed

Göka, Erol; Yüksel, Fatih Volkan; Göral, F Sevinç

2006-01-01

Melanie Klein, one of the pioneers of Object Relations Theory, first defined "projective identification", which is regarded as one of the most efficacious psychoanalytic concepts after the discovery of the "unconscious". Examination of the literature on "projective identification" shows that there are various perspectives and theories suggesting different uses of this concept. Some clinicians argue that projective identification is a primitive defense mechanism observed in severe psychopathologies like psychotic disorder and borderline personality disorder, where the intra-psychic structure has been damaged severely. Others suggest it to be an indispensable part of the transference and counter-transference between the therapist and the patient during psychotherapy and it can be used as a treatment material in the therapy by a skillful therapist. The latter group expands the use of the concept through normal daily relationships by stating that projective identification is one type of communication and part of the main human relation mechanism operating in all close relationships. Therefore, they suggest that projective identification has benign forms experienced in human relations as well as malign forms seen in psychopathologies. Thus, discussions about the definition of the concept appear complex. In order to clarify and overcome the complexity of the concept, Melanie Klein's and other most important subsequent approaches are discussed in this review article. Thereby, the article aims to explain its important function in understanding the psychopathologies, psychotherapeutic relationships and different areas of normal human relations.

Seasonality of absolute humidity explains seasonality of influenza-like illness in Vietnam.

PubMed

Thai, Pham Quang; Choisy, Marc; Duong, Tran Nhu; Thiem, Vu Dinh; Yen, Nguyen Thu; Hien, Nguyen Tran; Weiss, Daniel J; Boni, Maciej F; Horby, Peter

2015-12-01

Experimental and ecological studies have shown the role of climatic factors in driving the epidemiology of influenza. In particular, low absolute humidity (AH) has been shown to increase influenza virus transmissibility and has been identified to explain the onset of epidemics in temperate regions. Here, we aim to study the potential climatic drivers of influenza-like illness (ILI) epidemiology in Vietnam, a tropical country characterized by a high diversity of climates. We specifically focus on quantifying and explaining the seasonality of ILI. We used 18 years (1993-2010) of monthly ILI notifications aggregated by province (52) and monthly climatic variables (minimum, mean, maximum temperatures, absolute and relative humidities, rainfall and hours of sunshine) from 67 weather stations across Vietnam. Seasonalities were quantified from global wavelet spectra, using the value of the power at the period of 1 year as a measure of the intensity of seasonality. The 7 climatic time series were characterized by 534 summary statistics which were entered into a regression tree to identify factors associated with the seasonality of AH. Results were extrapolated to the global scale using simulated climatic times series from the NCEP/NCAR project. The intensity of ILI seasonality in Vietnam is best explained by the intensity of AH seasonality. We find that ILI seasonality is weak in provinces experiencing weak seasonal fluctuations in AH (annual power <17.6), whereas ILI seasonality is strongest in provinces with pronounced AH seasonality (power >17.6). In Vietnam, AH and ILI are positively correlated. Our results identify a role for AH in driving the epidemiology of ILI in a tropical setting. However, in contrast to temperate regions, high rather than low AH is associated with increased ILI activity. Fluctuation in AH may be the climate factor that underlies and unifies the seasonality of ILI in both temperate and tropical regions. Alternatively, the mechanism of action of

MUFFINN: cancer gene discovery via network analysis of somatic mutation data.

PubMed

Cho, Ara; Shim, Jung Eun; Kim, Eiru; Supek, Fran; Lehner, Ben; Lee, Insuk

2016-06-23

A major challenge for distinguishing cancer-causing driver mutations from inconsequential passenger mutations is the long-tail of infrequently mutated genes in cancer genomes. Here, we present and evaluate a method for prioritizing cancer genes accounting not only for mutations in individual genes but also in their neighbors in functional networks, MUFFINN (MUtations For Functional Impact on Network Neighbors). This pathway-centric method shows high sensitivity compared with gene-centric analyses of mutation data. Notably, only a marginal decrease in performance is observed when using 10 % of TCGA patient samples, suggesting the method may potentiate cancer genome projects with small patient populations.

A model for diagnosing and explaining multiple disorders.

PubMed

Jamieson, P W

1991-08-01

The ability to diagnose multiple interacting disorders and explain them in a coherent causal framework has only partially been achieved in medical expert systems. This paper proposes a causal model for diagnosing and explaining multiple disorders whose key elements are: physician-directed hypotheses generation, object-oriented knowledge representation, and novel explanation heuristics. The heuristics modify and link the explanations to make the physician aware of diagnostic complexities. A computer program incorporating the model currently is in use for diagnosing peripheral nerve and muscle disorders. The program successfully diagnoses and explains interactions between diseases in terms of underlying pathophysiologic concepts. The model offers a new architecture for medical domains where reasoning from first principles is difficult but explanation of disease interactions is crucial for the system's operation.

Explaining Errors in Children's Questions

ERIC Educational Resources Information Center

Rowland, Caroline F.

2007-01-01

The ability to explain the occurrence of errors in children's speech is an essential component of successful theories of language acquisition. The present study tested some generativist and constructivist predictions about error on the questions produced by ten English-learning children between 2 and 5 years of age. The analyses demonstrated that,…

Promoter Methylation of PTEN Is a Significant Prognostic Factor in Melanoma Survival.

PubMed

Roh, Mi Ryung; Gupta, Sameer; Park, Kyu-Hyun; Chung, Kee Yang; Lauss, Martin; Flaherty, Keith T; Jönsson, Göran; Rha, Sun Young; Tsao, Hensin

2016-05-01

Structural compromise of the tumor suppressor gene, phosphatase and tensin homolog (PTEN), occurs in 10% of melanoma specimens, and loss of PTEN expression through DNA methylation of the PTEN promoter region has also been reported in a number of other malignancies. However, the role of PTEN promoter methylation in melanoma is not well understood. We thus sought to elucidate the prevalence of PTEN promoter methylation in melanoma specimens, its relationship to clinical features, and its impact on the outcome of patients with melanoma. PTEN promoter methylation data were acquired from an archived primary Korean melanoma cohort (KMC) of 158 patients and, for validation, 234 patients from The Cancer Genome Atlas melanoma (TCGA-MEL) cohort. Hierarchical clustering was performed to identify PTEN "high methylated" and "low methylated" samples. Subsequently, differences in clinical features and outcomes based on PTEN promoter methylation status were then analyzed using SPSS and R. In the KMC, all tumors were acquired from primary tumors and 65.7% (n = 105) were acral or mucosal by site, whereas in the TCGA-MEL cohort, 90.5% of the tumors were from regional lymph node and distant metastatic lesions. Overall, 17.7% and 45.7% of the specimens harbored BRAF mutations in the KMC and TCGA-MEL cohort, respectively. Neuroblastoma RAS viral oncogene homolog was mutated in 12.2% and 26.9% of the tumors in the KMC and TCGA-MEL cohort, respectively. In the KMC, 31 cases (19.6%) were included in the high methylated group versus 142 cases (60.7%) in the TCGA-MEL cohort (P < 0.001). Multivariate Cox-regression analysis revealed promoter methylation of PTEN to be an independent negative prognostic factor for survival in both the KMC (hazard ratio 3.76, 95% confidence interval = 1.24-11.12, P = 0.017) and TCGA-MEL cohort (HR 1.88, 95% confidence interval = 1.13-3.12, P = 0.015). Our results indicate that PTEN promoter methylation is an independent predictor for impaired survival in

Guia para la Elaboracion y Evaluacion de Proyectos de Investigacion (Guidelines for Reporting and Evaluating Research Projects).

ERIC Educational Resources Information Center

Morles, Victor

This article establishes guidelines for conducting and evaluating research projects according to a scientific methodology. The organizational format suggested here follows an outline with elements and details that should be considered in an investigation. Each part of the proposed outline is explained, and terms are defined. Project evaluation is…

Reform-based science teaching: A mixed-methods approach to explaining variation in secondary science teacher practice

NASA Astrophysics Data System (ADS)

Jetty, Lauren E.

The purpose of this two-phase, sequential explanatory mixed-methods study was to understand and explain the variation seen in secondary science teachers' enactment of reform-based instructional practices. Utilizing teacher socialization theory, this mixed-methods analysis was conducted to determine the relative influence of secondary science teachers' characteristics, backgrounds and experiences across their teacher development to explain the range of teaching practices exhibited by graduates from three reform-oriented teacher preparation programs. Data for this study were obtained from the Investigating the Meaningfulness of Preservice Programs Across the Continuum of Teaching (IMPPACT) Project, a multi-university, longitudinal study funded by NSF. In the first quantitative phase of the study, data for the sample (N=120) were collected from three surveys from the IMPPACT Project database. Hierarchical multiple regression analysis was used to examine the separate as well as the combined influence of factors such as teachers' personal and professional background characteristics, beliefs about reform-based science teaching, feelings of preparedness to teach science, school context, school culture and climate of professional learning, and influences of the policy environment on the teachers' use of reform-based instructional practices. Findings indicate three blocks of variables, professional background, beliefs/efficacy, and local school context added significant contribution to explaining nearly 38% of the variation in secondary science teachers' use of reform-based instructional practices. The five variables that significantly contributed to explaining variation in teachers' use of reform-based instructional practices in the full model were, university of teacher preparation, sense of preparation for teaching science, the quality of professional development, science content focused professional, and the perceived level of professional autonomy. Using the results

Development and Assessment of Self-explaining Skills in College Chemistry Instruction

NASA Astrophysics Data System (ADS)

Villalta-Cerdas, Adrian

The prevalent trend in chemistry instruction relies on what has been described as the classroom game. In this model, students take a passive role and the instructor does all the explaining (thinking), and learning is trivialized to knowing the correct answers (memorizing) and being able to produce them when prompted (regurgitating). The generation of explanations is central to scientific and technological development. In the process of figuring out explanations, the generation of inferences relies on the application of skills associated with scientific behaviors (e.g., analytical reasoning and critical thinking). The process of explanation generation causes a deeper analysis and revision of the scientific models, thus impacting the conceptual understanding of such models. Although the process of generating authentic explanations is closer to the experience of doing science, this process is seldom replicated in science instruction. Self-explaining refers to the generation of inferences about causal connections between objects and events. In science, this may be summarized as making sense of how and why actual or hypothetical phenomena take place. Research findings in educational psychology show that implementing activities that elicit self-explaining improves learning in general and specifically enhances authentic learning in the sciences. Research also suggests that self-explaining influences many aspects of cognition, including acquisition of problem-solving skills and conceptual understanding. Although the evidence that links self-explaining and learning is substantial, most of the research has been conducted in experimental settings. The purpose of this work was to advance knowledge in this area by investigating the effect of different self-explaining tasks on self-explaining behavior and the effect of engaging in different levels of self-explaining on learning chemistry concepts. Unlike most of the research in the field, this work did not focus on advancing

A Gene Expression Profile of BRCAness That Predicts for Responsiveness to Platinum and PARP Inhibitors

DTIC Science & Technology

2017-02-01

To) 15 July 2010 – 2 Nov.2016 4 . TITLE AND SUBTITLE A Gene Expression Profile of BRCAness That Predicts for Responsiveness to Platinum and PARP...resistance in vitro, and to investigate the mechanism for this effect. The major goal for Aim 4 was to determine the reproducibility of the BRCAness...we used the epithelial ovarian cancer (EOC) dataset from The Cancer Genome Atlas (TCGA) ( 4 ). The TCGA dataset is a unique tool for these studies as

Independent Study Projects Guide. Talented and Gifted Students, Number 2.

ERIC Educational Resources Information Center

Alice Independent School District, TX.

Intended for secondary student use in the Talented and Gifted Students Program, the guide lists independent study activities in eight areas. It is explained that areas not usually covered in traditional courses of study are included to encourage indepth and open ended exploration of special interests, and that the projects focus on enhancing…

Shoes on the Highway: Discarded Footwear Inspires a Playwriting Project.

ERIC Educational Resources Information Center

Johnson, Maureen Brady

2003-01-01

Explains a drama assignment based on pictures of discarded shoes. Notes that through character creation, imaginative storytelling, and strong conflicting objectives, students write a 10-minute play about how the shoe got where it was. Outlines the final project, in which these plays would then be presented in a dramatic reading session. (PM)

Project LIFE Annual Report, September 1, 1972-August 31, 1973.

ERIC Educational Resources Information Center

Pfau, Glen S.

Presented is the annual (contract year 1972-73) report of Project LIFE (Language Improvement to Facilitate Education), a program to develop an instructional system to assist handicapped preschool and elementary aged children to acquire a functional language system. The prime teaching modality of the program is explained to be the filmstrip which…

The Rise and Fall of a Second-Generation CBNRM Project in Zambia: Insights from a Project Perspective

NASA Astrophysics Data System (ADS)

Lyons, Andrew

2013-02-01

Since the advent of community-based natural resource management (CBNRM) in the mid-1980s, scholars and practitioners have sought to explain the uneven performance of CBNRM programs. Most CBNRM assessments examine the underlying principles of community-based conservation, the local social and ecological contexts, and connections with larger political and historical patterns. In this article, I argue that analysis of the potential and pitfalls of CBNRM also requires an understanding of the institutional history and internal dynamics of projects that implement CBNRM reforms. Drawing upon theory and methods from development ethnography and public policy, I examine the rise and fall of CONASA, a second-generation CBNRM project in Zambia that operated from 2001 to 2004. CONASA was constituted from a merger of organizations and discourses to provide continuity with previous projects. Its ambitious suite of activities included support for household livelihoods, community-based resource management, policy analysis, advocacy, and conservation enterprises at local, national, and transboundary levels. While individual activities were largely successful, CONASA's hybrid origins and logframe-centric management created fissures between its holistic design and operational logics, and hindered its ability to develop a broader narrative and maintain key alliances. This case study illustrates the importance of understanding the interplay between project design and operational context to fully appreciate the possibilities and limitations of project-mode conservation.

Project demonstration of wind turbine electricity: Interconnecting a northern Michigan fruit farm with a major utility

NASA Astrophysics Data System (ADS)

Amon, D. M.

1982-10-01

A project to interconnect a farm wind turbine with a utility is reported. Included are a summary of accomplishments and daily major events, correspondence relevant to the project (letters explaining the delay of installation, extending the period of performance, tax credits, net energy sellback legislation, etc.), publicity, legal aspects, maintenance and repair, analysis of test data, and accounting.

Students Explaining Science—Assessment of Science Communication Competence

NASA Astrophysics Data System (ADS)

Kulgemeyer, Christoph; Schecker, Horst

2013-12-01

Science communication competence (SCC) is an important educational goal in the school science curricula of several countries. However, there is a lack of research about the structure and the assessment of SCC. This paper specifies the theoretical framework of SCC by a competence model. We developed a qualitative assessment method for SCC that is based on an expert-novice dialog: an older student (explainer, expert) explains a physics phenomenon to a younger peer (addressee, novice) in a controlled test setting. The explanations are video-recorded and analysed by qualitative content analysis. The method was applied in a study with 46 secondary school students as explainers. Our aims were (a) to evaluate whether our model covers the relevant features of SCC, (b) to validate the assessment method and (c) to find characteristics of addressee-adequate explanations. A performance index was calculated to quantify the explainers' levels of competence on an ordinal scale. We present qualitative and quantitative evidence that the index is adequate for assessment purposes. It correlates with results from a written SCC test and a perspective taking test (convergent validity). Addressee-adequate explanations can be characterized by use of graphical representations and deliberate switches between scientific and everyday language.

Metric analysis and data validation across FORTRAN projects

NASA Technical Reports Server (NTRS)

Basili, Victor R.; Selby, Richard W., Jr.; Phillips, Tsai-Yun

1983-01-01

The desire to predict the effort in developing or explaining the quality of software has led to the proposal of several metrics. As a step toward validating these metrics, the Software Engineering Laboratory (SEL) has analyzed the software science metrics, cyclomatic complexity, and various standard program measures for their relation to effort (including design through acceptance testing), development errors (both discrete and weighted according to the amount of time to locate and fix), and one another. The data investigated are collected from a project FORTRAN environment and examined across several projects at once, within individual projects and by reporting accuracy checks demonstrating the need to validate a database. When the data comes from individual programmers or certain validated projects, the metrics' correlations with actual effort seem to be strongest. For modules developed entirely by individual programmers, the validity ratios induce a statistically significant ordering of several of the metrics' correlations. When comparing the strongest correlations, neither software science's E metric cyclomatic complexity not source lines of code appears to relate convincingly better with effort than the others.

Explaining DAMPE results by dark matter with hierarchical lepton-specific Yukawa interactions

NASA Astrophysics Data System (ADS)

Liu, Guoli; Wang, Fei; Wang, Wenyu; Yang, Jin-Min

2018-02-01

We propose to interpret the DAMPE electron excess at 1.5 TeV through scalar or Dirac fermion dark matter (DM) annihilation with doubly charged scalar mediators that have lepton-specific Yukawa couplings. The hierarchy of such lepton-specific Yukawa couplings is generated through the Froggatt-Nielsen mechanism, so that the dark matter annihilation products can be dominantly electrons. Stringent constraints from LEP2 on intermediate vector boson production can be evaded in our scenarios. In the case of scalar DM, we discuss one scenario with DM annihilating directly to leptons and another scenario with DM annihilating to scalar mediators followed by their decays. We also discuss the Breit-Wigner resonant enhancement and the Sommerfeld enhancement in the case where the s-wave annihilation process is small or helicity-suppressed. With both types of enhancement, constraints on the parameters can be relaxed and new ways for model building can be opened in explaining the DAMPE results. Supported by National Natural Science Foundation of China (11105124, 11105125, 11375001, 11675147, 11675242), the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences (Y5KF121CJ1), the Innovation Talent project of Henan Province (15HASTIT017), the Young-Talent Foundation of Zhengzhou University, the CAS Center for Excellence in Particle Physics (CCEPP), the CAS Key Research Program of Frontier Sciences and a Key R&D Program of Ministry of Science and Technology of China (2017YFA0402200-04)

Explainable expert systems: A research program in information processing

NASA Technical Reports Server (NTRS)

Paris, Cecile L.

1993-01-01

Our work in Explainable Expert Systems (EES) had two goals: to extend and enhance the range of explanations that expert systems can offer, and to ease their maintenance and evolution. As suggested in our proposal, these goals are complementary because they place similar demands on the underlying architecture of the expert system: they both require the knowledge contained in a system to be explicitly represented, in a high-level declarative language and in a modular fashion. With these two goals in mind, the Explainable Expert Systems (EES) framework was designed to remedy limitations to explainability and evolvability that stem from related fundamental flaws in the underlying architecture of current expert systems.

Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes

PubMed Central

Tokar, Tomas; Pastrello, Chiara; Ramnarine, Varune R.; Zhu, Chang-Qi; Craddock, Kenneth J.; Pikor, Larrisa A.; Vucic, Emily A.; Vary, Simon; Shepherd, Frances A.; Tsao, Ming-Sound; Lam, Wan L.; Jurisica, Igor

2018-01-01

In many cancers, significantly down- or upregulated genes are found within chromosomal regions with DNA copy number alteration opposite to the expression changes. Generally, this paradox has been overlooked as noise, but can potentially be a consequence of interference of epigenetic regulatory mechanisms, including microRNA-mediated control of mRNA levels. To explore potential associations between microRNAs and paradoxes in non-small-cell lung cancer (NSCLC) we curated and analyzed lung adenocarcinoma (LUAD) data, comprising gene expressions, copy number aberrations (CNAs) and microRNA expressions. We integrated data from 1,062 tumor samples and 241 normal lung samples, including newly-generated array comparative genomic hybridization (aCGH) data from 63 LUAD samples. We identified 85 “paradoxical” genes whose differential expression consistently contrasted with aberrations of their copy numbers. Paradoxical status of 70 out of 85 genes was validated on sample-wise basis using The Cancer Genome Atlas (TCGA) LUAD data. Of these, 41 genes are prognostic and form a clinically relevant signature, which we validated on three independent datasets. By meta-analysis of results from 9 LUAD microRNA expression studies we identified 24 consistently-deregulated microRNAs. Using TCGA-LUAD data we showed that deregulation of 19 of these microRNAs explains differential expression of the paradoxical genes. Our results show that deregulation of paradoxical genes is crucial in LUAD and their expression pattern is maintained epigenetically, defying gene copy number status. PMID:29507679

A Little Knowledge of Ground Motion: Explaining 3-D Physics-Based Modeling to Engineers

NASA Astrophysics Data System (ADS)

Porter, K.

2014-12-01

Users of earthquake planning scenarios require the ground-motion map to be credible enough to justify costly planning efforts, but not all ground-motion maps are right for all uses. There are two common ways to create a map of ground motion for a hypothetical earthquake. One approach is to map the median shaking estimated by empirical attenuation relationships. The other uses 3-D physics-based modeling, in which one analyzes a mathematical model of the earth's crust near the fault rupture and calculates the generation and propagation of seismic waves from source to ground surface by first principles. The two approaches produce different-looking maps. The more-familiar median maps smooth out variability and correlation. Using them in a planning scenario can lead to a systematic underestimation of damage and loss, and could leave a community underprepared for realistic shaking. The 3-D maps show variability, including some very high values that can disconcert non-scientists. So when the USGS Science Application for Risk Reduction's (SAFRR) Haywired scenario project selected 3-D maps, it was necessary to explain to scenario users—especially engineers who often use median maps—the differences, advantages, and disadvantages of the two approaches. We used authority, empirical evidence, and theory to support our choice. We prefaced our explanation with SAFRR's policy of using the best available earth science, and cited the credentials of the maps' developers and the reputation of the journal in which they published the maps. We cited recorded examples from past earthquakes of extreme ground motions that are like those in the scenario map. We explained the maps on theoretical grounds as well, explaining well established causes of variability: directivity, basin effects, and source parameters. The largest mapped motions relate to potentially unfamiliar extreme-value theory, so we used analogies to human longevity and the average age of the oldest person in samples of

Proteogenomic characterization of human colon and rectal cancer

PubMed Central

Zhang, Bing; Wang, Jing; Wang, Xiaojing; Zhu, Jing; Liu, Qi; Shi, Zhiao; Chambers, Matthew C.; Zimmerman, Lisa J.; Shaddox, Kent F.; Kim, Sangtae; Davies, Sherri R.; Wang, Sean; Wang, Pei; Kinsinger, Christopher R.; Rivers, Robert C.; Rodriguez, Henry; Townsend, R. Reid; Ellis, Matthew J.C.; Carr, Steven A.; Tabb, David L.; Coffey, Robert J.; Slebos, Robbert J.C.; Liebler, Daniel C.

2014-01-01

Summary We analyzed proteomes of colon and rectal tumors previously characterized by the Cancer Genome Atlas (TCGA) and performed integrated proteogenomic analyses. Somatic variants displayed reduced protein abundance compared to germline variants. mRNA transcript abundance did not reliably predict protein abundance differences between tumors. Proteomics identified five proteomic subtypes in the TCGA cohort, two of which overlapped with the TCGA “MSI/CIMP” transcriptomic subtype, but had distinct mutation, methylation, and protein expression patterns associated with different clinical outcomes. Although copy number alterations showed strong cis- and trans-effects on mRNA abundance, relatively few of these extend to the protein level. Thus, proteomics data enabled prioritization of candidate driver genes. The chromosome 20q amplicon was associated with the largest global changes at both mRNA and protein levels; proteomics data highlighted potential 20q candidates including HNF4A, TOMM34 and SRC. Integrated proteogenomic analysis provides functional context to interpret genomic abnormalities and affords a new paradigm for understanding cancer biology. PMID:25043054

Explaining Support Vector Machines: A Color Based Nomogram

PubMed Central

Van Belle, Vanya; Van Calster, Ben; Van Huffel, Sabine; Suykens, Johan A. K.; Lisboa, Paulo

2016-01-01

Problem setting Support vector machines (SVMs) are very popular tools for classification, regression and other problems. Due to the large choice of kernels they can be applied with, a large variety of data can be analysed using these tools. Machine learning thanks its popularity to the good performance of the resulting models. However, interpreting the models is far from obvious, especially when non-linear kernels are used. Hence, the methods are used as black boxes. As a consequence, the use of SVMs is less supported in areas where interpretability is important and where people are held responsible for the decisions made by models. Objective In this work, we investigate whether SVMs using linear, polynomial and RBF kernels can be explained such that interpretations for model-based decisions can be provided. We further indicate when SVMs can be explained and in which situations interpretation of SVMs is (hitherto) not possible. Here, explainability is defined as the ability to produce the final decision based on a sum of contributions which depend on one single or at most two input variables. Results Our experiments on simulated and real-life data show that explainability of an SVM depends on the chosen parameter values (degree of polynomial kernel, width of RBF kernel and regularization constant). When several combinations of parameter values yield the same cross-validation performance, combinations with a lower polynomial degree or a larger kernel width have a higher chance of being explainable. Conclusions This work summarizes SVM classifiers obtained with linear, polynomial and RBF kernels in a single plot. Linear and polynomial kernels up to the second degree are represented exactly. For other kernels an indication of the reliability of the approximation is presented. The complete methodology is available as an R package and two apps and a movie are provided to illustrate the possibilities offered by the method. PMID:27723811

Road user behaviour changes following a self-explaining roads intervention.

PubMed

Mackie, Hamish W; Charlton, Samuel G; Baas, Peter H; Villasenor, Pablo C

2013-01-01

The self-explaining roads (SER) approach uses road designs that evoke correct expectations and driving behaviours from road users to create a safe and user-friendly road network. Following the implementation of an SER process and retrofitting of local and collector roads in a suburb within Auckland City, lower speeds on local roads and less variation in speed on both local and collector roads were achieved, along with a closer match between actual and perceived safe speeds. Preliminary analyses of crash data shows that the project has resulted in a 30% reduction crash numbers and an 86% reduction in crash costs per annum, since the road changes were completed. In order to further understand the outcomes from this project, a study was carried out to measure the effects of the SER intervention on the activity and behaviour of all road users. Video was collected over nine separate days, at nine different locations, both before and after SER construction. Road user behaviour categories were developed for all potential road users at different location types and then used to code the video data. Following SER construction, on local roads there was a relatively higher proportion of pedestrians, less uniformity in vehicle lane keeping and less indicating by motorists along with less through traffic, reflecting a more informal/low speed local road environment. Pedestrians were less constrained on local roads following SER construction, possibly reflecting a perceptually safer and more user-friendly environment. These behaviours were not generally evident on collector roads, a trend also shown by the previous study of speed changes. Given that one of the objectives of SER is to match road user behaviour with functionally different road categories, the road user behaviour differences demonstrated on different road types within the SER trial area provides further reinforcement of a successful SER trial. Copyright © 2012 Elsevier Ltd. All rights reserved.

The Value of DNA Sequencing - TCGA

Cancer.gov

DNA sequencing: what it tells us about DNA changes in cancer, how looking across many tumors will help to identify meaningful changes and potential drug targets, and how genomics is changing the way we think about cancer.

Anomalies and contradictions in an airport construction project: a historical analysis based on Cultural-Historical Activity Theory.

PubMed

Lopes, Manoela Gomes Reis; Vilela, Rodolfo Andrade de Gouveia; Querol, Marco Antônio Pereira

2018-02-19

Large construction projects involve the functioning of a complex activity system (AS) in network format. Anomalies such as accidents, delays, reworks, etc., can be explained by contradictions that emerge historically in the system. The aim of this study was to analyze the history of an airport construction project to understand the current contradictions and anomalies in the AS and how they emerged. A case study was conducted for this purpose, combining Collective Work Analysis, interviews, observations, and analysis of documents that provided the basis for sessions in the Change Laboratory, where a participant timeline was elaborated with the principal events during the construction project. Based on the timeline, a historical analysis of the airport's AS revealed critical historical events and contradictions that explained the anomalies that occurred during the project. The analysis showed that the airport had been planned for construction with politically determined deadlines that were insufficient and inconsistent with the project's complexity. The choice of the contract modality, which assigned responsibility to a joint venture for all of the project's phases, was another critical historical event, because it allowed launching the construction before a definitive executive project had been drafted. There were also different cultures in companies working together for the first time in the context of a project with time pressures and outsourcing of activities without the necessary coordination. Identifying these contradictions and their historical origins proved essential for understanding the current situation and efforts to prevent similar situations in the future.

Explaining Ethnic Disparities in Preterm Birth in Argentina and Ecuador

PubMed Central

Wehby, George L.; Pawluk, Mariela; Nyarko, Kwame A.; López-Camelo, Jorge S.

2017-01-01

Background Little is understood about racial/ethnic disparities in infant health in South America. We quantified the extent to which the disparity in preterm birth rate (PTB; < 37 gestational weeks) between infants of Native only ancestry and those of European only ancestry in Argentina and Ecuador are explained by household socioeconomic, demographic, healthcare use, and geographic location indicators. Methods The samples included 5199 infants born between 2000 and 2011 from Argentina and 1579 infants born between 2001 and 2011 from Ecuador. An Oaxaca-Blinder type decomposition model adapted to binary outcomes was estimated to explain the disparity in PTB risk across groups of variables and specific variables. Results Maternal use of prenatal care services significantly explained the PTB disparity, by nearly 57% and 30% in Argentina and Ecuador, respectively. Household socioeconomic status explained an additional 26% of the PTB disparity in Argentina. Conclusions Differences in maternal use of prenatal care may partly explain ethnic disparities in PTB in Argentina and Ecuador. Improving access to prenatal care may reduce ethnic disparities in PTB risk in these countries. PMID:27875924

HPMSS(High Precision Magnetic Survey System) and InterRidge

NASA Astrophysics Data System (ADS)

Isezaki, N.; Sayanagi, K.

2012-12-01

From the beginning of 1990s to the beginning of 2000s, the Japanese group of IntreRidge conducted many cruises for three component magnetic survey using Shipboard Three Component Magnetometer (STCM) and Deep Towed Three Component Magnetometer (DTCM) in the world wide oceans. We have been developing HPMSS during this time with support of Dr.Tamaki(the late representative of InterRidge Japan) who understood the advantages of three component geomagnetic anomalies (TCGA). TCGA measured by STCM determines the direction of geomagnetic anomaly lineations precisely at every point where TCGA were observed, which playes the important role in magnetic anomaly lineation analysis. Even in the beginning of 2000s, almost all marine magnetic scientists believed that the total intensity anomly (TIA) is the better data than TCGA for analysis because the scalar magnetometers (e.g. proton precession magnetometer) have the better accuracy than any other magnetometers (e.g.flux gate magnetometer (FGM)). We employed the high accrate gyroscope (e.g.ring lase gyroscope (RLG)/optical fiber gyroscope (OFG)) to improve the accuracy of STCM/DTCM equipped with FGM. Moreover we employed accurate and precise FGM which was selected among the market. Finally we developed the new magnetic survey system with high precision usable as airborn, shipboard and dee-ptowed magnetometers which we call HPMSS(High Precision Magnetic Survey System). As an optional equipment, we use LAN to communicate between a data aquisiitin part and a data logging part, and GPS for a position fix. For the deep-towed survey, we use the acoustic position fix (super short base line method) and the acoustic communication to monitor the DTCM status. First we used HPMSS to obtain the magnetization structure of the volcanic island, Aogashima located 300km south of Tokyo using a hellcopter in 2006 and 2009. Next we used HPMSS installed in DTCM in 2010,2011 and 2012 using R/V Bosei-maru belonging to Tokai University. Also we used

Explaining social class differences in depression and well-being.

PubMed

Stansfeld, S A; Head, J; Marmot, M G

1998-01-01

Work characteristics, including skill discretion and decision authority, explain most of the socioeconomic status gradient in well-being and depression in middle-aged British civil servants from the Whitehall II Study, London. Social support explained about one-third of the gradient, life events and material difficulties less than one-third. Socioeconomic status was measured by employment grade. Work characteristics were based on the Karasek model, social support was measured by the Close Persons Questionnaire, depression by the General Health Questionnaire and well-being by the Affect Balance Scale. Despite a small contribution from social selective factors measured by upward mobility, the psychosocial work environment explained most of the cross-sectional socioeconomic status gradient in well-being and depression.

Do changes in connectivity explain desertification?

USDA-ARS?s Scientific Manuscript database

Desertification, broad-scale land degradation in drylands, is a major environmental hazard facing inhabitants of the world’s deserts as well as an important component of global change. There is no unifying framework that simply and effectively explains different forms of desertification. Here we arg...

The Role of Early-Life Educational Quality and Literacy in Explaining Racial Disparities in Cognition in Late Life

PubMed Central

Gross, Alden L.; Shih, Regina A.; Sachs, Bonnie C.; Glymour, M. Maria; Bangen, Katherine J.; Benitez, Andreana; Skinner, Jeannine; Schneider, Brooke C.; Manly, Jennifer J.

2015-01-01

Objectives. Racial disparities in late-life cognition persist even after accounting for educational attainment. We examined whether early-life educational quality and literacy in later life help explain these disparities. Method. We used longitudinal data from the Washington Heights-Inwood Columbia Aging Project (WHICAP). Educational quality (percent white students; urban/rural school; combined grades in classroom) was operationalized using canonical correlation analysis. Late-life literacy (reading comprehension and ability, writing) was operationalized using confirmatory factor analysis. We examined whether these factors attenuated race-related differences in late-life cognition. Results. The sample consisted of 1,679U.S.-born, non-Hispanic, community-living adults aged 65–102 (71% black, 29% white; 70% women). Accounting for educational quality and literacy reduced disparities by 29% for general cognitive functioning, 26% for memory, and 32% for executive functioning but did not predict differences in rate of cognitive change. Discussion. Early-life educational quality and literacy in late life explain a substantial portion of race-related disparities in late-life cognitive function. PMID:24584038

Observed an aerial phenomenon that you can't explain? The UAP Observations Reporting Scheme as a tool for demystifying UFOs and stimulating interest in Science

NASA Astrophysics Data System (ADS)

Ailleris, P.

2011-10-01

We present the website's extensive and well illustrated list of misidentifications and describe how people can further check details and develop their knowledge (e.g. satellite paths, stars/planets charts, characteristics of meteors, pictures of sprites, clouds classification). A short illustrated list of cases will be featured, both explained and inexplicable; and outreach activities and partnerships with relevant astronomical projects (e.g. Astronomers without Borders, The World at Night) will be described. We will underline that the project definitely fulfills a need in relation to demystifying UFO events, providing education on pseudo-scientific information, while keeping an attitude of scientific openmindedness. For these reasons, we will encourage the planetary scientists community to further advertise the project's existence and the amateur astronomers and societies who receive questions about UFOs to redirect those queries to the websit.

Using Metaphors to Explain Molecular Testing to Cancer Patients.

PubMed

Pinheiro, Ana P M; Pocock, Rachel H; Dixon, Margie D; Shaib, Walid L; Ramalingam, Suresh S; Pentz, Rebecca D

2017-04-01

Molecular testing to identify targetable molecular alterations is routine practice for several types of cancer. Explaining the underlying molecular concepts can be difficult, and metaphors historically have been used in medicine to provide a common language between physicians and patients. Although previous studies have highlighted the use and effectiveness of metaphors to help explain germline genetic concepts to the general public, this study is the first to describe the use of metaphors to explain molecular testing to cancer patients in the clinical setting. Oncologist-patient conversations about molecular testing were recorded, transcribed verbatim, and coded. If a metaphor was used, patients were asked to explain it and assess its helpfulness. Sixty-six patients participated. Nine oncologists used metaphors to describe molecular testing; 25 of 66 (38%) participants heard a metaphor, 13 of 25 (52%) were questioned, 11 of 13 (85%) demonstrated understanding and reported the metaphor as being useful. Seventeen metaphors (bus driver, boss, switch, battery, circuit, broken light switch, gas pedal, key turning off an engine, key opening a lock, food for growth, satellite and antenna, interstate, alternate circuit, traffic jam, blueprint, room names, Florida citrus) were used to explain eight molecular testing terms (driver mutations, targeted therapy, hormones, receptors, resistance, exon specificity, genes, and cancer signatures). Because metaphors have proven to be a useful communication tool in other settings, these 17 metaphors may be useful for oncologists to adapt to their own setting to explain molecular testing terms. The Oncologist 2017;22:445-449 Implications for Practice: This article provides a snapshot of 17 metaphors that proved useful in describing 8 complicated molecular testing terms at 3 sites. As complex tumor sequencing becomes standard of care in clinics and widely used in clinical research, the use of metaphors may prove a useful communication

Capital Improvement Project Workshops: Anchorage--May 15, 1998; Juneau--May 19, 1998.

ERIC Educational Resources Information Center

Alaska State Dept. of Education, Juneau.

This workshop addresses the application process for capital improvement funding from the state, e.g., who should apply, applicant eligibility and evaluation criteria, the types of funding available, and project specifics to be included in application submissions. The evaluation and scoring process of applications is explained followed by the…

A Student Activity for the James Bay Hydro Project. The Geography Teacher.

ERIC Educational Resources Information Center

Green-Milberg, Patricia

1999-01-01

Provides activities for grades 6 to 8 that will promote student awareness and understanding of the use of hydropower in Canada, the benefits and drawbacks to hydropower, and also the drawbacks of electricity transmission lines. Explains that the activities focus on the James Bay Hydro Project in Canada. (CMK)

The Floating Lab Research Project: An Approach to Evaluating Field Programs.

ERIC Educational Resources Information Center

Brody, Michael J.

This report explains an evaluative study of the conceptual and affective development of students associated with the Floating Lab Program, an experiential field project sponsored by the University of New Hampshire and the Maine Sea Grant Program. The field program involved an opportunity for students to have hands-on experiences aboard a 65-foot…

Explaining the sex difference in dyslexia.

PubMed

Arnett, Anne B; Pennington, Bruce F; Peterson, Robin L; Willcutt, Erik G; DeFries, John C; Olson, Richard K

2017-06-01

Males are diagnosed with dyslexia more frequently than females, even in epidemiological samples. This may be explained by greater variance in males' reading performance. We expand on previous research by rigorously testing the variance difference theory, and testing for mediation of the sex difference by cognitive correlates. We developed an analytic framework that can be applied to group differences in any psychiatric disorder. Males' overrepresentation in the low performance tail of the reading distribution was accounted for by mean and variance differences across sex. There was no sex difference at the high performance tail. Processing speed (PS) and inhibitory control partially mediated the sex difference. Verbal reasoning emerged as a strength in males. Our results complement a previous finding that PS partially mediates the sex difference in symptoms of attention deficit/hyperactivity disorder (ADHD), and helps explain the sex difference in both dyslexia and ADHD and their comorbidity. © 2017 Association for Child and Adolescent Mental Health.

Explaining Success and Failure: Counterinsurgency in Malaya and India

DTIC Science & Technology

2010-12-01

bomb blasts Dalit Dalit is a term used for a lowest caste people in India who generally remain outside the traditional society and regarded...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS EXPLAINING SUCCESS AND FAILURE: COUNTERINSURGENCY IN MALAYA AND INDIA by...COVERED Master’s Thesis 4. TITLE AND SUBTITLE Explaining Success and Failure: Counterinsurgency in Malaya and India 6. AUTHOR(S) Deepak Aneel

Categorization of potential project cost overrun factors in construction industry

NASA Astrophysics Data System (ADS)

Karunakaran, P.; Abdullah, A. H.; Nagapan, S.; Sohu, S.; Kasvar, K. K.

2018-04-01

Cost overrun has been severely hit down the economy and reputations for many construction industry around the world. Many project management tools developed to control the budget of a project. However, the cost management is still considered poor as there are many cost overrun issues occurred in the construction industry. Thus, this paper aims to identify and cluster the potential construction project cost overrun factors according to their originating groups using the thematic approach. Basically, through literature review, all the potential factors that may cause cost overrun were screened thoroughly before they were clustered into seven (7) groups of the originating factors, namely project, contract, client, contractor, consultant, labour and external. Each potential factor was explained clearly with some examples based on the Malaysian case studies to illustrate the cost overrun scenario. These findings may aid in the future to highlight on how to mitigate the critical potential factors of cost overrun to reduce or overcome its impact on all the stakeholders involved.

In modelling effects of global warming, invalid assumptions lead to unrealistic projections.

PubMed

Lefevre, Sjannie; McKenzie, David J; Nilsson, Göran E

2018-02-01

In their recent Opinion, Pauly and Cheung () provide new projections of future maximum fish weight (W ∞ ). Based on criticism by Lefevre et al. (2017) they changed the scaling exponent for anabolism, d G . Here we find that changing both d G and the scaling exponent for catabolism, b, leads to the projection that fish may even become 98% smaller with a 1°C increase in temperature. This unrealistic outcome indicates that the current W ∞ is unlikely to be explained by the Gill-Oxygen Limitation Theory (GOLT) and, therefore, GOLT cannot be used as a mechanistic basis for model projections about fish size in a warmer world. © 2017 John Wiley & Sons Ltd.

Systems Analysis and Design for Decision Support Systems on Economic Feasibility of Projects

NASA Astrophysics Data System (ADS)

Balaji, S. Arun

2010-11-01

This paper discuss about need for development of the Decision Support System (DSS) software for economic feasibility of projects in Rwanda, Africa. The various economic theories needed and the corresponding formulae to compute payback period, internal rate of return and benefit cost ratio of projects are clearly given in this paper. This paper is also deals with the systems flow chart to fabricate the system in any higher level computing language. The various input requirements from the projects and the output needed for the decision makers are also included in this paper. The data dictionary used for input and output data structure is also explained.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Yitan; Xu, Yanxun; Helseth, Donald L.

Background: Genetic interactions play a critical role in cancer development. Existing knowledge about cancer genetic interactions is incomplete, especially lacking evidences derived from large-scale cancer genomics data. The Cancer Genome Atlas (TCGA) produces multimodal measurements across genomics and features of thousands of tumors, which provide an unprecedented opportunity to investigate the interplays of genes in cancer. Methods: We introduce Zodiac, a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood modelmore » derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes “Prior interaction map + TCGA data → Posterior interaction map.” Results: Zodiac provides molecular interactions for about 200 million pairs of genes. All the results are generated from a big-data analysis and organized into a comprehensive database allowing customized search. In addition, Zodiac provides data processing and analysis tools that allow users to customize the prior networks and update the genetic pathways of their interest. Zodiac is publicly available at www.compgenome.org/ZODIAC. Conclusions: Zodiac recapitulates and extends existing knowledge of molecular interactions in cancer. It can be used to explore novel gene-gene interactions, transcriptional regulation, and other types of molecular interplays in cancer.« less

Comparison of indium-labeled-leukocyte imaging with sequential technetium-gallium scanning in the diagnosis of low-grade musculoskeletal sepsis. A prospective study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merkel, K.D.; Brown, M.L.; Dewanjee, M.K.

We prospectively compared sequential technetium-gallium imaging with indium-labeled-leukocyte imaging in fifty patients with suspected low-grade musculoskeletal sepsis. Adequate images and follow-up examinations were obtained for forty-two patients. The presence or absence of low-grade sepsis was confirmed by histological and bacteriological examinations of tissue specimens taken at surgery in thirty of the forty-two patients. In these thirty patients, the sensitivity of sequential Tc-Ga imaging was 48 per cent, the specificity was 86 per cent, and the accuracy was 57 per cent, whereas the sensitivity of the indium-labeled-leukocyte technique was 83 per cent, the specificity was 86 per cent, and the accuracymore » was 83 per cent. When the additional twelve patients for whom surgery was deemed unnecessary were considered, the sensitivity of sequential Tc-Ga imaging was 50 per cent, the specificity was 78 per cent, and the accuracy was 62 per cent, as compared with a sensitivity of 83 per cent, a specificity of 94 per cent, and an accuracy of 88 per cent with the indium-labeled-leukocyte method. In patients with a prosthesis the indium-labeled-leukocyte image was 94 per cent accurate, compared with 75 per cent accuracy for sequential Tc-Ga imaging. Statistical analysis of these data demonstrated that the indium-labeled-leukocyte technique was superior to sequential Tc-Ga imaging in detecting areas of low-grade musculoskeletal sepsis.« less

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

PubMed

Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

2014-01-01

Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

A Multidisciplinary Biospecimen Bank of Renal Cell Carcinomas Compatible with Discovery Platforms at Mayo Clinic, Scottsdale, Arizona

PubMed Central

Ho, Thai H.; Nateras, Rafael Nunez; Yan, Huihuang; Park, Jin G.; Jensen, Sally; Borges, Chad; Lee, Jeong Heon; Champion, Mia D.; Tibes, Raoul; Bryce, Alan H.; Carballido, Estrella M.; Todd, Mark A.; Joseph, Richard W.; Wong, William W.; Parker, Alexander S.; Stanton, Melissa L.; Castle, Erik P.

2015-01-01

To address the need to study frozen clinical specimens using next-generation RNA, DNA, chromatin immunoprecipitation (ChIP) sequencing and protein analyses, we developed a biobank work flow to prospectively collect biospecimens from patients with renal cell carcinoma (RCC). We describe our standard operating procedures and work flow to annotate pathologic results and clinical outcomes. We report quality control outcomes and nucleic acid yields of our RCC submissions (N=16) to The Cancer Genome Atlas (TCGA) project, as well as newer discovery platforms, by describing mass spectrometry analysis of albumin oxidation in plasma and 6 ChIP sequencing libraries generated from nephrectomy specimens after histone H3 lysine 36 trimethylation (H3K36me3) immunoprecipitation. From June 1, 2010, through January 1, 2013, we enrolled 328 patients with RCC. Our mean (SD) TCGA RNA integrity numbers (RINs) were 8.1 (0.8) for papillary RCC, with a 12.5% overall rate of sample disqualification for RIN <7. Banked plasma had significantly less albumin oxidation (by mass spectrometry analysis) than plasma kept at 25°C (P<.001). For ChIP sequencing, the FastQC score for average read quality was at least 30 for 91% to 95% of paired-end reads. In parallel, we analyzed frozen tissue by RNA sequencing; after genome alignment, only 0.2% to 0.4% of total reads failed the default quality check steps of Bowtie2, which was comparable to the disqualification ratio (0.1%) of the 786-O RCC cell line that was prepared under optimal RNA isolation conditions. The overall correlation coefficients for gene expression between Mayo Clinic vs TCGA tissues ranged from 0.75 to 0.82. These data support the generation of high-quality nucleic acids for genomic analyses from banked RCC. Importantly, the protocol does not interfere with routine clinical care. Collections over defined time points during disease treatment further enhance collaborative efforts to integrate genomic information with outcomes. PMID

Implementing the "Marketing You" Project in Large Sections of Principles of Marketing

ERIC Educational Resources Information Center

Smith, Karen H.

2004-01-01

There is mounting pressure on business education to increase experiential learning at the same time that budget constraints are forcing universities to increase class size. This article explains the design and implementation of the "Marketing You" project in two large sections of Principles of Marketing to bring experiential learning into the…

The Short Life and Ignominious Death of ALA Video and Special Projects.

ERIC Educational Resources Information Center

Handman, Gary

1991-01-01

Discussion of videocassettes in our culture and the function of video collections in libraries focuses on the creation and demise of a unit sponsored by the American Library Association, the ALA Video and Special Projects. The unit's role is discussed and funding decisions that led to its demise are explained. (LRW)

A model to explain human voice production

NASA Astrophysics Data System (ADS)

Vilas Bôas, C. S. N.; Gobara, S. T.

2018-05-01

This article presents a device constructed with low-cost material to demonstrate and explain voice production. It also provides a contextualized, interdisciplinary approach to introduce the study of sound waves.

Sun light European Project

NASA Astrophysics Data System (ADS)

Soubielle, Marie-Laure

2015-04-01

2015 has been declared the year of light. Sunlight plays a major role in the world. From the sunbeams that heat our planet and feed our plants to the optical analysis of the sun or the modern use of sun particles in technologies, sunlight is everywhere and it is vital. This project aims to understand better the light of the Sun in a variety of fields. The experiments are carried out by students aged 15 to 20 in order to share their discoveries with Italian students from primary and secondary schools. The experiments will also be presented to a group of Danish students visiting our school in January. All experiments are carried out in English and involve teams of teachers. This project is 3 folds: part 1: Biological project = what are the mechanisms of photosynthesis? part 2: Optical project= what are the components of sunlight and how to use it? part 3: Technical project= how to use the energy of sunlight for modern devices? Photosynthesis project Biology and English Context:Photosynthesis is a process used by plants and other organisms to convert light energy, normally from the Sun, into chemical energy that can later fuel the organisms' activities. This chemical energy is stored in molecules which are synthesized from carbon dioxide and water. In most cases, oxygen is released as a waste product. Most plants perform photosynthesis. Photosynthesis maintains atmospheric oxygen levels and supplies all of the organic compounds and most of the energy necessary for life on Earth. Outcome: Our project consists in understanding the various steps of photosynthesis. Students will shoot a DVD of the experiments presenting the equipments required, the steps of the experiments and the results they have obtained for a better understanding of photosynthesis Digital pen project Electricity, Optics and English Context: Sunlight is a complex source of light based on white light that can be decomposed to explain light radiations or colours. This light is a precious source to create

Progress of the MAGDAS Project During 2013

NASA Astrophysics Data System (ADS)

Maeda, G.; Yoshikawa, A.; Abe, S.

2013-12-01

The magnetometer array of the MAGDAS Project is perhaps the largest magnetometer array in the world -- with 71 real time magnetometers deployed around the world. In this presentation we explain the latest status of this array and the latest data release policy. In addition, we describe various MAGDAS activities of this year, such as: (1) the ISWI and MAGDAS School in Africa, (2) the ISWI/MAGDAS presentation by the MAGDAS PI at Graz, Austria, and (3) the maintenance work done in the field for magnetometers.

Factors explaining children's responses to intravenous needle insertions.

PubMed

McCarthy, Ann Marie; Kleiber, Charmaine; Hanrahan, Kirsten; Zimmerman, M Bridget; Westhus, Nina; Allen, Susan

2010-01-01

Previous research shows that numerous child, parent, and procedural variables affect children's distress responses to procedures. Cognitive-behavioral interventions such as distraction are effective in reducing pain and distress for many children undergoing these procedures. The purpose of this report was to examine child, parent, and procedural variables that explain child distress during a scheduled intravenous insertion when parents are distraction coaches for their children. A total of 542 children, between 4 and 10 years of age, and their parents participated. Child age, gender, diagnosis, and ethnicity were measured by questions developed for this study. Standardized instruments were used to measure child experience with procedures, temperament, ability to attend, anxiety, coping style, and pain sensitivity. Questions were developed to measure parent variables, including ethnicity, gender, previous experiences, and expectations, and procedural variables, including use of topical anesthetics and difficulty of procedure. Standardized instruments were used to measure parenting style and parent anxiety, whereas a new instrument was developed to measure parent performance of distraction. Children's distress responses were measured with the Observation Scale of Behavioral Distress-Revised (behavioral), salivary cortisol (biological), Oucher Pain Scale (self-report), and parent report of child distress (parent report). Regression methods were used for data analyses. Variables explaining behavioral, child-report and parent-report measures include child age, typical coping response, and parent expectation of distress (p < .01). Level of parents' distraction coaching explained a significant portion of behavioral, biological, and parent-report distress measures (p < .05). Child impulsivity and special assistance at school also significantly explained child self-report of pain (p < .05). Additional variables explaining cortisol response were child's distress in the

Mentoring in 2 + 2 Programs: LISD/ACC 2 + 2 Articulation Project.

ERIC Educational Resources Information Center

Center for Occupational Research and Development, Inc., Waco, TX.

The role of mentoring in the 2 + 2 Instrumentation and Control (I&C) articulation project between the Leander Independent School District (LISD) and Austin Community College (ACC) is discussed in this document. Following a brief history of the origin and function of the mentor, the paper explains the need for the mentoring system in the I&C…

Explaining the Sex Difference in Dyslexia

ERIC Educational Resources Information Center

Arnett, Anne B.; Pennington, Bruce F.; Peterson, Robin L.; Willcutt, Erik G.; DeFries, John C.; Olson, Richard K.

2017-01-01

Background: Males are diagnosed with dyslexia more frequently than females, even in epidemiological samples. This may be explained by greater variance in males' reading performance. Methods: We expand on previous research by rigorously testing the variance difference theory, and testing for mediation of the sex difference by cognitive correlates.…

Explaining Teachers' Use of Textbooks

ERIC Educational Resources Information Center

Reichenberg, Monica

2016-01-01

In educational systems without comprehensive systems for regulating textbooks, teachers can exert considerable influence on the use of textbooks. However, existing research has not yet identified the mechanisms of this use. Accordingly, the aim of this article is to examine and explain teachers' strategic use of textbooks. I administered a…

Does a Corresponding Set of Variables for Explaining Voluntary Organizational Turnover Transfer to Explaining Voluntary Occupational Turnover?

ERIC Educational Resources Information Center

Blau, Gary

2007-01-01

This study proposed and tested corresponding sets of variables for explaining voluntary organizational versus occupational turnover for a sample of medical technologists. This study is believed to be the first test of the Rhodes and Doering (1983) occupational change model using occupational turnover data. Results showed that corresponding job…

LinkedOmics: analyzing multi-omics data within and across 32 cancer types.

PubMed

Vasaikar, Suhas V; Straub, Peter; Wang, Jing; Zhang, Bing

2018-01-04

The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application. The LinkFinder module allows flexible exploration of associations between a molecular or clinical attribute of interest and all other attributes, providing the opportunity to analyze and visualize associations between billions of attribute pairs for each cancer cohort. The LinkCompare module enables easy comparison of the associations identified by LinkFinder, which is particularly useful in multi-omics and pan-cancer analyses. The LinkInterpreter module transforms identified associations into biological understanding through pathway and network analysis. Using five case studies, we demonstrate that LinkedOmics provides a unique platform for biologists and clinicians to access, analyze and compare cancer multi-omics data within and across tumor types. LinkedOmics is freely available at http://www.linkedomics.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. | Office of Cancer Genomics

Cancer.gov

We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations (SCNAs) and 46 significantly mutated genes (SMGs). Eleven SCNAs and 11 SMGs had not been identified in previous TCGA studies of the individual tumor types. We found functionally significant estrogen receptor-regulated long non-coding RNAs (lncRNAs) and gene/lncRNA interaction networks.

Culturally appropriate organization of water and sewerage projects built through public private partnerships

PubMed Central

2017-01-01

This paper contributes to the pursuit of socially sustainable water and sanitation infrastructure for all people by discovering statistically robust relationships between Hofstede’s dimensions of cross-cultural comparison and the choice of contract award types, project type, and primary revenue sources. This analysis, which represents 973 projects distributed across 24 low- and middle-income nations, uses a World Bank dataset describing high capital cost water and sewerage projects funded through private investment. The results show that cultural dimensions explain variation in the choice of contract award types, project type, and primary revenue sources. These results provide empirical evidence that strategies for water and sewerage project organization are not culturally neutral. The data show, for example, that highly individualistic contexts are more likely to select competitive contract award types and to depend on user fees to provide the primary project revenue stream post-construction. By selecting more locally appropriate ways to organize projects, project stakeholders will be better able to pursue the construction of socially sustainable water and sewerage infrastructure. PMID:29200432

Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia

PubMed Central

Li, Yue; Liang, Minggao; Zhang, Zhaolei

2014-01-01

Gene expression is a combinatorial function of genetic/epigenetic factors such as copy number variation (CNV), DNA methylation (DM), transcription factors (TF) occupancy, and microRNA (miRNA) post-transcriptional regulation. At the maturity of microarray/sequencing technologies, large amounts of data measuring the genome-wide signals of those factors became available from Encyclopedia of DNA Elements (ENCODE) and The Cancer Genome Atlas (TCGA). However, there is a lack of an integrative model to take full advantage of these rich yet heterogeneous data. To this end, we developed RACER (Regression Analysis of Combined Expression Regulation), which fits the mRNA expression as response using as explanatory variables, the TF data from ENCODE, and CNV, DM, miRNA expression signals from TCGA. Briefly, RACER first infers the sample-specific regulatory activities by TFs and miRNAs, which are then used as inputs to infer specific TF/miRNA-gene interactions. Such a two-stage regression framework circumvents a common difficulty in integrating ENCODE data measured in generic cell-line with the sample-specific TCGA measurements. As a case study, we integrated Acute Myeloid Leukemia (AML) data from TCGA and the related TF binding data measured in K562 from ENCODE. As a proof-of-concept, we first verified our model formalism by 10-fold cross-validation on predicting gene expression. We next evaluated RACER on recovering known regulatory interactions, and demonstrated its superior statistical power over existing methods in detecting known miRNA/TF targets. Additionally, we developed a feature selection procedure, which identified 18 regulators, whose activities clustered consistently with cytogenetic risk groups. One of the selected regulators is miR-548p, whose inferred targets were significantly enriched for leukemia-related pathway, implicating its novel role in AML pathogenesis. Moreover, survival analysis using the inferred activities identified C-Fos as a potential AML

A self-updating road map of The Cancer Genome Atlas.

PubMed

Robbins, David E; Grüneberg, Alexander; Deus, Helena F; Tanik, Murat M; Almeida, Jonas S

2013-05-15

Since 2011, The Cancer Genome Atlas' (TCGA) files have been accessible through HTTP from a public site, creating entirely new possibilities for cancer informatics by enhancing data discovery and retrieval. Significantly, these enhancements enable the reporting of analysis results that can be fully traced to and reproduced using their source data. However, to realize this possibility, a continually updated road map of files in the TCGA is required. Creation of such a road map represents a significant data modeling challenge, due to the size and fluidity of this resource: each of the 33 cancer types is instantiated in only partially overlapping sets of analytical platforms, while the number of data files available doubles approximately every 7 months. We developed an engine to index and annotate the TCGA files, relying exclusively on third-generation web technologies (Web 3.0). Specifically, this engine uses JavaScript in conjunction with the World Wide Web Consortium's (W3C) Resource Description Framework (RDF), and SPARQL, the query language for RDF, to capture metadata of files in the TCGA open-access HTTP directory. The resulting index may be queried using SPARQL, and enables file-level provenance annotations as well as discovery of arbitrary subsets of files, based on their metadata, using web standard languages. In turn, these abilities enhance the reproducibility and distribution of novel results delivered as elements of a web-based computational ecosystem. The development of the TCGA Roadmap engine was found to provide specific clues about how biomedical big data initiatives should be exposed as public resources for exploratory analysis, data mining and reproducible research. These specific design elements align with the concept of knowledge reengineering and represent a sharp departure from top-down approaches in grid initiatives such as CaBIG. They also present a much more interoperable and reproducible alternative to the still pervasive use of data portals

Machine learning and deep analytics for biocomputing: call for better explainability.

PubMed

Petkovic, Dragutin; Kobzik, Lester; Re, Christopher

2018-01-01

The goals of this workshop are to discuss challenges in explainability of current Machine Leaning and Deep Analytics (MLDA) used in biocomputing and to start the discussion on ways to improve it. We define explainability in MLDA as easy to use information explaining why and how the MLDA approach made its decisions. We believe that much greater effort is needed to address the issue of MLDA explainability because of: 1) the ever increasing use and dependence on MLDA in biocomputing including the need for increased adoption by non-MLD experts; 2) the diversity, complexity and scale of biocomputing data and MLDA algorithms; 3) the emerging importance of MLDA-based decisions in patient care, in daily research, as well as in the development of new costly medical procedures and drugs. This workshop aims to: a) analyze and challenge the current level of explainability of MLDA methods and practices in biocomputing; b) explore benefits of improvements in this area; and c) provide useful and practical guidance to the biocomputing community on how to address these challenges and how to develop improvements. The workshop format is designed to encourage a lively discussion with panelists to first motivate and understand the problem and then to define next steps and solutions needed to improve MLDA explainability.

"Christmas Balls": a Christmas carol by the adolescent cancer patients of the Milan Youth Project.

PubMed

Ferrari, Andrea; Signoroni, Stefano; Silva, Matteo; Gaggiotti, Paola; Veneroni, Laura; Magni, Chiara; Casanova, Michela; Chiaravalli, Stefano; Capelletti, Mirko; Lapidari, Pietro; Clerici, Carlo Alfredo; Massimino, Maura

2017-03-24

The Youth Project is a program developed at the Pediatric Oncology Unit at the Istituto Nazionale Tumori in Milan, dedicated to adolescents and young adults with cancer. Among its various goals, the Youth Project organizes structured creative activities with the support of professionals, with the objective of offering young people a new way to express their hopes and fears. This article describes a project centered around music: patients created a Christmas carol with the help of musicians and authors. The adolescents explained with their own words the meaning of the lyrics, telling the story of a Christmas spent in a cancer hospital ward.

Creating a Project on Difference Equations with Primary Sources: Challenges and Opportunities

ERIC Educational Resources Information Center

Ruch, David

2014-01-01

This article discusses the creation of a student project about linear difference equations using primary sources. Early 18th-century developments in the area are outlined, focusing on efforts by Abraham De Moivre (1667-1754) and Daniel Bernoulli (1700-1782). It is explained how primary sources from these authors can be used to cover material…

Students' Development and Use of Models to Explain Electrostatic Interactions

NASA Astrophysics Data System (ADS)

Mayer, Kristin Elizabeth

The National Research Council (2012) recently published A Framework for K-12 Science Education that describes a vision for science classrooms where students engage in three dimensions--scientific and engineering practices, crosscutting concepts, and disciplinary core ideas--to explain phenomena or observations they can make about the universe around them. This vision of science instruction is a significant shift from current classroom instruction. This dissertation provides detailed examples of how students developed and used models to build causal explanations of phenomena. I co-taught classes that focused on having students develop and revise models of electric fields and atomic structure using a curriculum that was designed to align with the three-dimensional vision of learning. I developed case studies of eleven students from these classes. I analyzed the students' responses and interviewed the students throughout the school year. By comparing and contrasting the analysis across the analysis of students' interviews, I identified four themes: 1) students could apply their ideas to explain novel and abstract phenomena; 2) students struggled to connect changes in their atomic models to evidence, but ended up with dynamic models of atomic structure that they could apply to explain phenomena; 3) students developed models of atomic structure that they applied to explain phenomena, but they did not use models of electric fields in this way; and 4) too much focus on details interfered with students' ability to apply their models to explain new phenomena. This dissertation highlights the importance of focusing on phenomena in classrooms that aim at aligning with three-dimensional learning. Students struggled to focus on specific content and apply their ideas to explain phenomena at the same time. In order to apply ideas to new context, students had to shift their focus from recalling ideas to applying the ideas they do have. A focus on phenomena allowed students to show

Critical Factors Explaining the Leadership Performance of High-Performing Principals

ERIC Educational Resources Information Center

Hutton, Disraeli M.

2018-01-01

The study explored critical factors that explain leadership performance of high-performing principals and examined the relationship between these factors based on the ratings of school constituents in the public school system. The principal component analysis with the use of Varimax Rotation revealed that four components explain 51.1% of the…

Young Children: Priority One. A Project Kit for Kiwanis Clubs--Addressing the Needs of Children, Prenatal through Age Five.

ERIC Educational Resources Information Center

Rice, C.; And Others

This Kiwanis Club project kit contains ideas and instructions for implementing programs that meet local needs in the areas of maternal and infant health, child care and development, parenting, and safety and pediatric trauma. The kit begins with an overview that explains how to assess need and how to plan, implement, and evaluate a project. Tip…

Role of miR-452-5p in the tumorigenesis of prostate cancer: A study based on the Cancer Genome Atl(TCGA), Gene Expression Omnibus (GEO), and bioinformatics analysis.

PubMed

Gao, Li; Zhang, Li-Jie; Li, Sheng-Hua; Wei, Li-Li; Luo, Bin; He, Rong-Quan; Xia, Shuang

2018-03-06

MiR-452-5p has been reported to be down-regulated in prostate cancer, affecting the development of this type of cancer. However, the molecular mechanism of miR-452-5p in prostate cancer remains unclear. Therefore, we investigated the network of target genes of miR-452-5p in prostate cancer using bioinformatics analyses. We first analyzed the expression profiles and prognostic value of miR-452-5p in prostate cancer tissues from a public database. Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG), PANTHER pathway analyses, and a disease ontology (DG) analysis were performed to find the molecular functions of the target genes from GSE datasets and miRWalk. Finally, we validated hub genes from the protein-protein interaction (PPI) networks of the target genes in the Human Protein Atlas (HPA) database and Gene Expression Profiling Interactive Analysis (GEPIA). Narrowing down the optimal target genes was conducted by seeking the common parts of up-regulated genes from GEPIA, down-regulated genes from GSE datasets, and predicted genes in miRWalk. Based on mining of GEO and ArrayExpress microarray chips and miRNA-Seq data in the TCGA database, which includes 1007 prostate cancer samples and 387 non-cancer samples, miR-452-5p is shown to be down-regulated in prostate cancer. GO, KEGG, and PANTHER pathway analyses suggested that the target genes might participate in important biological processes, such as transforming growth factor beta signaling and the positive regulation of brown fat cell differentiation and mesenchymal cell differentiation, as well as the Ras signaling pathway and pathways regulating the pluripotency of stem cells and arrhythmogenic right ventricular cardiomyopathy (ARVC). Nine genes-GABBR, PNISR, NTSR1, DOCK1, EREG, SFRP1, PTGS2, LEF1, and BMP2-were defined as hub genes in the PPI network. Three genes-FAM174B, SLC30A4, and SLIT1-were jointly shared by GEPIA, the GSE datasets, and miRWalk. Down-regulated miR-452-5p might play an

Thai visitors' expectations and experiences of explainer interaction within a science museum context.

PubMed

Kamolpattana, Supara; Chen, Ganigar; Sonchaeng, Pichai; Wilkinson, Clare; Willey, Neil; Bultitude, Karen

2015-01-01

In Western literature, there is evidence that museum explainers offer significant potential for enhancing visitors' learning through influencing their knowledge, content, action, behaviour and attitudes. However, little research has focused on the role of explainers in other cultural contexts. This study explored interactions between visitors and museum explainers within the setting of Thailand. Two questionnaires were distributed to 600 visitors and 41 museum explainers. The results demonstrated both potential similarities and differences with Western contexts. Explainers appeared to prefer didactic approaches, focussing on factual knowledge rather than encouraging deep learning. Two-way communication, however, appeared to be enhanced by the use of a 'pseudo-sibling relationship' by explainers. Traditional Thai social reserve was reduced through such approaches, with visitors taking on active learning roles. These findings have implications for training museum explainers in non-Western cultures, as well as museum communication practice more generally. © The Author(s) 2014.

Thai visitors’ expectations and experiences of explainer interaction within a science museum context

PubMed Central

Chen, Ganigar; Sonchaeng, Pichai; Wilkinson, Clare; Willey, Neil; Bultitude, Karen

2015-01-01

In Western literature, there is evidence that museum explainers offer significant potential for enhancing visitors’ learning through influencing their knowledge, content, action, behaviour and attitudes. However, little research has focused on the role of explainers in other cultural contexts. This study explored interactions between visitors and museum explainers within the setting of Thailand. Two questionnaires were distributed to 600 visitors and 41 museum explainers. The results demonstrated both potential similarities and differences with Western contexts. Explainers appeared to prefer didactic approaches, focussing on factual knowledge rather than encouraging deep learning. Two-way communication, however, appeared to be enhanced by the use of a ‘pseudo-sibling relationship’ by explainers. Traditional Thai social reserve was reduced through such approaches, with visitors taking on active learning roles. These findings have implications for training museum explainers in non-Western cultures, as well as museum communication practice more generally. PMID:24751689

Molecular approaches for classifying endometrial carcinoma.

PubMed

Piulats, Josep M; Guerra, Esther; Gil-Martín, Marta; Roman-Canal, Berta; Gatius, Sonia; Sanz-Pamplona, Rebeca; Velasco, Ana; Vidal, August; Matias-Guiu, Xavier

2017-04-01

Endometrial carcinoma is the most common cancer of the female genital tract. This review article discusses the usefulness of molecular techniques to classify endometrial carcinoma. Any proposal for molecular classification of neoplasms should integrate morphological features of the tumors. For that reason, we start with the current histological classification of endometrial carcinoma, by discussing the correlation between genotype and phenotype, and the most significant recent improvements. Then, we comment on some of the possible flaws of this classification, by discussing also the value of molecular pathology in improving them, including interobserver variation in pathologic interpretation of high grade tumors. Third, we discuss the importance of applying TCGA molecular approach to clinical practice. We also comment on the impact of intratumor heterogeneity in classification, and finally, we will discuss briefly, the usefulness of TCGA classification in tailoring immunotherapy in endometrial cancer patients. We suggest combining pathologic classification and the surrogate TCGA molecular classification for high-grade endometrial carcinomas, as an option to improve assessment of prognosis. Copyright © 2016 Elsevier Inc. All rights reserved.

Explaining Racial Disparities in Infant Health in Brazil

PubMed Central

Nyarko, Kwame A.; Lopez-Camelo, Jorge; Castilla, Eduardo E.

2015-01-01

Objectives. We sought to quantify how socioeconomic, health care, demographic, and geographic effects explain racial disparities in low birth weight (LBW) and preterm birth (PTB) rates in Brazil. Methods. We employed a sample of 8949 infants born between 1995 and 2009 in 15 cities and 7 provinces in Brazil. We focused on disparities in LBW (< 2500 g) and PTB (< 37 gestational weeks) prevalence between infants of African ancestry alone or African mixed with other ancestries, and European ancestry alone. We used a decomposition model to quantify the contributions of conceptually relevant factors to these disparities. Results. The model explained 45% to 94% of LBW and 64% to 94% of PTB disparities between the African ancestry groups and European ancestry. Differences in prenatal care use and geographic location were the most important contributors, followed by socioeconomic differences. The model explained the majority of the disparities for mixed African ancestry and part of the disparity for African ancestry alone. Conclusions. Public policies to improve children’s health should target prenatal care and geographic location differences to reduce health disparities between infants of African and European ancestries in Brazil. PMID:26313046

Explaining Racial Disparities in Infant Health in Brazil

PubMed Central

Nyarko, Kwame A.; Lopez-Camelo, Jorge; Castilla, Eduardo E.

2013-01-01

Objectives. We sought to quantify how socioeconomic, health care, demographic, and geographic effects explain racial disparities in low birth weight (LBW) and preterm birth (PTB) rates in Brazil. Methods. We employed a sample of 8949 infants born between 1995 and 2009 in 15 cities and 7 provinces in Brazil. We focused on disparities in LBW (< 2500 g) and PTB (< 37 gestational weeks) prevalence between infants of African ancestry alone or African mixed with other ancestries, and European ancestry alone. We used a decomposition model to quantify the contributions of conceptually relevant factors to these disparities. Results. The model explained 45% to 94% of LBW and 64% to 94% of PTB disparities between the African ancestry groups and European ancestry. Differences in prenatal care use and geographic location were the most important contributors, followed by socioeconomic differences. The model explained the majority of the disparities for mixed African ancestry and part of the disparity for African ancestry alone. Conclusions. Public policies to improve children’s health should target prenatal care and geographic location differences to reduce health disparities between infants of African and European ancestries in Brazil. PMID:23409894

Effects on survival of BAP1 and PBRM1 mutations in sporadic clear-cell renal-cell carcinoma: a retrospective analysis with independent validation.

PubMed

Kapur, Payal; Peña-Llopis, Samuel; Christie, Alana; Zhrebker, Leah; Pavía-Jiménez, Andrea; Rathmell, W Kimryn; Xie, Xian-Jin; Brugarolas, James

2013-02-01

Clear-cell renal-cell carcinomas display divergent clinical behaviours. However, the molecular genetic events driving these behaviours are unknown. We discovered that BAP1 is mutated in about 15% of clear-cell renal-cell carcinoma, and that BAP1 and PBRM1 mutations are largely mutually exclusive. The aim of this study was to investigate the clinicopathological significance of these molecular subtypes and to determine whether patients with BAP1-mutant and PBRM1-mutant tumours had different overall survival. In this retrospective analysis, we assessed 145 patients with primary clear-cell renal-cell carcinoma and defined PBRM1 and BAP1 mutation status from the University of Texas Southwestern Medical Center (UTSW), TX, USA, between 1998 and 2011. We classified patients into those with BAP1-mutant tumours and those with tumours exclusively mutated for PBRM1 (PBRM1-mutant). We used a second independent cohort (n=327) from The Cancer Genome Atlas (TCGA) for validation. In both cohorts, more than 80% of patients had localised or locoregional disease at presentation. Overall both cohorts were similar, although the TCGA had more patients with metastatic and higher-grade disease, and more TCGA patients presented before molecularly targeted therapies became available. The median overall survival in the UTSW cohort was significantly shorter for patients with BAP1-mutant tumours (4·6 years; 95% CI 2·1-7·2), than for patients with PBRM1-mutant tumours (10·6 years; 9·8-11·5), corresponding to a HR of 2·7 (95% CI 0·99-7·6, p=0·044). Median overall survival in the TCGA cohort was 1·9 years (95% CI 0·6-3·3) for patients with BAP1-mutant tumours and 5·4 years (4·0-6·8) for those with PBRM1-mutant tumours. A HR similar to the UTSW cohort was noted in the TCGA cohort (2·8; 95% CI 1·4-5·9; p=0·004). Patients with mutations in both BAP1 and PBRM1, although a minority (three in UTSW cohort and four in TCGA cohort), had the worst overall survival (median 2·1 years, 95

Commentary on "Effects on survival of BAP1 and PBRM1 mutations in sporadic clear-cell renal-cell carcinoma: a retrospective analysis with independent validation." Kapur P, Peña-Llopis S, Christie A, Zhrebker L, Pavía-Jiménez A, Rathmell WK, Xie XJ, Brugarolas J. Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX. Lancet Oncol 2013; 14(2):159-67. [Epub 2013 Jan 16]. doi: 10.1016/S1470-2045(12)70584-3.

PubMed

Boorjian, Stephen

2014-08-01

Clear-cell renal-cell carcinomas display divergent clinical behaviours. However, the molecular genetic events driving these behaviours are unknown. We discovered that BAP1 is mutated in about 15% of clear-cell renal-cell carcinoma, and that BAP1 and PBRM1 mutations are largely mutually exclusive. The aim of this study was to investigate the clinicopathological significance of these molecular subtypes and to determine whether patients with BAP1-mutant and PBRM1-mutant tumours had different overall survival. In this retrospective analysis, we assessed 145 patients with primary clear-cell renal-cell carcinoma and defined PBRM1 and BAP1 mutation status from the University of Texas Southwestern Medical Center (UTSW), TX, USA, between 1998 and 2011. We classified patients into those with BAP1-mutant tumours and those with tumours exclusively mutated for PBRM1 (PBRM1-mutant). We used a second independent cohort (n=327) from The Cancer Genome Atlas (TCGA) for validation. In both cohorts, more than 80% of patients had localised or locoregional disease at presentation. Overall both cohorts were similar, although the TCGA had more patients with metastatic and higher-grade disease, and more TCGA patients presented before molecularly targeted therapies became available. The median overall survival in the UTSW cohort was significantly shorter for patients with BAP1-mutant tumours (4·6 years; 95% CI 2·1-7·2), than for patients with PBRM1-mutant tumours (10·6 years; 9·8-11·5), corresponding to a HR of 2·7 (95% CI 0·99-7·6, p=0·044). Median overall survival in the TCGA cohort was 1·9 years (95% CI 0·6-3·3) for patients with BAP1-mutant tumours and 5·4 years (4·0-6·8) for those with PBRM1-mutant tumours. A HR similar to the UTSW cohort was noted in the TCGA cohort (2·8; 95% CI 1·4-5·9; p=0·004). Patients with mutations in both BAP1 and PBRM1, although a minority (three in UTSW cohort and four in TCGA cohort), had the worst overall survival (median 2·1 years, 95

The role of early-life educational quality and literacy in explaining racial disparities in cognition in late life.

PubMed

Sisco, Shannon; Gross, Alden L; Shih, Regina A; Sachs, Bonnie C; Glymour, M Maria; Bangen, Katherine J; Benitez, Andreana; Skinner, Jeannine; Schneider, Brooke C; Manly, Jennifer J

2015-07-01

Racial disparities in late-life cognition persist even after accounting for educational attainment. We examined whether early-life educational quality and literacy in later life help explain these disparities. We used longitudinal data from the Washington Heights-Inwood Columbia Aging Project (WHICAP). Educational quality (percent white students; urban/rural school; combined grades in classroom) was operationalized using canonical correlation analysis. Late-life literacy (reading comprehension and ability, writing) was operationalized using confirmatory factor analysis. We examined whether these factors attenuated race-related differences in late-life cognition. The sample consisted of 1,679 U.S.-born, non-Hispanic, community-living adults aged 65-102 (71% black, 29% white; 70% women). Accounting for educational quality and literacy reduced disparities by 29% for general cognitive functioning, 26% for memory, and 32% for executive functioning but did not predict differences in rate of cognitive change. Early-life educational quality and literacy in late life explain a substantial portion of race-related disparities in late-life cognitive function. © The Author 2014. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Topology Explains Why Automobile Sunshades Fold Oddly

ERIC Educational Resources Information Center

Feist, Curtis; Naimi, Ramin

2009-01-01

Automobile sunshades always fold into an "odd" number of loops. The explanation why involves elementary topology (braid theory and linking number, both explained in detail here with definitions and examples), and an elementary fact from algebra about symmetric group.

De-mystifying earned value management for ground based astronomy projects, large and small

NASA Astrophysics Data System (ADS)

Norton, Timothy; Brennan, Patricia; Mueller, Mark

2014-08-01

The scale and complexity of today's ground based astronomy projects have justifiably required Principal Investigator's and their project teams to adopt more disciplined management processes and tools in order to achieve timely and accurate quantification of the progress and relative health of their projects. Earned Value Management (EVM) is one such tool. Developed decades ago and used extensively in the defense and construction industries, and now a requirement of NASA projects greater than $20M; EVM has gained a foothold in ground-based astronomy projects. The intent of this paper is to de-mystify EVM by discussing the fundamentals of project management, explaining how EVM fits with existing principles, and describing key concepts every project can use to implement their own EVM system. This paper also discusses pitfalls to avoid during implementation and obstacles to its success. The authors report on their organization's most recent experience implementing EVM for the GMT-Consortium Large Earth Finder (G-CLEF) project. G-CLEF is a fiber-fed, optical echelle spectrograph that has been selected as a first light instrument for the Giant Magellan Telescope (GMT), planned for construction at the Las Campanas Observatory in Chile's Atacama Desert region.

Explaining and Influencing Chinese Arms Transfers

DTIC Science & Technology

1995-02-01

this volume: Jonathan W. Pierce [] Secretary: Laura Hall [] Circulation Manager : Myma Morgan INSS publishes McNair Papers to provoke thought and inform...their affiliated factories were directed to decentralize their decision-making processes, grant more autonomy to managers , use excess capacity to...intimacy of ties between Moscow and 10 EXPLAINING AND INFLUENCING CHINESE ARMS TRANSFERS New Dehli , and concem that the United States was still in retreat

Ability of matrix models to explain the past and predict the future of plant populations.

USGS Publications Warehouse

McEachern, Kathryn; Crone, Elizabeth E.; Ellis, Martha M.; Morris, William F.; Stanley, Amanda; Bell, Timothy; Bierzychudek, Paulette; Ehrlen, Johan; Kaye, Thomas N.; Knight, Tiffany M.; Lesica, Peter; Oostermeijer, Gerard; Quintana-Ascencio, Pedro F.; Ticktin, Tamara; Valverde, Teresa; Williams, Jennifer I.; Doak, Daniel F.; Ganesan, Rengaian; Thorpe, Andrea S.; Menges, Eric S.

2013-01-01

Uncertainty associated with ecological forecasts has long been recognized, but forecast accuracy is rarely quantified. We evaluated how well data on 82 populations of 20 species of plants spanning 3 continents explained and predicted plant population dynamics. We parameterized stage-based matrix models with demographic data from individually marked plants and determined how well these models forecast population sizes observed at least 5 years into the future. Simple demographic models forecasted population dynamics poorly; only 40% of observed population sizes fell within our forecasts' 95% confidence limits. However, these models explained population dynamics during the years in which data were collected; observed changes in population size during the data-collection period were strongly positively correlated with population growth rate. Thus, these models are at least a sound way to quantify population status. Poor forecasts were not associated with the number of individual plants or years of data. We tested whether vital rates were density dependent and found both positive and negative density dependence. However, density dependence was not associated with forecast error. Forecast error was significantly associated with environmental differences between the data collection and forecast periods. To forecast population fates, more detailed models, such as those that project how environments are likely to change and how these changes will affect population dynamics, may be needed. Such detailed models are not always feasible. Thus, it may be wiser to make risk-averse decisions than to expect precise forecasts from models.

Ability of matrix models to explain the past and predict the future of plant populations.

PubMed

Crone, Elizabeth E; Ellis, Martha M; Morris, William F; Stanley, Amanda; Bell, Timothy; Bierzychudek, Paulette; Ehrlén, Johan; Kaye, Thomas N; Knight, Tiffany M; Lesica, Peter; Oostermeijer, Gerard; Quintana-Ascencio, Pedro F; Ticktin, Tamara; Valverde, Teresa; Williams, Jennifer L; Doak, Daniel F; Ganesan, Rengaian; McEachern, Kathyrn; Thorpe, Andrea S; Menges, Eric S

2013-10-01

Uncertainty associated with ecological forecasts has long been recognized, but forecast accuracy is rarely quantified. We evaluated how well data on 82 populations of 20 species of plants spanning 3 continents explained and predicted plant population dynamics. We parameterized stage-based matrix models with demographic data from individually marked plants and determined how well these models forecast population sizes observed at least 5 years into the future. Simple demographic models forecasted population dynamics poorly; only 40% of observed population sizes fell within our forecasts' 95% confidence limits. However, these models explained population dynamics during the years in which data were collected; observed changes in population size during the data-collection period were strongly positively correlated with population growth rate. Thus, these models are at least a sound way to quantify population status. Poor forecasts were not associated with the number of individual plants or years of data. We tested whether vital rates were density dependent and found both positive and negative density dependence. However, density dependence was not associated with forecast error. Forecast error was significantly associated with environmental differences between the data collection and forecast periods. To forecast population fates, more detailed models, such as those that project how environments are likely to change and how these changes will affect population dynamics, may be needed. Such detailed models are not always feasible. Thus, it may be wiser to make risk-averse decisions than to expect precise forecasts from models. © 2013 Society for Conservation Biology.

Breast MRI radiomics: comparison of computer- and human-extracted imaging phenotypes.

PubMed

Sutton, Elizabeth J; Huang, Erich P; Drukker, Karen; Burnside, Elizabeth S; Li, Hui; Net, Jose M; Rao, Arvind; Whitman, Gary J; Zuley, Margarita; Ganott, Marie; Bonaccio, Ermelinda; Giger, Maryellen L; Morris, Elizabeth A

2017-01-01

In this study, we sought to investigate if computer-extracted magnetic resonance imaging (MRI) phenotypes of breast cancer could replicate human-extracted size and Breast Imaging-Reporting and Data System (BI-RADS) imaging phenotypes using MRI data from The Cancer Genome Atlas (TCGA) project of the National Cancer Institute. Our retrospective interpretation study involved analysis of Health Insurance Portability and Accountability Act-compliant breast MRI data from The Cancer Imaging Archive, an open-source database from the TCGA project. This study was exempt from institutional review board approval at Memorial Sloan Kettering Cancer Center and the need for informed consent was waived. Ninety-one pre-operative breast MRIs with verified invasive breast cancers were analysed. Three fellowship-trained breast radiologists evaluated the index cancer in each case according to size and the BI-RADS lexicon for shape, margin, and enhancement (human-extracted image phenotypes [HEIP]). Human inter-observer agreement was analysed by the intra-class correlation coefficient (ICC) for size and Krippendorff's α for other measurements. Quantitative MRI radiomics of computerised three-dimensional segmentations of each cancer generated computer-extracted image phenotypes (CEIP). Spearman's rank correlation coefficients were used to compare HEIP and CEIP. Inter-observer agreement for HEIP varied, with the highest agreement seen for size (ICC 0.679) and shape (ICC 0.527). The computer-extracted maximum linear size replicated the human measurement with p  < 10 -12 . CEIP of shape, specifically sphericity and irregularity, replicated HEIP with both p values < 0.001. CEIP did not demonstrate agreement with HEIP of tumour margin or internal enhancement. Quantitative radiomics of breast cancer may replicate human-extracted tumour size and BI-RADS imaging phenotypes, thus enabling precision medicine.

Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis

PubMed Central

Wu, Tsung-Jung; Schriml, Lynn M.; Chen, Qing-Rong; Colbert, Maureen; Crichton, Daniel J.; Finney, Richard; Hu, Ying; Kibbe, Warren A.; Kincaid, Heather; Meerzaman, Daoud; Mitraka, Elvira; Pan, Yang; Smith, Krista M.; Srivastava, Sudhir; Ward, Sari; Yan, Cheng; Mazumder, Raja

2015-01-01

Bio-ontologies provide terminologies for the scientific community to describe biomedical entities in a standardized manner. There are multiple initiatives that are developing biomedical terminologies for the purpose of providing better annotation, data integration and mining capabilities. Terminology resources devised for multiple purposes inherently diverge in content and structure. A major issue of biomedical data integration is the development of overlapping terms, ambiguous classifications and inconsistencies represented across databases and publications. The disease ontology (DO) was developed over the past decade to address data integration, standardization and annotation issues for human disease data. We have established a DO cancer project to be a focused view of cancer terms within the DO. The DO cancer project mapped 386 cancer terms from the Catalogue of Somatic Mutations in Cancer (COSMIC), The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium, Therapeutically Applicable Research to Generate Effective Treatments, Integrative Oncogenomics and the Early Detection Research Network into a cohesive set of 187 DO terms represented by 63 top-level DO cancer terms. For example, the COSMIC term ‘kidney, NS, carcinoma, clear_cell_renal_cell_carcinoma’ and TCGA term ‘Kidney renal clear cell carcinoma’ were both grouped to the term ‘Disease Ontology Identification (DOID):4467 / renal clear cell carcinoma’ which was mapped to the TopNodes_DOcancerslim term ‘DOID:263 / kidney cancer’. Mapping of diverse cancer terms to DO and the use of top level terms (DO slims) will enable pan-cancer analysis across datasets generated from any of the cancer term sources where pan-cancer means including or relating to all or multiple types of cancer. The terms can be browsed from the DO web site (http://www.disease-ontology.org) and downloaded from the DO’s Apache Subversion or GitHub repositories. Database URL: http://www.disease-ontology.org PMID

Weather explains high annual variation in butterfly dispersal

PubMed Central

Rytteri, Susu; Heikkinen, Risto K.; Heliölä, Janne; von Bagh, Peter

2016-01-01

Weather conditions fundamentally affect the activity of short-lived insects. Annual variation in weather is therefore likely to be an important determinant of their between-year variation in dispersal, but conclusive empirical studies are lacking. We studied whether the annual variation of dispersal can be explained by the flight season's weather conditions in a Clouded Apollo (Parnassius mnemosyne) metapopulation. This metapopulation was monitored using the mark–release–recapture method for 12 years. Dispersal was quantified for each monitoring year using three complementary measures: emigration rate (fraction of individuals moving between habitat patches), average residence time in the natal patch, and average distance moved. There was much variation both in dispersal and average weather conditions among the years. Weather variables significantly affected the three measures of dispersal and together with adjusting variables explained 79–91% of the variation observed in dispersal. Different weather variables became selected in the models explaining variation in three dispersal measures apparently because of the notable intercorrelations. In general, dispersal rate increased with increasing temperature, solar radiation, proportion of especially warm days, and butterfly density, and decreased with increasing cloudiness, rainfall, and wind speed. These results help to understand and model annually varying dispersal dynamics of species affected by global warming. PMID:27440662

Weather explains high annual variation in butterfly dispersal.

PubMed

Kuussaari, Mikko; Rytteri, Susu; Heikkinen, Risto K; Heliölä, Janne; von Bagh, Peter

2016-07-27

Weather conditions fundamentally affect the activity of short-lived insects. Annual variation in weather is therefore likely to be an important determinant of their between-year variation in dispersal, but conclusive empirical studies are lacking. We studied whether the annual variation of dispersal can be explained by the flight season's weather conditions in a Clouded Apollo (Parnassius mnemosyne) metapopulation. This metapopulation was monitored using the mark-release-recapture method for 12 years. Dispersal was quantified for each monitoring year using three complementary measures: emigration rate (fraction of individuals moving between habitat patches), average residence time in the natal patch, and average distance moved. There was much variation both in dispersal and average weather conditions among the years. Weather variables significantly affected the three measures of dispersal and together with adjusting variables explained 79-91% of the variation observed in dispersal. Different weather variables became selected in the models explaining variation in three dispersal measures apparently because of the notable intercorrelations. In general, dispersal rate increased with increasing temperature, solar radiation, proportion of especially warm days, and butterfly density, and decreased with increasing cloudiness, rainfall, and wind speed. These results help to understand and model annually varying dispersal dynamics of species affected by global warming. © 2016 The Author(s).

John Kay's Civil War: A Multimedia Internet Project for Middle School Social Studies.

ERIC Educational Resources Information Center

Olwell, Russell B.

1999-01-01

Uses letters of John Kay, a Union Army soldier, to initiate a technology-based project that illustrates reasons for fighting in the Civil War, the daily life of a soldier, and the tragedies families endured. Explains that students learn that history is filled with real people who lived and died for their beliefs. (CMK)

Nathan Glazer Explains the Black Faculty Gap.

ERIC Educational Resources Information Center

Glazer, Nathan

2003-01-01

Contends that the low number of academically high-scoring black students at selective colleges, combined with the attraction of alternate career opportunities, largely explains the shortage of black doctoral candidates. The lower grades black students receive at selective institutions may discourage them from choosing academic careers. Suggests…

Children's Theories and the Drive to Explain

NASA Astrophysics Data System (ADS)

Schwitzgebel, Eric

Debate has been growing in developmental psychology over how much the cognitive development of children is like theory change in science. Useful debate on this topic requires a clear understanding of what it would be for a child to have a theory. I argue that existing accounts of theories within philosophy of science and developmental psychology either are less precise than is ideal for the task or cannot capture everyday theorizing of the sort that children, if they theorize, must do. I then propose an account of theories that ties theories and explanation very closely together, treating theories primarily as products of a drive to explain. I clarify some of the positions people have taken regarding the theory theory of development, and I conclude by proposing that psychologists interested in the ''theory theory'' look for patterns of affect and arousal in development that would accompany the existence of a drive to explain.

HIV As Trojan Exosome: Immunological Paradox Explained?

PubMed

Hildreth, James E K

2017-01-01

The HIV pandemic is still a major global challenge, despite the widespread availability of antiretroviral drugs. An effective vaccine would be the ideal approach to bringing the pandemic to an end. However, developing an effective HIV vaccine has proven to be an elusive goal. Three major human HIV vaccine trials revealed a strong trend toward greater risk of infection among vaccine recipients versus controls. A similar observation was made in a macaque SIV vaccine study. The mechanism explaining this phenomenon is not known. Here, a model is presented that may explain the troubling results of vaccine studies and an immunological paradox of HIV pathogenesis: preferential infection of HIV-specific T cells. The central hypothesis of this perspective is that as "Trojan exosomes" HIV particles can directly activate HIV-specific T cells enhancing their susceptibility to infection. Understanding the biology of HIV as an exosome may provide insights that enable novel approaches to vaccine development.

Communication, coordination and cooperation in construction projects: business environment and human behaviours

NASA Astrophysics Data System (ADS)

Salah Alaloul, Wesam; Shahir Liew, Mohd; Zawawi, Noor Amila Wan

2017-12-01

The accomplishment of construction projects is extremely dependent on the integration of several stakeholders; therefore none of them has the control or the ability to accomplish the project alone. Each of them may influence and be influenced by the project management approach. There is no comprehensive theoretical platform for defining Communication, Coordination and Cooperation (3Cs) in the management of construction project. This paper deliberates the function of the 3Cs different theoretical perceptions. Through an analysis of selected articles from reputable academic journals in construction management, the business environment and human behaviour were identified as two main parts. A little has been done so far about the 3Cs, and how they are correlated with construction projects performance. Therefore, the objective of this paper is to explain the definitions and the association between the 3Cs. There is a significant link between communication and coordination. Coordination alternatively, is trust-based a logic of mutual and exchange. Consequently, cooperation is much more sophisticated, which needing more time and attempts.

Cellular projections from sensory hair cells form polarity-specific scaffolds during synaptogenesis

PubMed Central

Dow, Eliot; Siletti, Kimberly

2015-01-01

The assembly of a nervous system requires the extension of axons and dendrites to specific regions where they are matched with appropriate synaptic targets. Although the cues that guide long-range outgrowth have been characterized extensively, additional mechanisms are required to explain short-range guidance in neural development. Using a complementary combination of time-lapse imaging by fluorescence confocal microscopy and serial block-face electron microscopy, we identified a novel type of presynaptic projection that participates in the assembly of the vertebrate nervous system. Synapse formation by each hair cell of the zebrafish's lateral line occurs during a particular interval after the cell's birth. During the same period, projections emerge from the cellular soma, extending toward a specific subpopulation of mature hair cells and interacting with polarity-specific afferent nerve terminals. The terminals then extend along the projections to reach appropriately matched presynaptic sites, after which the projections recede. Our results suggest that presynaptic projections act as transient scaffolds for short-range partner matching, a mechanism that may occur elsewhere in the nervous system. PMID:25995190

Throughfall Displacement Experiment (TDE) Ecosystem Model Intercomparison Project Data Archive

DOE Data Explorer

Hanson, Paul J. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (USA); Amthor, Jeffrey S. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (USA); Baldocchi, Dennis D. [University of California, Berkeley; Grant, Robert F. [University of Alberta, Canada; Hartley, Anne E. [Ohio State University; Hui, Dafeng [University of Oklahoma; Hunt, Jr., E. Raymond [Agricultural Research Service, U.S. Department of Agriculture; Johnson, Dale W. [University of Nevada, Reno; Kimball, John S. [University of Montana; King, Anthony W. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (USA); Luo, Yiqi [University of Oklahoma; McNulty, Steven G. [Southern Global Change Program, U.S. Forest Service, U.S. Department of Agriculture; Sun, Ge [North Carolina State University, Raleigh, NC (USA); Thornton, Peter E. [University of Montana; Wang, Shusen [Geomatics Canada - Canada Centre for Remote Sensing Natural Resources, Canada; Williams, Matthew [University of Edinburgh, United Kingdom; Wilson, Kell B. [National Oceanic and Atmospheric Administration, U.S. Department of Commerce; Wullschleger, Stanley D. [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (USA)

2002-08-01

This archive provides and documents data from a project whose purpose is to compare the output of various ecosystem models when they are run with the data from the Throughfall Displacement Experiment (TDE) at Walker Branch Watershed, Oak Ridge, Tennessee. The project is not designed to determine which models are "best" for diagnosis (i.e., explaining the current functioning of the system) or prognosis (i.e., predicting the response of the system to future conditions), but, rather, to clarify similarities and differences among the models and their components, so that all models can be improved. Data archive: ftp://cdiac.ornl.gov/ftp/tdemodel/. TDE data archive web site: http://cdiac.ess-dive.lbl.gov/epubs/ndp/ndp078a/ndp078a.html.

Chernobyl post-accident management: the ETHOS project.

PubMed

Dubreuil, G H; Lochard, J; Girard, P; Guyonnet, J F; Le Cardinal, G; Lepicard, S; Livolsi, P; Monroy, M; Ollagnon, H; Pena-Vega, A; Pupin, V; Rigby, J; Rolevitch, I; Schneider, T

1999-10-01

consideration the problems of acceptability of decisions and the distrust of the population towards experts. These cannot be solved merely by a better communication strategy. This paper presents the main features of the methodological approach of the ETHOS project. It also explains how it is being implemented in the village of Olmany in the district of Stolyn (Brest region) in Belarus since March 1996, as well as its initial achievements.

Explaining Pregnancy Loss: Parents' and Physicians' Attributions.

ERIC Educational Resources Information Center

Dunn, Dana S.; And Others

1991-01-01

Asked 138 females and 56 of their male partners to explain why they believed their spontaneous abortion, fetal or neonatal death, or ectopic pregnancy occurred. Explanations for loss included blaming mother, physical problems with mother or fetus, fate, or no explanation. Physicians' explanations related to gestational age of fetus, although…

"Listen to My Story and You Will Know Me": Digital Stories as Student-Centered Collaborative Projects

ERIC Educational Resources Information Center

Vinogradova, Polina; Linville, Heather A.; Bickel, Beverly

2011-01-01

This article explores the power of English language learners' digital stories as student-centered projects and offers practical suggestions for language teachers interested in trying digital storytelling. The article explains pedagogical practices and digital storytelling in the context of contemporary scholarship on inclusive pedagogy,…

Does traffic-related air pollution explain associations of aircraft and road traffic noise exposure on children's health and cognition? A secondary analysis of the United Kingdom sample from the RANCH project.

PubMed

Clark, Charlotte; Crombie, Rosanna; Head, Jenny; van Kamp, Irene; van Kempen, Elise; Stansfeld, Stephen A

2012-08-15

The authors examined whether air pollution at school (nitrogen dioxide) is associated with poorer child cognition and health and whether adjustment for air pollution explains or moderates previously observed associations between aircraft and road traffic noise at school and children's cognition in the 2001-2003 Road Traffic and Aircraft Noise Exposure and Children's Cognition and Health (RANCH) project. This secondary analysis of a subsample of the United Kingdom RANCH sample examined 719 children who were 9-10 years of age from 22 schools around London's Heathrow airport for whom air pollution data were available. Data were analyzed using multilevel modeling. Air pollution exposure levels at school were moderate, were not associated with a range of cognitive and health outcomes, and did not account for or moderate associations between noise exposure and cognition. Aircraft noise exposure at school was significantly associated with poorer recognition memory and conceptual recall memory after adjustment for nitrogen dioxide levels. Aircraft noise exposure was also associated with poorer reading comprehension and information recall memory after adjustment for nitrogen dioxide levels. Road traffic noise was not associated with cognition or health before or after adjustment for air pollution. Moderate levels of air pollution do not appear to confound associations of noise on cognition and health, but further studies of higher air pollution levels are needed.

Does Traffic-related Air Pollution Explain Associations of Aircraft and Road Traffic Noise Exposure on Children's Health and Cognition? A Secondary Analysis of the United Kingdom Sample From the RANCH Project

PubMed Central

Clark, Charlotte; Crombie, Rosanna; Head, Jenny; van Kamp, Irene; van Kempen, Elise; Stansfeld, Stephen A.

2012-01-01

The authors examined whether air pollution at school (nitrogen dioxide) is associated with poorer child cognition and health and whether adjustment for air pollution explains or moderates previously observed associations between aircraft and road traffic noise at school and children's cognition in the 2001–2003 Road Traffic and Aircraft Noise Exposure and Children's Cognition and Health (RANCH) project. This secondary analysis of a subsample of the United Kingdom RANCH sample examined 719 children who were 9–10 years of age from 22 schools around London's Heathrow airport for whom air pollution data were available. Data were analyzed using multilevel modeling. Air pollution exposure levels at school were moderate, were not associated with a range of cognitive and health outcomes, and did not account for or moderate associations between noise exposure and cognition. Aircraft noise exposure at school was significantly associated with poorer recognition memory and conceptual recall memory after adjustment for nitrogen dioxide levels. Aircraft noise exposure was also associated with poorer reading comprehension and information recall memory after adjustment for nitrogen dioxide levels. Road traffic noise was not associated with cognition or health before or after adjustment for air pollution. Moderate levels of air pollution do not appear to confound associations of noise on cognition and health, but further studies of higher air pollution levels are needed. PMID:22842719

Explaining patterns in the ratification of global environmental treaties

NASA Technical Reports Server (NTRS)

Cook, David W.

1991-01-01

A study was made of the ratification behavior of 160 countries with respect to 38 global environmental treaties. The study identifies and explains patterns in the ratification of treaties, providing two means of assessing the likelihood that any given country will support global environmental treaties. National ratification totals reveal a pattern of high ratification by countries in Western Europe, North America, Japan, Australia, and New Zealand. A country's standing within the range of high to low ratification rates can be explained by the statistical model developed in the study. This research allows one to identify countries likely to support global environmental treaties.

Software for project-based learning of robot motion planning

NASA Astrophysics Data System (ADS)

Moll, Mark; Bordeaux, Janice; Kavraki, Lydia E.

2013-12-01

Motion planning is a core problem in robotics concerned with finding feasible paths for a given robot. Motion planning algorithms perform a search in the high-dimensional continuous space of robot configurations and exemplify many of the core algorithmic concepts of search algorithms and associated data structures. Motion planning algorithms can be explained in a simplified two-dimensional setting, but this masks many of the subtleties and complexities of the underlying problem. We have developed software for project-based learning of motion planning that enables deep learning. The projects that we have developed allow advanced undergraduate students and graduate students to reflect on the performance of existing textbook algorithms and their own variations on such algorithms. Formative assessment has been conducted at three institutions. The core of the software used for this teaching module is also used within the Robot Operating System, a widely adopted platform by the robotics research community. This allows for transfer of knowledge and skills to robotics research projects involving a large variety robot hardware platforms.

Explaining Autism: Its Discursive and Neuroanatomical Characteristics.

ERIC Educational Resources Information Center

Oller, John W., Jr.; Rascon, Dana

This paper reviews the existing empirical research on autism in the context of the semiotic theories of Charles S. Peirce. His ideas of the generalized logic of relations are seen as explaining the unusual associations (or lack thereof) in autism. Concepts of "indices" or signs singling out distinct objects, and "adinity" or…

A self-updating road map of The Cancer Genome Atlas

PubMed Central

Robbins, David E.; Grüneberg, Alexander; Deus, Helena F.; Tanik, Murat M.; Almeida, Jonas S.

2013-01-01

Motivation: Since 2011, The Cancer Genome Atlas’ (TCGA) files have been accessible through HTTP from a public site, creating entirely new possibilities for cancer informatics by enhancing data discovery and retrieval. Significantly, these enhancements enable the reporting of analysis results that can be fully traced to and reproduced using their source data. However, to realize this possibility, a continually updated road map of files in the TCGA is required. Creation of such a road map represents a significant data modeling challenge, due to the size and fluidity of this resource: each of the 33 cancer types is instantiated in only partially overlapping sets of analytical platforms, while the number of data files available doubles approximately every 7 months. Results: We developed an engine to index and annotate the TCGA files, relying exclusively on third-generation web technologies (Web 3.0). Specifically, this engine uses JavaScript in conjunction with the World Wide Web Consortium’s (W3C) Resource Description Framework (RDF), and SPARQL, the query language for RDF, to capture metadata of files in the TCGA open-access HTTP directory. The resulting index may be queried using SPARQL, and enables file-level provenance annotations as well as discovery of arbitrary subsets of files, based on their metadata, using web standard languages. In turn, these abilities enhance the reproducibility and distribution of novel results delivered as elements of a web-based computational ecosystem. The development of the TCGA Roadmap engine was found to provide specific clues about how biomedical big data initiatives should be exposed as public resources for exploratory analysis, data mining and reproducible research. These specific design elements align with the concept of knowledge reengineering and represent a sharp departure from top-down approaches in grid initiatives such as CaBIG. They also present a much more interoperable and reproducible alternative to the still

Transcriptional diversity of long-term glioblastoma survivors

PubMed Central

Gerber, Naamit K.; Goenka, Anuj; Turcan, Sevin; Reyngold, Marsha; Makarov, Vladimir; Kannan, Kasthuri; Beal, Kathryn; Omuro, Antonio; Yamada, Yoshiya; Gutin, Phillip; Brennan, Cameron W.; Huse, Jason T.; Chan, Timothy A.

2014-01-01

Background Glioblastoma (GBM) is a highly aggressive type of glioma with poor prognosis. However, a small number of patients live much longer than the median survival. A better understanding of these long-term survivors (LTSs) may provide important insight into the biology of GBM. Methods We identified 7 patients with GBM, treated at Memorial Sloan-Kettering Cancer Center (MSKCC), with survival >48 months. We characterized the transcriptome of each patient and determined rates of MGMT promoter methylation and IDH1 and IDH2 mutational status. We identified LTSs in 2 independent cohorts (The Cancer Genome Atlas [TCGA] and NCI Repository for Molecular Brain Neoplasia Data [REMBRANDT]) and analyzed the transcriptomal characteristics of these LTSs. Results The median overall survival of our cohort was 62.5 months. LTSs were distributed between the proneural (n = 2), neural (n = 2), classical (n = 2), and mesenchymal (n = 1) subtypes. Similarly, LTS in the TCGA and REMBRANDT cohorts demonstrated diverse transcriptomal subclassification identities. The majority of the MSKCC LTSs (71%) were found to have methylation of the MGMT promoter. None of the patients had an IDH1 or IDH2 mutation, and IDH mutation occurred in a minority of the TCGA LTSs as well. A set of 60 genes was found to be differentially expressed in the MSKCC and TCGA LTSs. Conclusions While IDH mutant proneural tumors impart a better prognosis in the short-term, survival beyond 4 years does not require IDH mutation and is not dictated by a single transcriptional subclass. In contrast, MGMT methylation continues to have strong prognostic value for survival beyond 4 years. These findings have substantial impact for understanding GBM biology and progression. PMID:24662514

TCGA study of genetic drivers of melanoma

Cancer.gov

A comprehensive analysis of the genome of cutaneous melanoma has provided new insights into the roles of frequently mutated cancer genes and other genomic alterations that drive the development of this disease.

Placing and preserving priorities: projects, productivity, progress and people

PubMed Central

Babiak, John

1998-01-01

High throughput screening (HTS) involves using automated equipment to test a large number of samples against a defined molecular target to identify a reasonable number of active molecules in a timely fashion. Major factors which can influence priorities for the limited resources of the HTS group are projects, productivity, progress and people. The challenge to the HTS group is to provide excellent and timely screening services, but still devote efforts to new technologies and personnel development. This article explains why these factors are so important. PMID:18924829

How Employees Remain Happy: Explaining a Paradox

ERIC Educational Resources Information Center

Hutton, Dorothy M.; Atkinson, Barbara; Judd, Priya; Darling, Julie; Tran, Linh; Cummins, Robert A.

2004-01-01

This paper draws on subjective quality of life theory to explain findings from three studies of quality of work life. The studies were conducted with 346 regional process workers, metropolitan employment officers and nurses. The results support the adoption of the theory of homeostasis as an explanation for findings on subjective wellbeing at work…

Prognostic value of DNA repair based stratification of hepatocellular carcinoma

PubMed Central

Lin, Zhuo; Xu, Shi-Hao; Wang, Hai-Qing; Cai, Yi-Jing; Ying, Li; Song, Mei; Wang, Yu-Qun; Du, Shan-Jie; Shi, Ke-Qing; Zhou, Meng-Tao

2016-01-01

Aberrant activation of DNA repair is frequently associated with tumor progression and response to therapy in hepatocellular carcinoma (HCC). Bioinformatics analyses of HCC data in the Cancer Genome Atlas (TCGA) were performed to define DNA repair based molecular classification that could predict the prognosis of patients with HCC. Furthermore, we tested its predictive performance in 120 independent cases. Four molecular subgroups were identified on the basis of coordinate DNA repair cluster (CDRC) comprising 15 genes in TCGA dataset. Increasing expression of CDRC genes were significantly associated with TP53 mutation. High CDRC was significantly correlated with advanced tumor grades, advanced pathological stage and increased vascular invasion rate. Multivariate Cox regression analysis indicated that the molecular subgrouping was an independent prognostic parameter for both overall survival (p = 0.004, hazard ratio (HR): 2.989) and tumor-free survival (p = 0.049, HR: 3.366) in TCGA dataset. Similar results were also obtained by analyzing the independent cohort. These data suggest that distinct dysregulation of DNA repair constituents based molecular classes in HCC would be useful for predicting prognosis and designing clinical trials for targeted therapy. PMID:27174663

Efficient exploration of pan-cancer networks by generalized covariance selection and interactive web content

PubMed Central

Kling, Teresia; Johansson, Patrik; Sanchez, José; Marinescu, Voichita D.; Jörnsten, Rebecka; Nelander, Sven

2015-01-01

Statistical network modeling techniques are increasingly important tools to analyze cancer genomics data. However, current tools and resources are not designed to work across multiple diagnoses and technical platforms, thus limiting their applicability to comprehensive pan-cancer datasets such as The Cancer Genome Atlas (TCGA). To address this, we describe a new data driven modeling method, based on generalized Sparse Inverse Covariance Selection (SICS). The method integrates genetic, epigenetic and transcriptional data from multiple cancers, to define links that are present in multiple cancers, a subset of cancers, or a single cancer. It is shown to be statistically robust and effective at detecting direct pathway links in data from TCGA. To facilitate interpretation of the results, we introduce a publicly accessible tool (cancerlandscapes.org), in which the derived networks are explored as interactive web content, linked to several pathway and pharmacological databases. To evaluate the performance of the method, we constructed a model for eight TCGA cancers, using data from 3900 patients. The model rediscovered known mechanisms and contained interesting predictions. Possible applications include prediction of regulatory relationships, comparison of network modules across multiple forms of cancer and identification of drug targets. PMID:25953855

Disadvantaged persons' participation in health promotion projects: some structural dimensions.

PubMed

Boyce, W F

2001-05-01

A structural perspective was used in studying community participation of disadvantaged groups (poor women, street youth, and disabled persons) in health promotion projects. Five community projects in the Canadian Health Promotion Contribution Program were examined in a comparative case study utilizing in-depth interviews, documents, and secondary sources. Analysis revealed relatively low numbers and restricted range of participants, difficulties in recruiting and maintaining participants, declining rates of active participation over time, and limited target group influence and power. This paper reports on the relationship between various dimensions of structure (social-cultural, organizational, political-legal-economic) and the community participation process. Participation was influenced by structural factors such as bureaucratic rules and regulators, perceived minority group rights and relations, agency reputations and responsibilities, available resources, and organizational roles. Control of projects by target group members, rather than by service agencies, was an important overall organizational structural factor which allowed community members to achieve influence in projects. The study concludes that a conceptual model based on structural factors is useful in explaining how key factors from federal and local levels can restrict or facilitate the community participation process.

Do Lower-Body Dimensions and Body Composition Explain Vertical Jump Ability?

PubMed

Caia, Johnpaul; Weiss, Lawrence W; Chiu, Loren Z F; Schilling, Brian K; Paquette, Max R; Relyea, George E

2016-11-01

Caia, J, Weiss, LW, Chiu, LZF, Schilling, BK, Paquette, MR, and Relyea, GE. Do lower-body dimensions and body composition explain vertical jump ability? J Strength Cond Res 30(11): 3073-3083, 2016-Vertical jump (VJ) capability is integral to the level of success attained by individuals participating in numerous sport and physical activities. Knowledge of factors related to jump performance may help with talent identification and/or optimizing training prescription. Although myriad variables are likely related to VJ, this study focused on determining if various lower-body dimensions and/or body composition would explain some of the variability in performance. Selected anthropometric dimensions were obtained from 50 university students (25 men and 25 women) on 2 occasions separated by 48 or 72 hours. Estimated body fat percentage (BF%), height, body weight, hip width, pelvic width, bilateral quadriceps angle (Q-angle), and bilateral longitudinal dimensions of the feet, leg, thigh, and lower limb were obtained. Additionally, participants completed countermovement VJs. Analysis showed BF% to have the highest correlation with countermovement VJ displacement (r = -0.76, p < 0.001). When examining lower-body dimensions, right-side Q-angle displayed the strongest association with countermovement VJ displacement (r = -0.58, p < 0.001). Regression analysis revealed that 2 different pairs of variables accounted for the greatest variation (66%) in VJ: (a) BF% and sex and (b) BF% and body weight. Regression models involving BF% and lower-body dimensions explained up to 61% of the variance observed in VJ. Although the variance explained by BF% may be increased by using several lower-body dimensions, either sex identification or body weight explains comparatively more. Therefore, these data suggest that the lower-body dimensions measured herein have limited utility in explaining VJ performance.

Explaining Achievement in Higher Education

ERIC Educational Resources Information Center

Jansen, Ellen P. W. A.; Bruinsma, Marjon

2005-01-01

This research project investigated the relationship between students' pre-entry characteristics, perceptions of the learning environment, reported work discipline, the use of deep information processing strategies, and academic achievement. Ability measured by grade-point average in pre-university education was the most important predictor of…

Spatially tuned normalization explains attention modulation variance within neurons.

PubMed

Ni, Amy M; Maunsell, John H R

2017-09-01

Spatial attention improves perception of attended parts of a scene, a behavioral enhancement accompanied by modulations of neuronal firing rates. These modulations vary in size across neurons in the same brain area. Models of normalization explain much of this variance in attention modulation with differences in tuned normalization across neurons (Lee J, Maunsell JHR. PLoS One 4: e4651, 2009; Ni AM, Ray S, Maunsell JHR. Neuron 73: 803-813, 2012). However, recent studies suggest that normalization tuning varies with spatial location both across and within neurons (Ruff DA, Alberts JJ, Cohen MR. J Neurophysiol 116: 1375-1386, 2016; Verhoef BE, Maunsell JHR. eLife 5: e17256, 2016). Here we show directly that attention modulation and normalization tuning do in fact covary within individual neurons, in addition to across neurons as previously demonstrated. We recorded the activity of isolated neurons in the middle temporal area of two rhesus monkeys as they performed a change-detection task that controlled the focus of spatial attention. Using the same two drifting Gabor stimuli and the same two receptive field locations for each neuron, we found that switching which stimulus was presented at which location affected both attention modulation and normalization in a correlated way within neurons. We present an equal-maximum-suppression spatially tuned normalization model that explains this covariance both across and within neurons: each stimulus generates equally strong suppression of its own excitatory drive, but its suppression of distant stimuli is typically less. This new model specifies how the tuned normalization associated with each stimulus location varies across space both within and across neurons, changing our understanding of the normalization mechanism and how attention modulations depend on this mechanism. NEW & NOTEWORTHY Tuned normalization studies have demonstrated that the variance in attention modulation size seen across neurons from the same cortical

Can the inherence heuristic explain vitalistic reasoning?

PubMed

Bastian, Brock

2014-10-01

Inherence is an important component of psychological essentialism. By drawing on vitalism as a way in which to explain this link, however, the authors appear to conflate causal explanations based on fixed features with those based on general causal forces. The disjuncture between these two types of explanatory principles highlights potential new avenues for the inherence heuristic.

Learning to apply models of materials while explaining their properties

NASA Astrophysics Data System (ADS)

Karpin, Tiia; Juuti, Kalle; Lavonen, Jari

2014-09-01

Background:Applying structural models is important to chemistry education at the upper secondary level, but it is considered one of the most difficult topics to learn. Purpose:This study analyses to what extent in designed lessons students learned to apply structural models in explaining the properties and behaviours of various materials. Sample:An experimental group is 27 Finnish upper secondary school students and control group included 18 students from the same school. Design and methods:In quasi-experimental setting, students were guided through predict, observe, explain activities in four practical work situations. It was intended that the structural models would encourage students to learn how to identify and apply appropriate models when predicting and explaining situations. The lessons, organised over a one-week period, began with a teacher's demonstration and continued with student experiments in which they described the properties and behaviours of six household products representing three different materials. Results:Most students in the experimental group learned to apply the models correctly, as demonstrated by post-test scores that were significantly higher than pre-test scores. The control group showed no significant difference between pre- and post-test scores. Conclusions:The findings indicate that the intervention where students engage in predict, observe, explain activities while several materials and models are confronted at the same time, had a positive effect on learning outcomes.

Generalizing MOND to explain the missing mass in galaxy clusters

NASA Astrophysics Data System (ADS)

Hodson, Alistair O.; Zhao, Hongsheng

2017-02-01

Context. MOdified Newtonian Dynamics (MOND) is a gravitational framework designed to explain the astronomical observations in the Universe without the inclusion of particle dark matter. MOND, in its current form, cannot explain the missing mass in galaxy clusters without the inclusion of some extra mass, be it in the form of neutrinos or non-luminous baryonic matter. We investigate whether the MOND framework can be generalized to account for the missing mass in galaxy clusters by boosting gravity in high gravitational potential regions. We examine and review Extended MOND (EMOND), which was designed to increase the MOND scale acceleration in high potential regions, thereby boosting the gravity in clusters. Aims: We seek to investigate galaxy cluster mass profiles in the context of MOND with the primary aim at explaining the missing mass problem fully without the need for dark matter. Methods: Using the assumption that the clusters are in hydrostatic equilibrium, we can compute the dynamical mass of each cluster and compare the result to the predicted mass of the EMOND formalism. Results: We find that EMOND has some success in fitting some clusters, but overall has issues when trying to explain the mass deficit fully. We also investigate an empirical relation to solve the cluster problem, which is found by analysing the cluster data and is based on the MOND paradigm. We discuss the limitations in the text.

Being in the World: An Existential Inquiry of Knowing One's Self through a Personal Project--In the Context of Dissertation Survival

ERIC Educational Resources Information Center

Kitajima, Tomoe

2012-01-01

This study--a philosophical exploration, partly in an autoethnographical account-provides an empirical demonstration that one's personal project has a strong and positive impact on the dissertation process both for endurance to complete the process and for quality of the product. The concept of project is often explained as one's pursuit…

Project Ice Storm: Prenatal Maternal Stress Affects Cognitive and Linguistic Functioning in 5 1/2-Year-Old Children

ERIC Educational Resources Information Center

Laplante, David P.; Brunet, Alain; Schmitz, Norbert; Ciampi, Antonio; King, Suzanne

2008-01-01

The study used data from Project Ice Storm to determine the extent to which exposure to prenatal maternal stress due to a natural disaster can explain variance in the intellectual and language performance of offspring at age 5 1/2.

The relationship between observational scale and explained variance in benthic communities

PubMed Central

Flood, Roger D.; Frisk, Michael G.; Garza, Corey D.; Lopez, Glenn R.; Maher, Nicole P.

2018-01-01

This study addresses the impact of spatial scale on explaining variance in benthic communities. In particular, the analysis estimated the fraction of community variation that occurred at a spatial scale smaller than the sampling interval (i.e., the geographic distance between samples). This estimate is important because it sets a limit on the amount of community variation that can be explained based on the spatial configuration of a study area and sampling design. Six benthic data sets were examined that consisted of faunal abundances, common environmental variables (water depth, grain size, and surficial percent cover), and sonar backscatter treated as a habitat proxy (categorical acoustic provinces). Redundancy analysis was coupled with spatial variograms generated by multiscale ordination to quantify the explained and residual variance at different spatial scales and within and between acoustic provinces. The amount of community variation below the sampling interval of the surveys (< 100 m) was estimated to be 36–59% of the total. Once adjusted for this small-scale variation, > 71% of the remaining variance was explained by the environmental and province variables. Furthermore, these variables effectively explained the spatial structure present in the infaunal community. Overall, no scale problems remained to compromise inferences, and unexplained infaunal community variation had no apparent spatial structure within the observational scale of the surveys (> 100 m), although small-scale gradients (< 100 m) below the observational scale may be present. PMID:29324746

Teaching With Projections in the Geosciences: Windows to Enlightenment or Barriers to Understanding?

NASA Astrophysics Data System (ADS)

Mogk, D. W.

2009-12-01

Geoscientists are trained to represent multi-component datasets by projecting onto relatively simple diagrams on two-dimensional surfaces. These projections are used to represent a variety of phenomena ranging from spatial relations to physico-chemical processes. By using projections, it is possible to create simple diagrams as models or analogs of complex and heterogeneous natural systems using a limited number of well-defined “end-member” variables. Although projections are widely used in professional practice, the construction, use and interpretation of these diagrams often presents formidable barriers to student learning. This is largely due to the fact that diagrams that display projected data are the composite product of underlying scientific and mathematical principles, spatial relations on the diagrams may serve as proxies for physical or chemical properties or processes (thus co-mingling spatial reasoning with conceptual reasoning), there are myriad hidden or understood assumptions in the creation of the projections, and projections seek to decrease the “dimensionality” (or degrees of freedom) of multi-component (or multi-variable) systems. Additional layers of information may be superposed on projected diagrams by contouring data, using color or other symbols to distinguish discrete populations of data, imposing gradients of related variables (e.g. isotherms on composition diagrams), or using multiple projections to demonstrate time sequences that elucidate processes (e.g. before/after relations conveyed in animations). Thus, the simple forms of graphical projections may belie numerous layers of information that attempt to explain complex and sophisticated relationships in nature. In striving for simplicity in presentation, diagrams that present projected data may confound student understanding due to lack of knowledge about the inherent complexities in their development. Recall Plato’s Myth of the Cave (Republic, Book 7): the shadow on the wall

Project-Based Method as an Effective Means of Interdisciplinary Interaction While Teaching a Foreign Language

ERIC Educational Resources Information Center

Bondar, Irina Alekseevna; Kulbakova, Renata Ivanovna; Svintorzhitskaja, Irina Andreevna; Pilat, Larisa Pavlovna; Zavrumov, Zaur Aslanovich

2016-01-01

The article explains how to use a project-based method as an effective means of interdisciplinary interaction when teaching a foreign language on the example of The Institute of service, tourism and design (branch) of the North Caucasus Federal University (Pyatigorsk, Stavropol Territory Russia). The article holds the main objectives of the…

Enhancing the Internationalisation of Distance Education in the Biological Sciences: The DUNE Project and Genetic Engineering.

ERIC Educational Resources Information Center

Leach, C. K.; And Others

1997-01-01

Describes the Distance Educational Network of Europe (DUNE) project that aims at enhancing the development of distance education in an international context. Highlights issues relating to the delivery of distance-learning courses in a transnational forum. Describes the genetic engineering course that aims at explaining the core techniques of…

Modeling the determinants of the social impacts of agricultural development projects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmadvand, Mostafa, E-mail: Ahmadvand_2000@yahoo.co; Karami, Ezatollah, E-mail: ekarami@shirazu.ac.i; Iman, Mohammad Taghi, E-mail: Iman@shirazu.ac.i

2011-01-15

In an attempt to help policy-makers improve the social sustainability of development projects, this study identifies the key determinants of farmers' attitudes relating to the social impacts of the floodwater spreading project (FWSP) on the Gareh-Bygone plain in Iran. In order to analyze the links between the various factors that affect the experience of social impact, a theoretical framework was developed. Stratified random sampling was used to survey 138 farm households from the four villages in the region. One male and one female from each house were interviewed face-to-face using a questionnaire, resulting in a total of 276 interviews. Structuralmore » factors were found to be the largest contribution to stakeholders' attitudes relating to the social impacts of the project. Results from a cluster analysis suggested that the level of floodwater information, level of participation, water access, ownership change, and environmental worldview were the most important factors explaining attitude towards social impact of the FWSP.« less

Using cultural-historical activity theory to analyze social service practices evolving from the Norwegian HUSK projects.

PubMed

Foot, Kirsten

2015-01-01

The HUSK projects catalyzed innovation in the practices of providing social services that could yield useful insights both within and outside of Norway if analyzed in these two ways: (a) retrospective analysis of the development of individual HUSK projects in light of their cultural-historical contexts, and (b) comparative analysis of the efforts to advance multi-sector collaboration in some of the HUSK projects. Such analyses require a practice-based research approach that takes into account culture and history. In this article the author explains how cultural-historical activity theory provides such an approach, illustrated via several HUSK cases. The author suggests five questions for future analyses of the HUSK projects and argues that insights gleaned from such analyses could contribute significantly to research on-and the provision of-social services.

Usage of Electric Vehicle Supply Equipment Along the Corridors between the EV Project Major Cities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mindy Kirkpatrick

The report explains how the EVSE are being used along the corridors between the EV Project cities. The EV Project consists of a nationwide collaboration between Idaho National Laboratory (INL), ECOtality North America, Nissan, General Motors, and more than 40 other city, regional and state governments, and electric utilities. The purpose of the EV Project is to demonstrate the deployment and use of approximately 14,000 Level II (208-240V) electric vehicle supply equipment (EVSE) and 300 fast chargers in 16 major cities. This research investigates the usage of all currently installed EV Project commercial EVSE along major interstate corridors. ESRI ArcMapmore » software products are utilized to create geographic EVSE data layers for analysis and visualization of commercial EVSE usage. This research locates the crucial interstate corridors lacking sufficient commercial EVSE and targets locations for future commercial EVSE placement. The results and methods introduced in this research will be used by INL for the duration of the EV Project.« less

The role of ethics in data governance of large neuro-ICT projects.

PubMed

Stahl, Bernd Carsten; Rainey, Stephen; Harris, Emma; Fothergill, B Tyr

2018-05-14

We describe current practices of ethics-related data governance in large neuro-ICT projects, identify gaps in current practice, and put forward recommendations on how to collaborate ethically in complex regulatory and normative contexts. We undertake a survey of published principles of data governance of large neuro-ICT projects. This grounds an approach to a normative analysis of current data governance approaches. Several ethical issues are well covered in the data governance policies of neuro-ICT projects, notably data protection and attribution of work. Projects use a set of similar policies to ensure users behave appropriately. However, many ethical issues are not covered at all. Implementation and enforcement of policies remain vague. The data governance policies we investigated indicate that the neuro-ICT research community is currently close-knit and that shared assumptions are reflected in infrastructural aspects. This explains why many ethical issues are not explicitly included in data governance policies at present. With neuro-ICT research growing in scale, scope, and international involvement, these shared assumptions should be made explicit and reflected in data governance.

The Waves and Tsunamis Project

NASA Astrophysics Data System (ADS)

Lavin, M.; Strohschneider, D.; Maichle, R.; Frashure, K.; Micozzi, N.; Stephen, R. A.

2005-12-01

The goals of the Waves and Tsunamis Project are "to make waves real" to middle school students and to teach them some fundamental concepts of waves. The curriculum was designed in Fall 2004 (before the Sumatra Tsunami) and involves an ocean scientist classroom visit, hands-on demonstrations, and an interactive website designed to explain ocean wave properties. The website is called 'The Plymouth Wave Lab' and it has had more than 40,000 hits since the Sumatra event. One inexpensive and interesting demonstration is based on a string composed of alternating elastic bands and paper clips. Washers can be added to the paper clips to construct strings with varying mass. For example, a tapered string with mass decreasing in the wave propagation direction is an analog of tsunami waves propagating from deep to shallow water. The Waves and Tsunamis Project evolved as a collaborative effort involving an ocean science researcher and middle school science teachers. It was carried out through the direction of the Centers of Ocean Science Education Excellence New England (COSEE-NE) Ocean Science Education Institute (OSEI). COSEE-NE is involved in developing models for sustainable involvement of ocean science researchers in K-12 education ( http://necosee.net ). This work is supported by the National Science Foundation.

Conceptual Foundations of Systems Biology Explaining Complex Cardiac Diseases.

PubMed

Louridas, George E; Lourida, Katerina G

2017-02-21

Systems biology is an important concept that connects molecular biology and genomics with computing science, mathematics and engineering. An endeavor is made in this paper to associate basic conceptual ideas of systems biology with clinical medicine. Complex cardiac diseases are clinical phenotypes generated by integration of genetic, molecular and environmental factors. Basic concepts of systems biology like network construction, modular thinking, biological constraints (downward biological direction) and emergence (upward biological direction) could be applied to clinical medicine. Especially, in the field of cardiology, these concepts can be used to explain complex clinical cardiac phenotypes like chronic heart failure and coronary artery disease. Cardiac diseases are biological complex entities which like other biological phenomena can be explained by a systems biology approach. The above powerful biological tools of systems biology can explain robustness growth and stability during disease process from modulation to phenotype. The purpose of the present review paper is to implement systems biology strategy and incorporate some conceptual issues raised by this approach into the clinical field of complex cardiac diseases. Cardiac disease process and progression can be addressed by the holistic realistic approach of systems biology in order to define in better terms earlier diagnosis and more effective therapy.

Does sexual selection explain human sex differences in aggression?

PubMed

Archer, John

2009-08-01

I argue that the magnitude and nature of sex differences in aggression, their development, causation, and variability, can be better explained by sexual selection than by the alternative biosocial version of social role theory. Thus, sex differences in physical aggression increase with the degree of risk, occur early in life, peak in young adulthood, and are likely to be mediated by greater male impulsiveness, and greater female fear of physical danger. Male variability in physical aggression is consistent with an alternative life history perspective, and context-dependent variability with responses to reproductive competition, although some variability follows the internal and external influences of social roles. Other sex differences, in variance in reproductive output, threat displays, size and strength, maturation rates, and mortality and conception rates, all indicate that male aggression is part of a sexually selected adaptive complex. Physical aggression between partners can be explained using different evolutionary principles, arising from the conflicts of interest between males and females entering a reproductive alliance, combined with variability following differences in societal gender roles. In this case, social roles are particularly important since they enable both the relatively equality in physical aggression between partners from Western nations, and the considerable cross-national variability, to be explained.

Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data.

PubMed

Robinson, Kelly M; Crabtree, Jonathan; Mattick, John S A; Anderson, Kathleen E; Dunning Hotopp, Julie C

2017-01-25

A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome. Through careful consideration of all of the bacterial taxa present in the cancer types investigated, their relative abundance, and batch effects, we were able to identify some read pairs from certain taxa as likely resulting from contamination. In particular, the presence of Mycobacterium tuberculosis complex in the ovarian serous cystadenocarcinoma (OV) and glioblastoma multiforme (GBM) samples was correlated with the sequencing center of the samples. Additionally, there was a correlation between the presence of Ralstonia spp. and two specific plates of acute myeloid leukemia (AML) samples. At the end, associations remained between Pseudomonas-like and Acinetobacter-like read pairs in AML, and Pseudomonas-like read pairs in stomach adenocarcinoma (STAD) that could not be explained through batch effects or systematic contamination as seen in other samples. This approach suggests that it is possible to identify bacteria that may be present in human tumor samples from public genome sequencing data that can be examined further experimentally. More weight should be given to this approach in the future when bacterial associations with diseases are suspected.

EXPLAINING THE ASSOCIATION BETWEEN INCARCERATION AND DIVORCE*

PubMed Central

Siennick, Sonja E.; Stewart, Eric A.; Staff, Jeremy

2014-01-01

Recent studies have suggested that incarceration dramatically increases the odds of divorce, but we know little about the mechanisms that explain the association. This study uses prospective longitudinal data from a subset of married young adults in the National Longitudinal Study of Adolescent Health (N = 1,919) to examine whether incarceration is associated with divorce indirectly via low marital love, economic strain, relationship violence, and extramarital sex. The findings confirmed that incarcerations occurring during, but not before, a marriage were associated with an increased hazard of divorce. Incarcerations occurring during marriage also were associated with less marital love, more relationship violence, more economic strain, and greater odds of extramarital sex. Above-average levels of economic strain were visible among respondents observed preincarceration, but only respondents observed postincarceration showed less marital love, more relationship violence, and higher odds of extramarital sex than did respondents who were not incarcerated during marriage. These relationship problems explained approximately 40 percent of the association between incarceration and marital dissolution. These findings are consistent with theoretical predictions that a spouse’s incarceration alters the rewards and costs of the marriage and the relative attractiveness of alternative partners. PMID:25598544

How to deal with petabytes of data: the LHC Grid project

NASA Astrophysics Data System (ADS)

Britton, D.; Lloyd, S. L.

2014-06-01

We review the Grid computing system developed by the international community to deal with the petabytes of data coming from the Large Hadron Collider at CERN in Geneva with particular emphasis on the ATLAS experiment and the UK Grid project, GridPP. Although these developments were started over a decade ago, this article explains their continued relevance as part of the ‘Big Data’ problem and how the Grid has been forerunner of today's cloud computing.

Explaining the Origins and Expansion of Mass Education.

ERIC Educational Resources Information Center

Boli, John; And Others

1985-01-01

Theories of mass education that emphasize processes of differentiation or the reproduction of inequalities ignore the universal and institutional character of mass education. A theoretical framework emphasizing individualism and the rationalization of individual and collective authority better explains the relationship of mass education to…

Legal Issues of Ambient Intelligence in the SERENITY Project

NASA Astrophysics Data System (ADS)

Krausová, Alžběta; Dumortier, Jos

The successful functionality of the solutions proposed by the SERENITY project will only be achieved when they fit into the existing legal framework. Therefore, when developing software and hardware solutions, developers must respect requirements set out by law. The aim of this chapter is to define legal challenges that arise with the advent of the Ambient Intelligence, and to explain how SERENITY deals with the challenge of legal compliance. To do this, we will first describe how the legal requirements are translated into a machinereadable form in the SERENITY project, and introduce the concept of so called legal patterns. The application of relevant legal principles on data protection will be illustrated using two particular scenarios. We will then focus on practical legal problems related to daily operations of SERENITY technical solutions. Finally, we conclude with an evaluation of the SERENITY approach and its outcomes

Thermally-assisted Magma Emplacement Explains Restless Calderas

NASA Astrophysics Data System (ADS)

Amoruso, A.; Crescentini, L.; D'Antonio, M.; Acocella, V.

2017-12-01

Many calderas show repeated unrest over centuries. Though probably induced by magma, this unique behaviour is not understood and its dynamics remains elusive. To better understand these restless calderas, we interpret deformation data and build thermal models of Campi Flegrei, Italy, which is the best-known, yet most dangerous calderas, lying to the west of Naples and restless since the 1950s at least.Our elaboration of the geodetic data indicates that the inflation and deflation of magmatic sources at the same location explain most deformation, at least since the build-up of the last 1538 AD eruption. However, such a repeated magma emplacement requires a persistently hot crust.Our thermal models show that the repeated emplacement was assisted by the thermal anomaly created by magma that was intruded at shallow depth 3 ka before the last eruption and, in turn, contributed to maintain the thermal anomaly itself. This may explain the persistence of the magmatic sources promoting the restless behaviour of the Campi Flegrei caldera; moreover, it explains the crystallization, re-melting and mixing among compositionally distinct magmas recorded in young volcanic rocks.Available information at other calderas highlights similarities to Campi Flegrei, in the pattern and cause of unrest. All monitored restless calderas have either geodetically (Yellowstone, Aira Iwo-Jima, Askja, Fernandina and, partly, Long Valley) or geophysically (Rabaul, Okmok) detected sill-like intrusions inducing repeated unrest. Some calderas (Yellowstone, Long Valley) also show stable deformation pattern, where inflation insists on and mimics the resurgence uplift. The common existence of sill-like sources, also responsible for stable deformation patterns, in restless calderas suggests close similarities to Campi Flegrei. This suggests a wider applicability of our model of thermally-assisted sill emplacement, to be tested by future studies to better understand not only the dynamics of restless

The Effect of Self-Explaining on Robust Learning

ERIC Educational Resources Information Center

Hausmann, Robert G. M.; VanLehn, Kurt

2010-01-01

Self-explaining is a domain-independent learning strategy that generally leads to a robust understanding of the domain material. However, there are two potential explanations for its effectiveness. First, self-explanation generates additional "content" that does not exist in the instructional materials. Second, when compared to…

The Role of Secondary Education in Explaining Competitiveness

ERIC Educational Resources Information Center

Baumann, Chris; Winzar, Hume

2016-01-01

The literature establishes that education drives economic performance, but the extent that education is associated with a country's competitiveness is empirically untested. Our study analyses Programme for International Student Assessment (PISA) data from 63 countries to ascertain education's role in explaining the competitiveness of a country.…

Accurate Projection Methods for the Incompressible Navier–Stokes Equations

DOE PAGES

Brown, David L.; Cortez, Ricardo; Minion, Michael L.

2001-04-10

This paper considers the accuracy of projection method approximations to the initial–boundary-value problem for the incompressible Navier–Stokes equations. The issue of how to correctly specify numerical boundary conditions for these methods has been outstanding since the birth of the second-order methodology a decade and a half ago. It has been observed that while the velocity can be reliably computed to second-order accuracy in time and space, the pressure is typically only first-order accurate in the L ∞-norm. Here, we identify the source of this problem in the interplay of the global pressure-update formula with the numerical boundary conditions and presentsmore » an improved projection algorithm which is fully second-order accurate, as demonstrated by a normal mode analysis and numerical experiments. In addition, a numerical method based on a gauge variable formulation of the incompressible Navier–Stokes equations, which provides another option for obtaining fully second-order convergence in both velocity and pressure, is discussed. The connection between the boundary conditions for projection methods and the gauge method is explained in detail.« less

Analysis of single nucleotide variants of HFE gene and association to survival in The Cancer Genome Atlas GBM data

PubMed Central

Zhang, Bo; Liu, Dajiang J.; Muscat, Joshua E.; Langan, Sara T.; Connor, James R.

2017-01-01

Human hemochromatosis protein (HFE) is involved in iron metabolism. Two major HFE polymorphisms, H63D and C282Y, have been associated with an increased risk of cancers. Previously, we reported decreased gender effects in overall survival based on H63D or C282Y HFE polymorphisms patients with glioblastoma multiforme (GBM). However, the effect of other single nucleotide variation (SNV) in the HFE gene on the cancer development and progression has not been systematically studied. To expand our finding in a larger sample, and to identify other HFE SNV, we analyzed the frequency of somatic SNV in HFE gene and its relationship to survival in GBM patients using The Cancer Genome Atlas (TCGA) GBM (Caucasian only) database. We found 9 SNVs with increased frequency in blood normal of TCGA GBM patients compared to the 1000Genome. Among 9 SNVs, 7 SNVs were located in the intron and 2 SNVs (i.e., H63D, C282Y) in the exon of HFE gene. The statistical analysis demonstrated that blood normal samples of TCGA GBM have more H63D (p = 0.0002, 95% Confidence interval (CI): 0.2119–0.3223) or C282Y (p = 0.0129, 95% CI: 0.0474–0.1159) HFE polymorphisms than 1000Genome. The Kaplan-Meier survival curve for the 264 GBM samples revealed no difference between wild type (WT) HFE and H63D, and WT HFE and C282Y GBM patients. In addition, there was no difference in the survival of male/female GBM patients based on HFE genotype. There was no correlation between HFE expression and survival. In conclusion, the current results suggest that somatic HFE polymorphisms do not impact GBM patients’ survival in the TCGA data set of GBM. PMID:28358914

Analysis of single nucleotide variants of HFE gene and association to survival in The Cancer Genome Atlas GBM data.

PubMed

Lee, Sang Y; Zhu, Junjia; Salzberg, Anna C; Zhang, Bo; Liu, Dajiang J; Muscat, Joshua E; Langan, Sara T; Connor, James R

2017-01-01

Human hemochromatosis protein (HFE) is involved in iron metabolism. Two major HFE polymorphisms, H63D and C282Y, have been associated with an increased risk of cancers. Previously, we reported decreased gender effects in overall survival based on H63D or C282Y HFE polymorphisms patients with glioblastoma multiforme (GBM). However, the effect of other single nucleotide variation (SNV) in the HFE gene on the cancer development and progression has not been systematically studied. To expand our finding in a larger sample, and to identify other HFE SNV, we analyzed the frequency of somatic SNV in HFE gene and its relationship to survival in GBM patients using The Cancer Genome Atlas (TCGA) GBM (Caucasian only) database. We found 9 SNVs with increased frequency in blood normal of TCGA GBM patients compared to the 1000Genome. Among 9 SNVs, 7 SNVs were located in the intron and 2 SNVs (i.e., H63D, C282Y) in the exon of HFE gene. The statistical analysis demonstrated that blood normal samples of TCGA GBM have more H63D (p = 0.0002, 95% Confidence interval (CI): 0.2119-0.3223) or C282Y (p = 0.0129, 95% CI: 0.0474-0.1159) HFE polymorphisms than 1000Genome. The Kaplan-Meier survival curve for the 264 GBM samples revealed no difference between wild type (WT) HFE and H63D, and WT HFE and C282Y GBM patients. In addition, there was no difference in the survival of male/female GBM patients based on HFE genotype. There was no correlation between HFE expression and survival. In conclusion, the current results suggest that somatic HFE polymorphisms do not impact GBM patients' survival in the TCGA data set of GBM.

FGFR3, as a receptor tyrosine kinase, is associated with differentiated biological functions and improved survival of glioma patients

PubMed Central

Wang, Zheng; Zhang, Chuanbao; Sun, Lihua; Liang, Jingshan; Liu, Xing; Li, Guanzhang; Yao, Kun; Zhang, Wei; Jiang, Tao

2016-01-01

Background Activation of receptor tyrosine kinases is common in Malignancies. FGFR3 fusion with TACC3 has been reported to have transforming effects in primary glioblastoma and display oncogenic activity in vitro and in vivo. We set out to investigate the role of FGFR3 in glioma through transcriptomic analysis. Results FGFR3 increased in Classical subtype and Neural subtype consistently in CGGA and TCGA cohort. Similar patterns of FGFR3 distribution through subtypes were observed in CGGA and TCGA samples. Gene ontology analysis was performed with genes that were significantly correlated with FGFR3 expression. We found that positively associated biological processes of FGFR3 were focused on differentiated cellular functions and neuronal activities, while negatively correlated biological processes focused on mitosis and cell cycle phase. Clinical investigation showed that higher FGFR3 expression predicted improved survival for glioma patients, especially in Proneural subtype. Moreover, FGFR3 showed very limited relevance with other receptor tyrosine kinases in glioma at transcriptome level. Materials and Methods FGFR3 expression data of glioma was obtained from Chinese Glioma Genome Atlas (CGGA) and TCGA (The Cancer Genome Atlas). In total, RNA sequencing data of 325 glioma samples and mRNA microarray data of 301 samples from CGGA dataset were enrolled into this study. To consolidate the findings that we have revealed in CGGA dataset, RNA-seq data of 672 glioma samples from TCGA dataset were used as a validation cohort. R language was used as the main tool to perform statistical analysis and graphical work. Conclusions FGFR3 expression increased in classical and neural subtypes and was associated with differentiated cellular functions. FGFR3 showed very limited correlation with other common receptor tyrosine kinases, and predicted improved survival for glioma patients. PMID:27829236

Transcriptional diversity of long-term glioblastoma survivors.

PubMed

Gerber, Naamit K; Goenka, Anuj; Turcan, Sevin; Reyngold, Marsha; Makarov, Vladimir; Kannan, Kasthuri; Beal, Kathryn; Omuro, Antonio; Yamada, Yoshiya; Gutin, Phillip; Brennan, Cameron W; Huse, Jason T; Chan, Timothy A

2014-09-01

Glioblastoma (GBM) is a highly aggressive type of glioma with poor prognosis. However, a small number of patients live much longer than the median survival. A better understanding of these long-term survivors (LTSs) may provide important insight into the biology of GBM. We identified 7 patients with GBM, treated at Memorial Sloan-Kettering Cancer Center (MSKCC), with survival >48 months. We characterized the transcriptome of each patient and determined rates of MGMT promoter methylation and IDH1 and IDH2 mutational status. We identified LTSs in 2 independent cohorts (The Cancer Genome Atlas [TCGA] and NCI Repository for Molecular Brain Neoplasia Data [REMBRANDT]) and analyzed the transcriptomal characteristics of these LTSs. The median overall survival of our cohort was 62.5 months. LTSs were distributed between the proneural (n = 2), neural (n = 2), classical (n = 2), and mesenchymal (n = 1) subtypes. Similarly, LTS in the TCGA and REMBRANDT cohorts demonstrated diverse transcriptomal subclassification identities. The majority of the MSKCC LTSs (71%) were found to have methylation of the MGMT promoter. None of the patients had an IDH1 or IDH2 mutation, and IDH mutation occurred in a minority of the TCGA LTSs as well. A set of 60 genes was found to be differentially expressed in the MSKCC and TCGA LTSs. While IDH mutant proneural tumors impart a better prognosis in the short-term, survival beyond 4 years does not require IDH mutation and is not dictated by a single transcriptional subclass. In contrast, MGMT methylation continues to have strong prognostic value for survival beyond 4 years. These findings have substantial impact for understanding GBM biology and progression. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

[Bioinformatics on vascular invasion markers in hepatocellular carcinoma via Big-Data analysis].

PubMed

Chen, Q; Qiu, X Q

2017-04-10

Objective: To investigate the biomarkers in hepatocellular carcinoma and their prognostic value via GEO (Gene Expression Omnibus) and TCGA (The Cancer Genome Atlas) database. Methods: Datasets of hepatocellular carcinoma were downloaded from GEO (GSE67140) and TCGA. MicroRNA in SNU423, SNU449, HepG2, Hep3B, SNU398 cell lines which had low or high invasion capabilities were investigated and verified, in 81 patients with and 91 without vascular invasion hepatocellular carcinoma. The prognostic value of these microRNAs were studied via TCGA database,obtained from 362 patients with hepatocellular carcinoma, through Kaplan-Meier and Multivariate Cox proportional hazard analysis. Target genes were analyzed by GO and KEGG. Results: Expressions of hsa-mir-1180, hsa-mir-149, hsa-mir-744 and hsa-mir-940 were all up regulated in high invasion capable cell lines (SNU423, SNU449) and vascular invasion patients with hepatocellular carcinoma (logFC>1, P <0.05). Results from the Survival analysis showed that hsa-mir-1180 ( HR =1.623, 95 % CI : 1.114-2.365, P =0.012), hsa-mir-149 ( HR =2.400, 95 % CI : 1.639-3.514) and hsa-mir-940 ( HR =1.704, 95 %CI : 1.188-2.443, P =0.004) were independent risk factors on the prognosis of patients with hepatocellular carcinoma ( P <0.05). The mechanism might be related to factors as immune response, focal adhesion and adherence junction signaling pathways. Conclusion: With TCGA and GEO data mining, we found that hsa-mir-1180, hsa-mir-149, hsa-mir-744 and hsa-mir-940 were all highly related to the prognosis of hepatocellular carcinoma, that enabled it to be used to further study the biomarkers related to the prognosis of hepatocellular carcinoma.

FGFR3, as a receptor tyrosine kinase, is associated with differentiated biological functions and improved survival of glioma patients.

PubMed

Wang, Zheng; Zhang, Chuanbao; Sun, Lihua; Liang, Jingshan; Liu, Xing; Li, Guanzhang; Yao, Kun; Zhang, Wei; Jiang, Tao

2016-12-20

Activation of receptor tyrosine kinases is common in Malignancies. FGFR3 fusion with TACC3 has been reported to have transforming effects in primary glioblastoma and display oncogenic activity in vitro and in vivo. We set out to investigate the role of FGFR3 in glioma through transcriptomic analysis. FGFR3 increased in Classical subtype and Neural subtype consistently in CGGA and TCGA cohort. Similar patterns of FGFR3 distribution through subtypes were observed in CGGA and TCGA samples. Gene ontology analysis was performed with genes that were significantly correlated with FGFR3 expression. We found that positively associated biological processes of FGFR3 were focused on differentiated cellular functions and neuronal activities, while negatively correlated biological processes focused on mitosis and cell cycle phase. Clinical investigation showed that higher FGFR3 expression predicted improved survival for glioma patients, especially in Proneural subtype. Moreover, FGFR3 showed very limited relevance with other receptor tyrosine kinases in glioma at transcriptome level. FGFR3 expression data of glioma was obtained from Chinese Glioma Genome Atlas (CGGA) and TCGA (The Cancer Genome Atlas). In total, RNA sequencing data of 325 glioma samples and mRNA microarray data of 301 samples from CGGA dataset were enrolled into this study. To consolidate the findings that we have revealed in CGGA dataset, RNA-seq data of 672 glioma samples from TCGA dataset were used as a validation cohort. R language was used as the main tool to perform statistical analysis and graphical work. FGFR3 expression increased in classical and neural subtypes and was associated with differentiated cellular functions. FGFR3 showed very limited correlation with other common receptor tyrosine kinases, and predicted improved survival for glioma patients.

Tuned Normalization Explains the Size of Attention Modulations

PubMed Central

Ni, Amy M.; Ray, Supratim; Maunsell, John H. R.

2012-01-01

SUMMARY The effect of attention on firing rates varies considerably within a single cortical area. The firing rate of some neurons is greatly modulated by attention while others are hardly affected. The reason for this variability across neurons is unknown. We found that the variability in attention modulation across neurons in area MT of macaques can be well explained by variability in the strength of tuned normalization across neurons. The presence of tuned normalization also explains a striking asymmetry in attention effects within neurons: when two stimuli are in a neuron’s receptive field, directing attention to the preferred stimulus modulates firing rates more than directing attention to the non-preferred stimulus. These findings show that much of the neuron-to-neuron variability in modulation of responses by attention depends on variability in the way the neurons process multiple stimuli, rather than differences in the influence of top-down signals related to attention. PMID:22365552

Functional traits explain ecosystem function through opposing mechanisms.

PubMed

Cadotte, Marc W

2017-08-01

The ability to explain why multispecies assemblages produce greater biomass compared to monocultures, has been a central goal in the quest to understand biodiversity effects on ecosystem function. Species contributions to ecosystem function can be driven by two processes: niche complementarity and a selection effect that is influenced by fitness (competitive) differences, and both can be approximated with measures of species' traits. It has been hypothesised that fitness differences are associated with few, singular traits while complementarity requires multidimensional trait measures. Here, using experimental data from plant assemblages, I show that the selection effect was strongest when trait dissimilarity was low, while complementarity was greatest with high trait dissimilarity. Selection effects were best explained by a single trait, plant height. Complementarity was correlated with dissimilarity across multiple traits, representing above and below ground processes. By identifying the relevant traits linked to ecosystem function, we obtain the ability to predict combinations of species that will maximise ecosystem function. © 2017 John Wiley & Sons Ltd/CNRS.

[Pay for performance explained by transaction costs theory].

PubMed

Gorbaneff, Yuri; Cortes, Ariel; Torres, Sergio; Yepes, Francisco

2011-01-01

To evaluate the ability of transaction costs theory to explain incentives in the health care chain. We performed a case study of CPS, a health insurance company in Bogota (Colombia), which preferred not to publish its name. CPS moves in the environment of high transaction costs and uses the hybrid form of governance at the outpatient level. Incentive intensity, administrative control and the contract all agree with the theory. At the hospital level, the market is used, despite greater uncertainty. Because of the discrete form (1.0) of the incentives and the absence of administrative control, it is difficult for CPS to relate payment to hospital performance. Transaction costs theory explains the configuration of incentives. Another contribution made by this theory to the literature is the criterion to differentiate between the market and the hybrid. We propose that the market uses discrete-type (1.0) incentives, while the hybrid uses continuous, commission-like incentives. Copyright © 2011 SESPAS. Published by Elsevier Espana. All rights reserved.

Tuned normalization explains the size of attention modulations.

PubMed

Ni, Amy M; Ray, Supratim; Maunsell, John H R

2012-02-23

The effect of attention on firing rates varies considerably within a single cortical area. The firing rate of some neurons is greatly modulated by attention while others are hardly affected. The reason for this variability across neurons is unknown. We found that the variability in attention modulation across neurons in area MT of macaques can be well explained by variability in the strength of tuned normalization across neurons. The presence of tuned normalization also explains a striking asymmetry in attention effects within neurons: when two stimuli are in a neuron's receptive field, directing attention to the preferred stimulus modulates firing rates more than directing attention to the nonpreferred stimulus. These findings show that much of the neuron-to-neuron variability in modulation of responses by attention depends on variability in the way the neurons process multiple stimuli, rather than differences in the influence of top-down signals related to attention. Copyright © 2012 Elsevier Inc. All rights reserved.

Content-Free Computer Supports for Self-Explaining: Modifiable Typing Interface and Prompting

ERIC Educational Resources Information Center

Chou, Chih-Yueh; Liang, Hung-Ta

2009-01-01

Self-explaining, which asks students to generate explanations while reading a text, is a self-constructive activity and is helpful for students' learning. Studies have revealed that prompts by a human tutor promote students' self-explanations. However, most studies on self-explaining focus on spoken self-explanations. This study investigates the…

On the explaining-away phenomenon in multivariate latent variable models.

PubMed

van Rijn, Peter; Rijmen, Frank

2015-02-01

Many probabilistic models for psychological and educational measurements contain latent variables. Well-known examples are factor analysis, item response theory, and latent class model families. We discuss what is referred to as the 'explaining-away' phenomenon in the context of such latent variable models. This phenomenon can occur when multiple latent variables are related to the same observed variable, and can elicit seemingly counterintuitive conditional dependencies between latent variables given observed variables. We illustrate the implications of explaining away for a number of well-known latent variable models by using both theoretical and real data examples. © 2014 The British Psychological Society.

Explaining formation of Astronomical Jets using Dynamic Universe Model

NASA Astrophysics Data System (ADS)

Naga Parameswara Gupta, Satyavarapu

2016-07-01

Astronomical jets are observed from the centres of many Galaxies including our own Milkyway. The formation of such jet is explained using SITA simulations of Dynamic Universe Model. For this purpose the path traced by a test neutron is calculated and depicted using a set up of one densemass of the mass equivalent to mass of Galaxy center, 90 stars with similar masses of stars near Galaxy center, mass equivalents of 23 Globular Cluster groups, 16 Milkyway parts, Andromeda and Triangulum Galaxies at appropriate distances. Five different kinds of theoretical simulations gave positive results The path travelled by this test neutron was found to be an astronomical jet emerging from Galaxy center. This is another result from Dynamic Universe Model. It solves new problems like a. Variable Mass Rocket Trajectory Problem b. Explaining Very long baseline interferometry (VLBI) observations c. Astronomical jets observed from Milkyway Center d. Prediction of Blue shifted Galaxies e. Explaining Pioneer Anomaly f. Prediction of New Horizons satellite trajectory etc. Dynamic Universe Model never reduces to General relativity on any condition. It uses a different type of mathematics based on Newtonian physics. This mathematics used here is simple and straightforward. As there are no differential equations present in Dynamic Universe Model, the set of equations give single solution in x y z Cartesian coordinates for every point mass for every time step

Uncertainty in Arctic climate projections traced to variability of downwelling longwave radiation

NASA Astrophysics Data System (ADS)

Krikken, Folmer; Bintanja, Richard; Hazeleger, WIlco; van Heerwaarden, Chiel

2017-04-01

The Arctic region has warmed rapidly over the last decades, and this warming is projected to increase. The uncertainty in these projections, i.e. intermodel spread, is however very large and a clear understanding of the sources behind the spread is so far still lacking. Here we use 31 state-of-the-art global climate models to show that variability of May downwelling radiation (DLR) in the models' control climate, primarily located at the land surrounding the Arctic ocean, explains 2/3 of the intermodel spread in projected Arctic warming under the RPC85 scenario. This variability is related to the combined radiative effect of the cloud radiative forcing (CRF) and the albedo response due to snowfall, which varies strongly between the models in these regions. This mechanism dampens or enhances yearly variability of DLR in the control climate but also dampens or enhances the climate response of DLR, sea ice cover and near surface temperature.

Using Physical Models to Explain a Division Algorithm.

ERIC Educational Resources Information Center

Vest, Floyd

1985-01-01

Develops a division algorithm in terms of familiar manipulations of concrete objects and presents it with a series of questions for diagnosis of students' understanding of the algorithm in terms of the concrete model utilized. Also offers general guidelines for using concrete illustrations to explain algorithms and other mathematical principles.…

Explaining the Socio-Economic Status School Completion Gap

ERIC Educational Resources Information Center

Polidano, Cain; Hanel, Barbara; Buddelmeyer, Hielke

2013-01-01

Relatively low rates of school completion among students from low socio-economic backgrounds is a key driver of intergenerational inequality. Linking data from the Programme for International Student Assessment with data from the Longitudinal Survey of Australian Youth, we use a decomposition framework to explain the gap in school completion rates…

Cases and Controversy: Guide to Teaching the Public Issues Series/Harvard Social Studies Project, and Supplement.

ERIC Educational Resources Information Center

Oliver, Donald W.; Newmann, Fred M.

This general guide presents an overview and explains the rationale of the teaching approach of the "Public Issues Series," units produced by the Harvard Social Studies Project to help students in grades 9-19 analyze and discuss human dilemmas related to public issues. (A detailed report on the nature, development, and evaluation of the Harvard…

Explaining the harmonic sequence paradox.

PubMed

Schmidt, Ulrich; Zimper, Alexander

2012-05-01

According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced. ©2011 The British Psychological Society.

Higher-order Traits and Happiness in the Workplace: The Importance of Occupational Project Scale for the Evaluation of Characteristic Adaptations.

PubMed

Buruk, Pelin; Şimşek, Ömer Faruk; Kocayörük, Ercan

2017-01-01

This study attempts to explain the relationship between job satisfaction and the Big Two, Stability and Plasticity, which are the higher-order traits of Big Five. Occupational Project, a narrative construct, was considered a mediator variable in this relationship. Occupational Project consists of affective and cognitive evaluations of an individual's work life as a project in terms of the completed (past), the ongoing (present) and the prospective (future) parts. The survey method was applied to a sample of 253 participants. The results supported the proposed model, in which Occupational Project mediated the relationship between the Big Two and both job satisfaction and affect in workplace. Discussion is focused on applying Occupational Project as a practical tool for management. Consideration of an employee's Occupational Project could provide management with a means to question, understand, intervene with and redefine the narrative quality of his/her occupational project that influences job satisfaction.

Deep Supervised, but Not Unsupervised, Models May Explain IT Cortical Representation

PubMed Central

Khaligh-Razavi, Seyed-Mahdi; Kriegeskorte, Nikolaus

2014-01-01

Inferior temporal (IT) cortex in human and nonhuman primates serves visual object recognition. Computational object-vision models, although continually improving, do not yet reach human performance. It is unclear to what extent the internal representations of computational models can explain the IT representation. Here we investigate a wide range of computational model representations (37 in total), testing their categorization performance and their ability to account for the IT representational geometry. The models include well-known neuroscientific object-recognition models (e.g. HMAX, VisNet) along with several models from computer vision (e.g. SIFT, GIST, self-similarity features, and a deep convolutional neural network). We compared the representational dissimilarity matrices (RDMs) of the model representations with the RDMs obtained from human IT (measured with fMRI) and monkey IT (measured with cell recording) for the same set of stimuli (not used in training the models). Better performing models were more similar to IT in that they showed greater clustering of representational patterns by category. In addition, better performing models also more strongly resembled IT in terms of their within-category representational dissimilarities. Representational geometries were significantly correlated between IT and many of the models. However, the categorical clustering observed in IT was largely unexplained by the unsupervised models. The deep convolutional network, which was trained by supervision with over a million category-labeled images, reached the highest categorization performance and also best explained IT, although it did not fully explain the IT data. Combining the features of this model with appropriate weights and adding linear combinations that maximize the margin between animate and inanimate objects and between faces and other objects yielded a representation that fully explained our IT data. Overall, our results suggest that explaining IT requires

Explainers' development of science-learner identities through participation in a community of practice

NASA Astrophysics Data System (ADS)

Richardson, Anne E.

The urgent environmental issues of today require science-literate adults to engage in business and political decisions to create solutions. Despite the need, few adults have the knowledge and skills of science literacy. This doctoral dissertation is an analytical case study examining the science-learner identity development of Exploratorium Field Trip Explainers. Located in San Francisco, CA, the Exploratorium is a museum of science, art, and human perception dedicated to nurturing curiosity and exploration. Data collected included semi-structured interviews with sixteen former Field Trip Explainers, participant observation of the current Field Trip Explainer Program, and review of relevant documentation. Data analysis employed constant comparative analysis, guided by the communities of practice theoretical framework (Wenger, 1998) and the National Research Council's (2009) Six Strands of Science Learning. Findings of this research indicate that Exploratorium Field Trip Explainers participate in a community of practice made up of a diverse group of people that values curiosity and openness to multiple ways of learning. Many participants entered the Field Trip Explainer Program with an understanding of science learning as a rigid process reserved for a select group of people; through participation in the Field Trip Explainer community of practice, participants developed an understanding of science learning as accessible and a part of everyday life. The findings of this case study have implications for research, theory, and practice in informal adult science learning, access of non-dominant groups to science learning, and adult workplace learning in communities of practice.

Direct Retrieval of Exterior Orientation Parameters Using A 2-D Projective Transformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seedahmed, Gamal H.

2006-09-01

Direct solutions are very attractive because they obviate the need for initial approximations associated with non-linear solutions. The Direct Linear Transformation (DLT) establishes itself as a method of choice for direct solutions in photogrammetry and other fields. The use of the DLT with coplanar object space points leads to a rank deficient model. This rank deficient model leaves the DLT defined up to a 2-D projective transformation, which makes the direct retrieval of the exterior orientation parameters (EOPs) a non-trivial task. This paper presents a novel direct algorithm to retrieve the EOPs from the 2-D projective transformation. It is basedmore » on a direct relationship between the 2-D projective transformation and the collinearity model using homogeneous coordinates representation. This representation offers a direct matrix correspondence between the 2-D projective transformation parameters and the collinearity model parameters. This correspondence lends itself to a direct matrix factorization to retrieve the EOPs. An important step in the proposed algorithm is a normalization process that provides the actual link between the 2-D projective transformation and the collinearity model. This paper explains the theoretical basis of the proposed algorithm as well as the necessary steps for its practical implementation. In addition, numerical examples are provided to demonstrate its validity.« less

Pre-service primary school teachers’ abilities in explaining water and air pollution scientifically

NASA Astrophysics Data System (ADS)

Lukmannudin; Sopandi, W.; Sujana, A.; Sukardi, R.

2018-05-01

The purpose of this study is to determine the ability of pre-service primary school teachers (PSPST) in explaining the phenomenon of water and air pollution scientifically. The research method used descriptive method of analysis with qualitative approach. The respondents were PSPTP at 4th semester. This study used a four-tier instrument diagnostic test. The number of subjects was 84 PSPTP at Universitas Pendidikan Indonesia, Kampus Daerah Sumedang. The results demonstrate the ability of PSPST in explaining water and air pollution scientifically. The results show that only 6% of PSPST who are able to explain the phenomenon of water pollution and only 4% of PSPST who are able to explain the phenomenon of air pollution. The fact should be attention for PSPST because these understanding are crucial in the process of learning activities in the classroom.

Why Compositional Convection Cannot Explain Substellar Objects’ Sharp Spectral-type Transitions

NASA Astrophysics Data System (ADS)

Leconte, Jérémy

2018-02-01

As brown dwarfs and young giant planets cool down, they are known to experience various chemical transitions—for example, from {CO} rich L-dwarfs to methane rich T-dwarfs. Those chemical transitions are accompanied by spectral transitions with sharpness that cannot be explained by chemistry alone. In a series of articles, Tremblin et al. proposed that some of the yet-unexplained features associated with these transitions could be explained by a reduction of the thermal gradient near the photosphere. To explain, in turn, this more isothermal profile, they invoke the presence of an instability analogous to fingering convection—compositional convection—triggered by the change in mean molecular weight of the gas due to the chemical transitions mentioned above. In this Letter, we use existing arguments to demonstrate that any turbulent transport, if present, would in fact increase the thermal gradient. This misinterpretation comes from the fact that turbulence mixes/homogenizes entropy (potential temperature) instead of temperature. So, while increasing transport, turbulence in an initially stratified atmosphere actually carries energy downward, whether it is due to fingering or any other type of compositional convection. These processes therefore cannot explain the features observed along the aforementioned transitions by reducing the thermal gradient in the atmosphere of substellar objects. Understanding the microphysical and dynamical properties of clouds at these transitions thus probably remains our best way forward.

Predator mimicry, not conspicuousness, explains the efficacy of butterfly eyespots

PubMed Central

De Bona, Sebastiano; Valkonen, Janne K.; López-Sepulcre, Andrés; Mappes, Johanna

2015-01-01

Large conspicuous eyespots on butterfly wings have been shown to deter predators. This has been traditionally explained by mimicry of vertebrate eyes, but recently the classic eye-mimicry hypothesis has been challenged. It is proposed that the conspicuousness of the eyespot, not mimicry, is what causes aversion due to sensory biases, neophobia or sensory overloads. We conducted an experiment to directly test whether the eye-mimicry or the conspicuousness hypothesis better explain eyespot efficacy. We used great tits (Parus major) as model predator, and tested their reaction towards animated images on a computer display. Birds were tested against images of butterflies without eyespots, with natural-looking eyespots, and manipulated spots with the same contrast but reduced resemblance to an eye, as well as images of predators (owls) with and without eyes. We found that mimetic eyespots were as effective as true eyes of owls and more efficient in eliciting an aversive response than modified, less mimetic but equally contrasting eyespots. We conclude that the eye-mimicry hypothesis explains our results better than the conspicuousness hypothesis and is thus likely to be an important mechanism behind the evolution of butterfly eyespots. PMID:25854889

Openings between Defective Endothelial Cells Explain Tumor Vessel Leakiness

PubMed Central

Hashizume, Hiroya; Baluk, Peter; Morikawa, Shunichi; McLean, John W.; Thurston, Gavin; Roberge, Sylvie; Jain, Rakesh K.; McDonald, Donald M.

2000-01-01

Leakiness of blood vessels in tumors may contribute to disease progression and is key to certain forms of cancer therapy, but the structural basis of the leakiness is unclear. We sought to determine whether endothelial gaps or transcellular holes, similar to those found in leaky vessels in inflammation, could explain the leakiness of tumor vessels. Blood vessels in MCa-IV mouse mammary carcinomas, which are known to be unusually leaky (functional pore size 1.2–2 μm), were compared to vessels in three less leaky tumors and normal mammary glands. Vessels were identified by their binding of intravascularly injected fluorescent cationic liposomes and Lycopersicon esculentum lectin and by CD31 (PECAM) immunoreactivity. The luminal surface of vessels in all four tumors had a defective endothelial monolayer as revealed by scanning electron microscopy. In MCa-IV tumors, 14% of the vessel surface was lined by poorly connected, overlapping cells. The most superficial lining cells, like endothelial cells, had CD31 immunoreactivity and fenestrae with diaphragms, but they had a branched phenotype with cytoplasmic projections as long as 50 μm. Some branched cells were separated by intercellular openings (mean diameter 1.7 μm; range, 0.3–4.7 μm). Transcellular holes (mean diameter 0.6 μm) were also present but were only 8% as numerous as intercellular openings. Some CD31-positive cells protruded into the vessel lumen; others sprouted into perivascular tumor tissue. Tumors in RIP-Tag2 mice had, in addition, tumor cell-lined lakes of extravasated erythrocytes. We conclude that some tumor vessels have a defective cellular lining composed of disorganized, loosely connected, branched, overlapping or sprouting endothelial cells. Openings between these cells contribute to tumor vessel leakiness and may permit access of macromolecular therapeutic agents to tumor cells. PMID:10751361

Explaining the motherhood wage penalty during the early occupational career.

PubMed

Staff, Jeremy; Mortimer, Jeylan T

2012-02-01

Prior research shows that mothers earn lower hourly wages than women without children, and that this maternal wage penalty cannot be fully explained by differences between mothers and other women in work experience and job characteristics. This research examines whether the residual motherhood wage penalty results from differences between mothers and other women in the accumulation of work interruptions and breaks in schooling. Using longitudinal data for 486 women followed from ages 19 to 31 in the Minnesota Youth Development Study, we find that accumulated months not in the labor force and not enrolled in school explain the residual pay gap between mothers and other women.

EXPLAINING THE MOTHERHOOD WAGE PENALTY DURING THE EARLY OCCUPATIONAL CAREER

PubMed Central

STAFF, JEREMY; MORTIMER, JEYLAN T.

2011-01-01

Prior research shows that mothers earn lower hourly wages than women without children, and that this maternal wage penalty cannot be fully explained by differences between mothers and other women in work experience and job characteristics. This research examines whether the residual motherhood wage penalty results from differences between mothers and other women in the accumulation of work interruptions and breaks in schooling. Using longitudinal data for 486 women followed from ages 19 to 31 in the Youth Development Study, we find that accumulated months not in the labor force and not enrolled in school explain the residual pay gap between mothers and other women. PMID:22037996

One project`s waste is another project`s resource

DOE Office of Scientific and Technical Information (OSTI.GOV)

Short, J.

1997-02-01

The author describes the efforts being made toward pollution prevention within the DOE complex, as a way to reduce overall project costs, in addition to decreasing the amount of waste to be handled. Pollution prevention is a concept which is trying to be ingrained into project planning. Part of the program involves the concept that ultimately the responsibility for waste comes back to the generator. Parts of the program involve efforts to reuse materials and equipment on new projects, to recycle wastes to generate offsetting revenue, and to increase awareness, accountability and incentives so as to stimulate action on thismore » plan. Summaries of examples are presented in tables.« less

Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation

PubMed Central

Xu, Yaomin; Guo, Xingyi; Sun, Jiayang; Zhao, Zhongming

2015-01-01

Motivation: Large-scale cancer genomic studies, such as The Cancer Genome Atlas (TCGA), have profiled multidimensional genomic data, including mutation and expression profiles on a variety of cancer cell types, to uncover the molecular mechanism of cancerogenesis. More than a hundred driver mutations have been characterized that confer the advantage of cell growth. However, how driver mutations regulate the transcriptome to affect cellular functions remains largely unexplored. Differential analysis of gene expression relative to a driver mutation on patient samples could provide us with new insights in understanding driver mutation dysregulation in tumor genome and developing personalized treatment strategies. Results: Here, we introduce the Snowball approach as a highly sensitive statistical analysis method to identify transcriptional signatures that are affected by a recurrent driver mutation. Snowball utilizes a resampling-based approach and combines a distance-based regression framework to assign a robust ranking index of genes based on their aggregated association with the presence of the mutation, and further selects the top significant genes for downstream data analyses or experiments. In our application of the Snowball approach to both synthesized and TCGA data, we demonstrated that it outperforms the standard methods and provides more accurate inferences to the functional effects and transcriptional dysregulation of driver mutations. Availability and implementation: R package and source code are available from CRAN at http://cran.r-project.org/web/packages/DESnowball, and also available at http://bioinfo.mc.vanderbilt.edu/DESnowball/. Contact: zhongming.zhao@vanderbilt.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25192743

Knowledge Growth of Mathematics Teachers during Professional Activity Based on the Task of Lesson Explaining

ERIC Educational Resources Information Center

Peng, Aihui

2007-01-01

"Lesson explaining" has been developed in China from an evaluative resource to an effective form of teacher professional development with the value of emphasizing teacher reflective practice. This paper begins with a general description of lesson explaining. Then an example of "explaining" a mathematics lesson for teaching…

How to explain Si isotopes of chert?

NASA Astrophysics Data System (ADS)

Liu, Y.

2016-12-01

The variations of d30Si values in diagenetic chert and chert- associated BIFs over time can be used to reconstruct the environmental conditions of the early Earth, and become a hot topic in the Si isotope society. However, there are several different views of explaining the variation of d30Si values over time. Moreover, there are disputes in explaining the distribution of Si isotope in several main reservoirs in surface systems. Those disagreements are caused by lacking key Si isotope fractionation factors associated with the formation processes of chert and its altered products. There are many unexplained observations about Si isotope distributions in Earth's surface systems (Opfergelt and Delmelle, 2012). For example, the deduced Si isotope equilibrium fractionation factors by Rayleigh model at ambient temperature between clay and the solution D30Siclay-solution = -1.5 ‰ and -2.05 ‰ (Hughes et al., 2013) obviously disagree with common sense, which dictates that stiffer chemical bonds will enrich heavier isotopes, i.e., the precipitated minerals will preferentially incorporate heavy isotopes relative to aqueous H4SiO4 due to their shorter Si-O bonds. Another similar case is the fractionation between quartz and solution. Most field observations suggested that solution will be enriched with heavier Si isotope compared to quartz, conflicting to the fact that quartz is the one with much shorter Si-O bonds than aqueous H4SiO4 (ca. 1.610Å vs. 1.639Å). Here we provide equilibrium and kinetic Si isotope fractionation factors associated with the formation of amorphous quartz and other secondary minerals in polymerization, co-precipitation and adsorption processes. The adsorption processes of silica gel to Fe-hydroxides have been carefully examined. The Si isotope fractionations due to the formation of mono-dentate to quadru-dentate adsorbed Fe-Si complexes have been calculated. These data can explain well the experimental observations (e.g., Zheng et al., 2016) and

Explaining seeing? Disentangling qualia from perceptual organization.

PubMed

Ibáñez, Agustin; Bekinschtein, Tristan

2010-09-01

Abstract Visual perception and integration seem to play an essential role in our conscious phenomenology. Relatively local neural processing of reentrant nature may explain several visual integration processes (feature binding or figure-ground segregation, object recognition, inference, competition), even without attention or cognitive control. Based on the above statements, should the neural signatures of visual integration (via reentrant process) be non-reportable phenomenological qualia? We argue that qualia are not required to understand this perceptual organization.

How Much of Language Acquisition Does Operant Conditioning Explain?

PubMed

Sturdy, Christopher B; Nicoladis, Elena

2017-01-01

Since the 1950s, when Chomsky argued that Skinner's arguments could not explain syntactic acquisition, psychologists have generally avoided explicitly invoking operant or instrumental conditioning as a learning mechanism for language among human children. In this article, we argue that this is a mistake. We focus on research that has been done on language learning in human infants and toddlers in order to illustrate our points. Researchers have ended up inventing learning mechanisms that, in actual practice, not only resemble but also in fact are examples of operant conditioning (OC) by any other name they select. We argue that language acquisition researchers should proceed by first ruling out OC before invoking alternative learning mechanisms. While it is possible that OC cannot explain all of the language acquisition, simple learning mechanisms that work across species may have some explanatory power in children's language learning.

The formal Darwinism project: a mid-term report.

PubMed

Grafen, A

2007-07-01

For 8 years I have been pursuing in print an ambitious and at times highly technical programme of work, the 'Formal Darwinism Project', whose essence is to underpin and formalize the fitness optimization ideas used by behavioural ecologists, using a new kind of argument linking the mathematics of motion and the mathematics of optimization. The value of the project is to give stronger support to current practices, and at the same time sharpening theoretical ideas and suggesting principled resolutions of some untidy areas, for example, how to define fitness. The aim is also to unify existing free-standing theoretical structures, such as inclusive fitness theory, Evolutionary Stable Strategy (ESS) theory and bet-hedging theory. The 40-year-old misunderstanding over the meaning of fitness optimization between mathematicians and biologists is explained. Most of the elements required for a general theory have now been implemented, but not together in the same framework, and 'general time' remains to be developed and integrated with the other elements to produce a final unified theory of neo-Darwinian natural selection.

Interactions between Defining, Explaining and Classifying: The Case of Increasing and Decreasing Sequences

ERIC Educational Resources Information Center

Alcock, Lara; Simpson, Adrian

2017-01-01

This paper describes a study in which we investigated relationships between defining mathematical concepts--increasing and decreasing infinite sequences--explaining their meanings and classifying consistently with formal definitions. We explored the effect of defining, explaining or studying a definition on subsequent classification, and the…

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor

PubMed Central

Collado-Torres, Leonardo; Nellore, Abhinav; Jaffe, Andrew E.

2017-01-01

The recount2 resource is composed of over 70,000 uniformly processed human RNA-seq samples spanning TCGA and SRA, including GTEx. The processed data can be accessed via the recount2 website and the recountBioconductor package. This workflow explains in detail how to use the recountpackage and how to integrate it with other Bioconductor packages for several analyses that can be carried out with the recount2 resource. In particular, we describe how the coverage count matrices were computed in recount2 as well as different ways of obtaining public metadata, which can facilitate downstream analyses. Step-by-step directions show how to do a gene-level differential expression analysis, visualize base-level genome coverage data, and perform an analyses at multiple feature levels. This workflow thus provides further information to understand the data in recount2 and a compendium of R code to use the data. PMID:29043067

Weaker dental enamel explains dental decay.

PubMed

Vieira, Alexandre R; Gibson, Carolyn W; Deeley, Kathleen; Xue, Hui; Li, Yong

2015-01-01

Dental caries continues to be the most prevalent bacteria-mediated non-contagious disease of humankind. Dental professionals assert the disease can be explained by poor oral hygiene and a diet rich in sugars but this does not account for caries free individuals exposed to the same risk factors. In order to test the hypothesis that amount of amelogenin during enamel development can influence caries susceptibility, we generated multiple strains of mice with varying levels of available amelogenin during dental development. Mechanical tests showed that dental enamel developed with less amelogenin is "weaker" while the dental enamel of animals over-expressing amelogenin appears to be more resistant to acid dissolution.

Boosted Regression Tree Models to Explain Watershed ...

EPA Pesticide Factsheets

Boosted regression tree (BRT) models were developed to quantify the nonlinear relationships between landscape variables and nutrient concentrations in a mesoscale mixed land cover watershed during base-flow conditions. Factors that affect instream biological components, based on the Index of Biotic Integrity (IBI), were also analyzed. Seasonal BRT models at two spatial scales (watershed and riparian buffered area [RBA]) for nitrite-nitrate (NO2-NO3), total Kjeldahl nitrogen, and total phosphorus (TP) and annual models for the IBI score were developed. Two primary factors — location within the watershed (i.e., geographic position, stream order, and distance to a downstream confluence) and percentage of urban land cover (both scales) — emerged as important predictor variables. Latitude and longitude interacted with other factors to explain the variability in summer NO2-NO3 concentrations and IBI scores. BRT results also suggested that location might be associated with indicators of sources (e.g., land cover), runoff potential (e.g., soil and topographic factors), and processes not easily represented by spatial data indicators. Runoff indicators (e.g., Hydrological Soil Group D and Topographic Wetness Indices) explained a substantial portion of the variability in nutrient concentrations as did point sources for TP in the summer months. The results from our BRT approach can help prioritize areas for nutrient management in mixed-use and heavily impacted watershed

Explaining socio-demographic differences in disengagement from sports in adolescence.

PubMed

Prins, Richard G; Kamphuis, Carlijn B M; van Empelen, Pepijn; Beenackers, Mariëlle A; Brug, Johannes; Mackenbach, Johan P; Oenema, Anke

2013-10-01

The purpose of this longitudinal study is to identify risk groups for disengagement from sports during adolescence. In addition, it will be explored whether cognitive and environmental factors can explain socio-demographic differences in disengagement from sports. Data were obtained from the Environmental Determinants of Obesity in Rotterdam Schoolchildren study, and 357 adolescents were eligible for analysis. Socio-demographics (gender, ethnicity, education), individual cognitions and neighbourhood perceptions were assessed at baseline (2005/2006), and sports participation at baseline and at follow-up (2007/2008). Two dichotomous outcome variables were constructed: (i) disengagement from sports (yes/no) and (ii) ceased compliance with the fitnorm (i.e. cease engaging in sports ≥3 times/wk) (yes/no). In logistic regression and mediation analyses, we identified socio-demographic differences in the two outcomes. Subsequently, we applied mediation analyses to identify the contribution of cognitive and environmental explanatory factors of the socio-demographic differences. Girls [odds ratio (OR): 2.5, 95% confidence interval (CI): 1.5-4.5] were more likely than boys to disengage from sports. Girls (OR: 2.5, 95% CI: 1.4-4.2), adolescents of non-Western background (OR: 1.8, 95% CI: 1.0-3.0) and those in lower educational levels (OR: 1.7, 95% CI: 1.0-2.9) were more likely to cease compliance with the fitnorm. Perceived neighbourhood safety partly explained gender differences in disengagement from sports (8%). Intention partly explained ethnical (32%) and educational differences (37%) in ceasing compliance with the fitnorm. Girls, lower-educated adolescents and those with a non-Western background showed more pronounced reductions in sports participation and compliance with the fitnorm. Intention and perceived neighbourhood safety could partially explain these differences.

What explains the relation between family poverty and childhood depressive symptoms?

PubMed

Tracy, Melissa; Zimmerman, Frederick J; Galea, Sandro; McCauley, Elizabeth; Stoep, Ann Vander

2008-10-01

The relation between low socioeconomic status (SES) and depression has been well documented in adult populations. A number of studies suggest that family SES may be associated with depression among children and adolescents as well, although the evidence is mixed. We assessed the relation between family income and depressive symptoms among 457 children aged 11-13 years and examined pathways that may explain this relation. In-person interviews of children and their caregivers were conducted, including assessment of family income and administration of the Computer-based Diagnostic Interview Schedule for Children (C-DISC). Family income was significantly associated with depressive symptoms, with children in the lowest income group (<$35,000) reporting a mean of 8.12 symptoms compared to 6.27 symptoms in the middle income group ($35,000-$74,999) and 5.13 symptoms in the highest income group (> or = $75,000; p<0.001). Controlling for the number of stressful life events experienced in the past 6 months attenuated the effect of low family income on depressive symptoms by 28%. Indicators of the family environment explained 45% and neighborhood median household income and aggravated assault rate explained 12% of the relation. The family environment, including parental divorce or separation and perceived parental support, appears to explain most of the relation between low family income and childhood depressive symptoms. Further exploration of the pathways between family SES and depression may suggest potential interventions to reduce the occurrence and persistence of depressive symptoms in children.

The Multi-SAG project: filling the MultiDark simulations with semi-analytic galaxies

NASA Astrophysics Data System (ADS)

Vega-Martínez, C. A.; Cora, S. A.; Padilla, N. D.; Muñoz Arancibia, A. M.; Orsi, A. A.; Ruiz, A. N.

2016-08-01

The semi-analytical model sag is a code of galaxy formation and evolution which is applied to halo catalogs and merger trees extracted from cosmological -body simulations of dark matter. This contribution describes the project of constructing a catalog of simulated galaxies by adapting and applying the model sag over two dark matter simulations of the spanish MultiDark Project publicly available. Those simulations have particles, each, in boxes with sizes of 1000 Mpc and 400 Mpc respectively with Planck cosmological parameters. They cover a large range of masses and have halo mass resolutions of , therefore each simulation is able to produce more than 150 millions of simulated galaxies. A detailed description of the method is explained, and the first statistical results are shown.

Explaining mastitis incidence in Dutch dairy farming: the influence of farmers' attitudes and behaviour.

PubMed

Jansen, J; van den Borne, B H P; Renes, R J; van Schaik, G; Lam, T J G M; Leeuwis, C

2009-11-15

When mastitis incidence increases, either infection pressure has increased or cows' resistance has decreased. This usually indicates that farm management is not optimal. Numerous quantitative studies have demonstrated the effect of management practices on mastitis. In most of these studies, the identified risk factors could explain only part of the variance in mastitis incidence on farms. Several studies suggest that the unexplained variance is caused by farmers' attitudes towards different aspects of mastitis treatment and preventive behaviour. This study aims to determine, to quantify and to specify the extent to which farmers' attitudes, over and above farmers' behaviour, are factors that explain the variation in mastitis incidence, measured in terms of the quantifiable effect of management factors. An extensive survey on self-reported attitudes, behaviour and mastitis incidence was conducted on 336 Dutch dairy farms. Results of multiple linear regression analyses show that farmers' self-reported behaviour and attitudes together explain 48%, 31% and 23% of the variation within, respectively, the average farm bulk milk somatic cell count (BMSCC), the clinical mastitis incidence and the combined clinical and subclinical mastitis incidence. Both behaviour and attitudes explain part of the variance. However, most of the variance in all three dependant measures is explained solely by the attitude variables. The variation in BMSCC value is best explained by (1) farmers' normative frame of reference about mastitis, (2) farmers' perceptions about the control of mastitis and (3) the perceived effect of a BMSCC penalty level. The variation in clinical mastitis is best explained by farmers' perceptions about mastitis control. The variation in the combined clinical and subclinical mastitis incidence rate is best explained by the perceived effect of a BMSCC penalty level and the frequency of contact with others. The results of this study show that farmers' attitudes are a

Explaining ecological clusters of maternal depression in South Western Sydney

PubMed Central

2014-01-01

Background The aim of the qualitative study reported here was to: 1) explain the observed clustering of postnatal depressive symptoms in South Western Sydney; and 2) identify group-level mechanisms that would add to our understanding of the social determinants of maternal depression. Methods Critical realism provided the methodological underpinning for the study. The setting was four local government areas in South Western Sydney, Australia. Child and Family practitioners and mothers in naturally occurring mothers groups were interviewed. Results Using an open coding approach to maximise emergence of patterns and relationships we have identified seven theoretical concepts that might explain the observed spatial clustering of maternal depression. The theoretical concepts identified were: Community-level social networks; Social Capital and Social Cohesion; "Depressed community"; Access to services at the group level; Ethnic segregation and diversity; Supportive social policy; and Big business. Conclusions We postulate that these regional structural, economic, social and cultural mechanisms partially explain the pattern of maternal depression observed in families and communities within South Western Sydney. We further observe that powerful global economic and political forces are having an impact on the local situation. The challenge for policy and practice is to support mothers and their families within this adverse regional and global-economic context. PMID:24460690

Genetic pleiotropy explains associations between musical auditory discrimination and intelligence.

PubMed

Mosing, Miriam A; Pedersen, Nancy L; Madison, Guy; Ullén, Fredrik

2014-01-01

Musical aptitude is commonly measured using tasks that involve discrimination of different types of musical auditory stimuli. Performance on such different discrimination tasks correlates positively with each other and with intelligence. However, no study to date has explored these associations using a genetically informative sample to estimate underlying genetic and environmental influences. In the present study, a large sample of Swedish twins (N = 10,500) was used to investigate the genetic architecture of the associations between intelligence and performance on three musical auditory discrimination tasks (rhythm, melody and pitch). Phenotypic correlations between the tasks ranged between 0.23 and 0.42 (Pearson r values). Genetic modelling showed that the covariation between the variables could be explained by shared genetic influences. Neither shared, nor non-shared environment had a significant effect on the associations. Good fit was obtained with a two-factor model where one underlying shared genetic factor explained all the covariation between the musical discrimination tasks and IQ, and a second genetic factor explained variance exclusively shared among the discrimination tasks. The results suggest that positive correlations among musical aptitudes result from both genes with broad effects on cognition, and genes with potentially more specific influences on auditory functions.

Genetic Pleiotropy Explains Associations between Musical Auditory Discrimination and Intelligence

PubMed Central

Mosing, Miriam A.; Pedersen, Nancy L.; Madison, Guy; Ullén, Fredrik

2014-01-01

Musical aptitude is commonly measured using tasks that involve discrimination of different types of musical auditory stimuli. Performance on such different discrimination tasks correlates positively with each other and with intelligence. However, no study to date has explored these associations using a genetically informative sample to estimate underlying genetic and environmental influences. In the present study, a large sample of Swedish twins (N = 10,500) was used to investigate the genetic architecture of the associations between intelligence and performance on three musical auditory discrimination tasks (rhythm, melody and pitch). Phenotypic correlations between the tasks ranged between 0.23 and 0.42 (Pearson r values). Genetic modelling showed that the covariation between the variables could be explained by shared genetic influences. Neither shared, nor non-shared environment had a significant effect on the associations. Good fit was obtained with a two-factor model where one underlying shared genetic factor explained all the covariation between the musical discrimination tasks and IQ, and a second genetic factor explained variance exclusively shared among the discrimination tasks. The results suggest that positive correlations among musical aptitudes result from both genes with broad effects on cognition, and genes with potentially more specific influences on auditory functions. PMID:25419664

What Explains Patterns of Diversification and Richness among Animal Phyla?

PubMed Central

Jezkova, Tereza; Wiens, John J.

2016-01-01

Animal phyla vary dramatically in species richness (from 1 species to >1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g. sponges), parasitic worms (e.g. nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ~74% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, non-marine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (~67%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g. head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across >80% of all extant, described species. PMID:28221832

Explaining ecological clusters of maternal depression in South Western Sydney.

PubMed

Eastwood ED, John; Kemp, Lynn; Jalaludin, Bin

2014-01-24

The aim of the qualitative study reported here was to: 1) explain the observed clustering of postnatal depressive symptoms in South Western Sydney; and 2) identify group-level mechanisms that would add to our understanding of the social determinants of maternal depression. Critical realism provided the methodological underpinning for the study. The setting was four local government areas in South Western Sydney, Australia. Child and Family practitioners and mothers in naturally occurring mothers groups were interviewed. Using an open coding approach to maximise emergence of patterns and relationships we have identified seven theoretical concepts that might explain the observed spatial clustering of maternal depression. The theoretical concepts identified were: Community-level social networks; Social Capital and Social Cohesion; "Depressed community"; Access to services at the group level; Ethnic segregation and diversity; Supportive social policy; and Big business. We postulate that these regional structural, economic, social and cultural mechanisms partially explain the pattern of maternal depression observed in families and communities within South Western Sydney. We further observe that powerful global economic and political forces are having an impact on the local situation. The challenge for policy and practice is to support mothers and their families within this adverse regional and global-economic context.

What Explains Patterns of Diversification and Richness among Animal Phyla?

PubMed

Jezkova, Tereza; Wiens, John J

2017-03-01

Animal phyla vary dramatically in species richness (from one species to >1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g., sponges), parasitic worms (e.g., nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ∼74% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, nonmarine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (∼67%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g., head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across >80% of all extant, described species.

How Much of Language Acquisition Does Operant Conditioning Explain?

PubMed Central

Sturdy, Christopher B.; Nicoladis, Elena

2017-01-01

Since the 1950s, when Chomsky argued that Skinner’s arguments could not explain syntactic acquisition, psychologists have generally avoided explicitly invoking operant or instrumental conditioning as a learning mechanism for language among human children. In this article, we argue that this is a mistake. We focus on research that has been done on language learning in human infants and toddlers in order to illustrate our points. Researchers have ended up inventing learning mechanisms that, in actual practice, not only resemble but also in fact are examples of operant conditioning (OC) by any other name they select. We argue that language acquisition researchers should proceed by first ruling out OC before invoking alternative learning mechanisms. While it is possible that OC cannot explain all of the language acquisition, simple learning mechanisms that work across species may have some explanatory power in children’s language learning. PMID:29163295

Self-Explaining Effect in General Chemistry Instruction: Eliciting Overt Categorical Behaviours by Design

ERIC Educational Resources Information Center

Villalta-Cerdas, Adrian; Sandi-Urena, Santiago

2014-01-01

Self-explaining refers to the generation of inferences about causal connections between objects and events. In science, this may be summarised as making sense of how and why actual or hypothetical phenomena take place. Research findings in educational psychology show that implementing activities that elicit self-explaining improves learning in…

Project management of life-science research projects: project characteristics, challenges and training needs.

PubMed

Beukers, Margot W

2011-02-01

Thirty-four project managers of life-science research projects were interviewed to investigate the characteristics of their projects, the challenges they faced and their training requirements. A set of ten discriminating parameters were identified based on four project categories: contract research, development, discovery and call-based projects--projects set up to address research questions defined in a call for proposals. The major challenges these project managers are faced with relate to project members, leadership without authority and a lack of commitment from the respective organization. Two-thirds of the project managers indicated that they would be interested in receiving additional training, mostly on people-oriented, soft skills. The training programs that are currently on offer, however, do not meet their needs. Copyright © 2010 Elsevier Ltd. All rights reserved.

EST databases and web tools for EST projects.

PubMed

Shen, Yao-Qing; O'Brien, Emmet; Koski, Liisa; Lang, B Franz; Burger, Gertraud

2009-01-01

This chapter outlines key considerations for constructing and implementing an EST database. Instead of showing the technological details step by step, emphasis is put on the design of an EST database suited to the specific needs of EST projects and how to choose the most suitable tools. Using TBestDB as an example, we illustrate the essential factors to be considered for database construction and the steps for data population and annotation. This process employs technologies such as PostgreSQL, Perl, and PHP to build the database and interface, and tools such as AutoFACT for data processing and annotation. We discuss these in comparison to other available technologies and tools, and explain the reasons for our choices.

Interactions between psychosocial and built environment factors in explaining older adults' physical activity.

PubMed

Carlson, Jordan A; Sallis, James F; Conway, Terry L; Saelens, Brian E; Frank, Lawrence D; Kerr, Jacqueline; Cain, Kelli L; King, Abby C

2012-01-01

To evaluate ecological model predictions of cross-level interactions among psychosocial and environmental correlates of physical activity in 719 community-dwelling older adults in the Baltimore, Maryland and Seattle, Washington areas during 2005-2008. Walkability, access to parks and recreation facilities and moderate-to-vigorous physical activity (MVPA) minutes per week (min/week) were measured objectively. Neighborhood aesthetics, walking facilities, social support, self-efficacy, barriers and transportation and leisure walking min/week were self-reported. Walkability interacted with social support in explaining total MVPA (B=13.71) and with social support (B=7.90), self-efficacy (B=7.66) and barriers (B=-8.26) in explaining walking for transportation. Aesthetics interacted with barriers in explaining total MVPA (B=-12.20) and walking facilities interacted with self-efficacy in explaining walking for leisure (B=-10.88; Ps<.05). Summarizing across the interactions, living in a supportive environment (vs. unsupportive) was related to 30-59 more min/week of physical activity for participants with more positive psychosocial attributes, but only 0-28 more min/week for participants with less positive psychosocial attributes. Results supported synergistic interactions between built environment and psychosocial factors in explaining physical activity among older adults. Findings suggest multilevel interventions may be most effective in increasing physical activity. Copyright © 2011 Elsevier Inc. All rights reserved.

Does geography or ecology best explain 'cultural' variation among chimpanzee communities?

PubMed

Kamilar, Jason M; Marshack, Joshua L

2012-02-01

Much attention has been paid to geographic variation in chimpanzee behavior, but few studies have applied quantitative techniques to explain this variation. Here, we apply methods typically utilized in macroecology to explain variation in the putative cultural traits of chimpanzees. We analyzed published data containing 39 behavioral traits from nine chimpanzee communities. We used a canonical correspondence analysis to examine the relative importance of environmental characteristics and geography, which may be a proxy for inter-community gene flow and/or social transmission, for explaining geographic variation in chimpanzee behavior. We found that geography, and longitude in particular, was the best predictor of behavioral variation. Chimpanzee communities in close longitudinal proximity to each other exhibit similar behavioral repertoires, independent of local ecological factors. No ecological variables were significantly related to behavioral variation. These results support the idea that inter-community dispersal patterns have played a major role in structuring behavioral variation. We cannot be certain whether behavioral variation has a genetic basis, is the result of innovation and diffusion, or a combination of the two. Copyright © 2011 Elsevier Ltd. All rights reserved.

Explaining resource consumption among non-normal neonates

PubMed Central

Schwartz, Rachel M.; Michelman, Thomas; Pezzullo, John; Phibbs, Ciaran S.

1991-01-01

The adoption by Medicare in 1983 of prospective payment using diagnosis-related groups (DRGs) has stimulated research to develop case-mix grouping schemes that more accurately predict resource consumption by patients. In this article, the authors explore a new method designed to improve case-mix classification for newborns through the use of birth weight in combination with DRGs to adjust the unexplained case-mix severity. Although the findings are developmental in nature, they reveal that the model significantly improves our ability to explain resource use. PMID:10122360

The boundaries of instance-based learning theory for explaining decisions from experience.

PubMed

Gonzalez, Cleotilde

2013-01-01

Most demonstrations of how people make decisions in risky situations rely on decisions from description, where outcomes and their probabilities are explicitly stated. But recently, more attention has been given to decisions from experience where people discover these outcomes and probabilities through exploration. More importantly, risky behavior depends on how decisions are made (from description or experience), and although prospect theory explains decisions from description, a comprehensive model of decisions from experience is yet to be found. Instance-based learning theory (IBLT) explains how decisions are made from experience through interactions with dynamic environments (Gonzalez et al., 2003). The theory has shown robust explanations of behavior across multiple tasks and contexts, but it is becoming unclear what the theory is able to explain and what it does not. The goal of this chapter is to start addressing this problem. I will introduce IBLT and a recent cognitive model based on this theory: the IBL model of repeated binary choice; then I will discuss the phenomena that the IBL model explains and those that the model does not. The argument is for the theory's robustness but also for clarity in terms of concrete effects that the theory can or cannot account for. Copyright © 2013 Elsevier B.V. All rights reserved.

Microhabitat and Climatic Niche Change Explain Patterns of Diversification among Frog Families.

PubMed

Moen, Daniel S; Wiens, John J

2017-07-01

A major goal of ecology and evolutionary biology is to explain patterns of species richness among clades. Differences in rates of net diversification (speciation minus extinction over time) may often explain these patterns, but the factors that drive variation in diversification rates remain uncertain. Three important candidates are climatic niche position (e.g., whether clades are primarily temperate or tropical), rates of climatic niche change among species within clades, and microhabitat (e.g., aquatic, terrestrial, arboreal). The first two factors have been tested separately in several studies, but the relative importance of all three is largely unknown. Here we explore the correlates of diversification among families of frogs, which collectively represent ∼88% of amphibian species. We assemble and analyze data on phylogeny, climate, and microhabitat for thousands of species. We find that the best-fitting phylogenetic multiple regression model includes all three types of variables: microhabitat, rates of climatic niche change, and climatic niche position. This model explains 67% of the variation in diversification rates among frog families, with arboreal microhabitat explaining ∼31%, niche rates ∼25%, and climatic niche position ∼11%. Surprisingly, we show that microhabitat can have a much stronger influence on diversification than climatic niche position or rates of climatic niche change.

Weaker Dental Enamel Explains Dental Decay

PubMed Central

Vieira, Alexandre R.; Gibson, Carolyn W.; Deeley, Kathleen; Xue, Hui; Li, Yong

2015-01-01

Dental caries continues to be the most prevalent bacteria-mediated non-contagious disease of humankind. Dental professionals assert the disease can be explained by poor oral hygiene and a diet rich in sugars but this does not account for caries free individuals exposed to the same risk factors. In order to test the hypothesis that amount of amelogenin during enamel development can influence caries susceptibility, we generated multiple strains of mice with varying levels of available amelogenin during dental development. Mechanical tests showed that dental enamel developed with less amelogenin is “weaker” while the dental enamel of animals over-expressing amelogenin appears to be more resistant to acid dissolution. PMID:25885796

Bell Test experiments explained without entanglement

NASA Astrophysics Data System (ADS)

Boyd, Jeffrey

2011-04-01

by Jeffrey H. Boyd. Jeffreyhboyd@gmail.com. John Bell proposed a test of what was called "local realism." However that is a different view of reality than we hold. Bell incorrectly assumed the validity of wave particle dualism. According to our model waves are independent of particles; wave interference precedes the emission of a particle. This results in two conclusions. First the proposed inequalities that apply to "local realism" in Bell's theorem do not apply to this model. The alleged mathematics of "local realism" is therefore wrong. Second, we can explain the Bell Test experimental results (such as the experiments done at Innsbruck) without any need for entanglement, non-locality, or particle superposition.

A step-by-step methodology for enterprise interoperability projects

NASA Astrophysics Data System (ADS)

Chalmeta, Ricardo; Pazos, Verónica

2015-05-01

Enterprise interoperability is one of the key factors for enhancing enterprise competitiveness. Achieving enterprise interoperability is an extremely complex process which involves different technological, human and organisational elements. In this paper we present a framework to help enterprise interoperability. The framework has been developed taking into account the three domains of interoperability: Enterprise Modelling, Architecture and Platform and Ontologies. The main novelty of the framework in comparison to existing ones is that it includes a step-by-step methodology that explains how to carry out an enterprise interoperability project taking into account different interoperability views, like business, process, human resources, technology, knowledge and semantics.

Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub-classification.

PubMed

Shimoni, Yishai

2018-02-01

One of the goals of cancer research is to identify a set of genes that cause or control disease progression. However, although multiple such gene sets were published, these are usually in very poor agreement with each other, and very few of the genes proved to be functional therapeutic targets. Furthermore, recent findings from a breast cancer gene-expression cohort showed that sets of genes selected randomly can be used to predict survival with a much higher probability than expected. These results imply that many of the genes identified in breast cancer gene expression analysis may not be causal of cancer progression, even though they can still be highly predictive of prognosis. We performed a similar analysis on all the cancer types available in the cancer genome atlas (TCGA), namely, estimating the predictive power of random gene sets for survival. Our work shows that most cancer types exhibit the property that random selections of genes are more predictive of survival than expected. In contrast to previous work, this property is not removed by using a proliferation signature, which implies that proliferation may not always be the confounder that drives this property. We suggest one possible solution in the form of data-driven sub-classification to reduce this property significantly. Our results suggest that the predictive power of random gene sets may be used to identify the existence of sub-classes in the data, and thus may allow better understanding of patient stratification. Furthermore, by reducing the observed bias this may allow more direct identification of biologically relevant, and potentially causal, genes.

Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub-classification

PubMed Central

2018-01-01

One of the goals of cancer research is to identify a set of genes that cause or control disease progression. However, although multiple such gene sets were published, these are usually in very poor agreement with each other, and very few of the genes proved to be functional therapeutic targets. Furthermore, recent findings from a breast cancer gene-expression cohort showed that sets of genes selected randomly can be used to predict survival with a much higher probability than expected. These results imply that many of the genes identified in breast cancer gene expression analysis may not be causal of cancer progression, even though they can still be highly predictive of prognosis. We performed a similar analysis on all the cancer types available in the cancer genome atlas (TCGA), namely, estimating the predictive power of random gene sets for survival. Our work shows that most cancer types exhibit the property that random selections of genes are more predictive of survival than expected. In contrast to previous work, this property is not removed by using a proliferation signature, which implies that proliferation may not always be the confounder that drives this property. We suggest one possible solution in the form of data-driven sub-classification to reduce this property significantly. Our results suggest that the predictive power of random gene sets may be used to identify the existence of sub-classes in the data, and thus may allow better understanding of patient stratification. Furthermore, by reducing the observed bias this may allow more direct identification of biologically relevant, and potentially causal, genes. PMID:29470520

On the influence of simulated SST warming on rainfall projections in the Indo-Pacific domain: an AGCM study

NASA Astrophysics Data System (ADS)

Zhang, Huqiang; Zhao, Y.; Moise, A.; Ye, H.; Colman, R.; Roff, G.; Zhao, M.

2018-02-01

Significant uncertainty exists in regional climate change projections, particularly for rainfall and other hydro-climate variables. In this study, we conduct a series of Atmospheric General Circulation Model (AGCM) experiments with different future sea surface temperature (SST) warming simulated by a range of coupled climate models. They allow us to assess the extent to which uncertainty from current coupled climate model rainfall projections can be attributed to their simulated SST warming. Nine CMIP5 model-simulated global SST warming anomalies have been super-imposed onto the current SSTs simulated by the Australian climate model ACCESS1.3. The ACCESS1.3 SST-forced experiments closely reproduce rainfall means and interannual variations as in its own fully coupled experiments. Although different global SST warming intensities explain well the inter-model difference in global mean precipitation changes, at regional scales the SST influence vary significantly. SST warming explains about 20-25% of the patterns of precipitation changes in each of the four/five models in its rainfall projections over the oceans in the Indo-Pacific domain, but there are also a couple of models in which different SST warming explains little of their precipitation pattern changes. The influence is weaker again for rainfall changes over land. Roughly similar levels of contribution can be attributed to different atmospheric responses to SST warming in these models. The weak SST influence in our study could be due to the experimental setup applied: superimposing different SST warming anomalies onto the same SSTs simulated for current climate by ACCESS1.3 rather than directly using model-simulated past and future SSTs. Similar modelling and analysis from other modelling groups with more carefully designed experiments are needed to tease out uncertainties caused by different SST warming patterns, different SST mean biases and different model physical/dynamical responses to the same underlying

Genetic drivers of papillary renal cell carcinoma - TCGA

Cancer.gov

A comprehensive genomic analysis of 161 tumors from people with papillary renal cell carcinoma (PRCC) – the second most common form of kidney cancer –provided insights into the molecular basis of this cancer and may inform its classification and treatment.

Reinvigorating GBM Research with Hope for Therapies - TCGA

Cancer.gov

Dr. Antonio Iavarone and his research group at Columbia University have discovered the first recurrent gene fusion in glioblastoma. Find out how they did it and potential implications in this Case Study.

Mathematical Representation Ability by Using Project Based Learning on the Topic of Statistics

NASA Astrophysics Data System (ADS)

Widakdo, W. A.

2017-09-01

Seeing the importance of the role of mathematics in everyday life, mastery of the subject areas of mathematics is a must. Representation ability is one of the fundamental ability that used in mathematics to make connection between abstract idea with logical thinking to understanding mathematics. Researcher see the lack of mathematical representation and try to find alternative solution to dolve it by using project based learning. This research use literature study from some books and articles in journals to see the importance of mathematical representation abiliy in mathemtics learning and how project based learning able to increase this mathematical representation ability on the topic of Statistics. The indicators for mathematical representation ability in this research classifies namely visual representation (picture, diagram, graph, or table); symbolize representation (mathematical statement. Mathematical notation, numerical/algebra symbol) and verbal representation (written text). This article explain about why project based learning able to influence student’s mathematical representation by using some theories in cognitive psychology, also showing the example of project based learning that able to use in teaching statistics, one of mathematics topic that very useful to analyze data.

Reference Canopy Stomatal Conductance Explains Spatiotemporal Patterns of Tree Transpiration

NASA Astrophysics Data System (ADS)

Loranty, M. M.; Mackay, D. S.; Ewers, B. E.; Kruger, E. L.; Traver, E.

2007-12-01

Increased heterogeneity in patterns of whole tree transpiration (EC) with increasing atmospheric vapor pressure deficit (D) suggests a dynamic response of sap flow velocity (JS) to environmental drivers. We hypothesized that differences in reference stomatal conductance (GSref), stomatal conductance at D = 1kPa, would explain the spatiotemporal dynamics of JS. Using a coupled model of plant hydraulic and biochemical processes we tested this hypothesis with sap flux data for 106 aspen ( Populus tremuloides) and 108 sugar maple ( Acer saccharum) trees collected from plots using in 2-D cyclic sampling scheme during the summer of 2005 in northern Wisconsin. Inverse modeling is used to estimate GSref for each tree. For each species, trees from across the ranges of JS and diameter distributions are compared. GSref explained temporal variability in spatial patterns of EC We explore several possible mechanistic explanations for differences in GSref among trees. Topoedaphic factors are considered to determine if location within a stand has an effect. We also consider competition with neighboring individuals as a possible explanation. Variations in GSref in aspen were explained in part by competition for light between neighboring individuals, while competition for light was not a significant factor for sugar maple. Based on simulation analysis we identify possible biochemical feedbacks as drivers of the variability in plant hydraulics. Other factors examined included micro-topography within both sites.

Explaining Common Variance Shared by Early Numeracy and Literacy

ERIC Educational Resources Information Center

Davidse, N. J.; De Jong, M. T.; Bus, A. G.

2014-01-01

How can it be explained that early literacy and numeracy share variance? We specifically tested whether the correlation between four early literacy skills (rhyming, letter knowledge, emergent writing, and orthographic knowledge) and simple sums (non-symbolic and story condition) reduced after taking into account preschool attention control,…

Which Mechanisms Explain Monetary Returns to International Student Mobility?

ERIC Educational Resources Information Center

Kratz, Fabian; Netz, Nicolai

2018-01-01

The authors develop a conceptual framework explaining monetary returns to international student mobility (ISM). Based on data from two German graduate panel surveys, they test this framework using growth curve models and Oaxaca-Blinder decompositions. The results indicate that ISM-experienced graduates enjoy a steeper wage growth after graduation…

[Research progress in molecular classification of gastric cancer].

PubMed

Zhou, Menglong; Li, Guichao; Zhang, Zhen

2016-09-25

Gastric cancer(GC) is a highly heterogeneous malignancy. The present widely used histopathological classifications have gradually failed to meet the needs of individualized diagnosis and treatment. Development of technologies such as microarray and next-generation sequencing (NGS) has allowed GC to be studied at the molecular level. Mechanisms about tumorigenesis and progression of GC can be elucidated in the aspects of gene mutations, chromosomal alterations, transcriptional and epigenetic changes, on the basis of which GC can be divided into several subtypes. The classifications of Tan's, Lei's, TCGA and ACRG are relatively comprehensive. Especially the TCGA and ACRG classifications have large sample size and abundant molecular profiling data, thus, the genomic characteristics of GC can be depicted more accurately. However, significant differences between both classifications still exist so that they cannot be substituted for each other. So far there is no widely accepted molecular classification of GC. Compared with TCGA classification, ACRG system may have more clinical significance in Chinese GC patients since the samples are mostly from Asian population and show better association with prognosis. The molecular classification of GC may provide the theoretical and experimental basis for early diagnosis, therapeutic efficacy prediction and treatment stratification while their clinical application is still limited. Future work should involve the application of molecular classifications in the clinical settings for improving the medical management of GC.

Combined image and genomic analysis of high-grade serous ovarian cancer reveals PTEN loss as a common driver event and prognostic classifier.

PubMed

Martins, Filipe C; Santiago, Ines de; Trinh, Anne; Xian, Jian; Guo, Anne; Sayal, Karen; Jimenez-Linan, Mercedes; Deen, Suha; Driver, Kristy; Mack, Marie; Aslop, Jennifer; Pharoah, Paul D; Markowetz, Florian; Brenton, James D

2014-12-17

TP53 and BRCA1/2 mutations are the main drivers in high-grade serous ovarian carcinoma (HGSOC). We hypothesise that combining tissue phenotypes from image analysis of tumour sections with genomic profiles could reveal other significant driver events. Automatic estimates of stromal content combined with genomic analysis of TCGA HGSOC tumours show that stroma strongly biases estimates of PTEN expression. Tumour-specific PTEN expression was tested in two independent cohorts using tissue microarrays containing 521 cases of HGSOC. PTEN loss or downregulation occurred in 77% of the first cohort by immunofluorescence and 52% of the validation group by immunohistochemistry, and is associated with worse survival in a multivariate Cox-regression model adjusted for study site, age, stage and grade. Reanalysis of TCGA data shows that hemizygous loss of PTEN is common (36%) and expression of PTEN and expression of androgen receptor are positively associated. Low androgen receptor expression was associated with reduced survival in data from TCGA and immunohistochemical analysis of the first cohort. PTEN loss is a common event in HGSOC and defines a subgroup with significantly worse prognosis, suggesting the rational use of drugs to target PI3K and androgen receptor pathways for HGSOC. This work shows that integrative approaches combining tissue phenotypes from images with genomic analysis can resolve confounding effects of tissue heterogeneity and should be used to identify new drivers in other cancers.

Explaining Warm Coronal Loops

NASA Technical Reports Server (NTRS)

Klimchuk, James A.; Karpen, Judy T.; Patsourakos, Spiros

2008-01-01

One of the great mysteries of coronal physics that has come to light in the last few years is the discovery that warn (- 1 INK) coronal loops are much denser than expected for quasi-static equilibrium. Both the excess densities and relatively long lifetimes of the loops can be explained with bundles of unresolved strands that are heated impulsively to very high temperatures. Since neighboring strands are at different stages of cooling, the composite loop bundle is multi-thermal, with the distribution of temperatures depending on the details of the "nanoflare storm." Emission hotter than 2 MK is predicted, but it is not clear that such emission is always observed. We consider two possible explanations for the existence of over-dense warm loops without corresponding hot emission: (1) loops are bundles of nanoflare heated strands, but a significant fraction of the nanoflare energy takes the form of a nonthermal electron beam rather then direct plasma heating; (2) loops are bundles of strands that undergo thermal nonequilibrium that results when steady heating is sufficiently concentrated near the footpoints. We present numerical hydro simulations of both of these possibilities and explore the observational consequences, including the production of hard X-ray emission and absorption by cool material in the corona.

Explaining regional variation in home care use by demand and supply variables.

PubMed

van Noort, Olivier; Schotanus, Fredo; van de Klundert, Joris; Telgen, Jan

2018-02-01

In the Netherlands, home care services like district nursing and personal assistance are provided by private service provider organizations and covered by private health insurance companies which bear legal responsibility for purchasing these services. To improve value for money, their procurement increasingly replaces fee-for-service payments with population based budgets. Setting appropriate population budgets requires adaptation to the legitimate needs of the population, whereas historical costs are likely to be influenced by supply factors as well, not all of which are necessarily legitimate. Our purpose is to explain home care costs in terms of demand and supply factors. This allows for adjusting historical cost patterns when setting population based budgets. Using expenses claims of 60 Dutch municipalities, we analyze eight demand variables and five supply variables with a multiple regression model to explain variance in the number of clients per inhabitant, costs per client and costs per inhabitant. Our models explain 69% of variation in the number of clients per inhabitant, 28% of costs per client and 56% of costs per inhabitant using demand factors. Moreover, we find that supply factors explain an additional 17-23% of variation. Predictors of higher utilization are home care organizations that are integrated with intramural nursing homes, higher competition levels among home care organizations and the availability of complementary services. Copyright © 2017. Published by Elsevier B.V.

A Conceptual Characterization of Online Videos Explaining Natural Selection

ERIC Educational Resources Information Center

Bohlin, Gustav; Göransson, Andreas; Höst, Gunnar E.; Tibell, Lena A. E.

2017-01-01

Educational videos on the Internet comprise a vast and highly diverse source of information. Online search engines facilitate access to numerous videos claiming to explain natural selection, but little is known about the degree to which the video content match key evolutionary content identified as important in evolution education research. In…

Explaining University Students' Effective Use of E-Learning Platforms

ERIC Educational Resources Information Center

Moreno, Valter; Cavazotte, Flavia; Alves, Isabela

2017-01-01

Students' success in e-learning programs depends on how they adopt and embed technology into their learning activities. Drawing on the Technology Acceptance Model, we propose a framework to explain students' intention to use e-learning platforms effectively, that is, their intention to fully exploit system's functionalities in leaning processes,…

Uncertainty of future projections of species distributions in mountainous regions.

PubMed

Tang, Ying; Winkler, Julie A; Viña, Andrés; Liu, Jianguo; Zhang, Yuanbin; Zhang, Xiaofeng; Li, Xiaohong; Wang, Fang; Zhang, Jindong; Zhao, Zhiqiang

2018-01-01

Multiple factors introduce uncertainty into projections of species distributions under climate change. The uncertainty introduced by the choice of baseline climate information used to calibrate a species distribution model and to downscale global climate model (GCM) simulations to a finer spatial resolution is a particular concern for mountainous regions, as the spatial resolution of climate observing networks is often insufficient to detect the steep climatic gradients in these areas. Using the maximum entropy (MaxEnt) modeling framework together with occurrence data on 21 understory bamboo species distributed across the mountainous geographic range of the Giant Panda, we examined the differences in projected species distributions obtained from two contrasting sources of baseline climate information, one derived from spatial interpolation of coarse-scale station observations and the other derived from fine-spatial resolution satellite measurements. For each bamboo species, the MaxEnt model was calibrated separately for the two datasets and applied to 17 GCM simulations downscaled using the delta method. Greater differences in the projected spatial distributions of the bamboo species were observed for the models calibrated using the different baseline datasets than between the different downscaled GCM simulations for the same calibration. In terms of the projected future climatically-suitable area by species, quantification using a multi-factor analysis of variance suggested that the sum of the variance explained by the baseline climate dataset used for model calibration and the interaction between the baseline climate data and the GCM simulation via downscaling accounted for, on average, 40% of the total variation among the future projections. Our analyses illustrate that the combined use of gridded datasets developed from station observations and satellite measurements can help estimate the uncertainty introduced by the choice of baseline climate information to

Uncertainty of future projections of species distributions in mountainous regions

PubMed Central

Tang, Ying; Viña, Andrés; Liu, Jianguo; Zhang, Yuanbin; Zhang, Xiaofeng; Li, Xiaohong; Wang, Fang; Zhang, Jindong; Zhao, Zhiqiang

2018-01-01

Multiple factors introduce uncertainty into projections of species distributions under climate change. The uncertainty introduced by the choice of baseline climate information used to calibrate a species distribution model and to downscale global climate model (GCM) simulations to a finer spatial resolution is a particular concern for mountainous regions, as the spatial resolution of climate observing networks is often insufficient to detect the steep climatic gradients in these areas. Using the maximum entropy (MaxEnt) modeling framework together with occurrence data on 21 understory bamboo species distributed across the mountainous geographic range of the Giant Panda, we examined the differences in projected species distributions obtained from two contrasting sources of baseline climate information, one derived from spatial interpolation of coarse-scale station observations and the other derived from fine-spatial resolution satellite measurements. For each bamboo species, the MaxEnt model was calibrated separately for the two datasets and applied to 17 GCM simulations downscaled using the delta method. Greater differences in the projected spatial distributions of the bamboo species were observed for the models calibrated using the different baseline datasets than between the different downscaled GCM simulations for the same calibration. In terms of the projected future climatically-suitable area by species, quantification using a multi-factor analysis of variance suggested that the sum of the variance explained by the baseline climate dataset used for model calibration and the interaction between the baseline climate data and the GCM simulation via downscaling accounted for, on average, 40% of the total variation among the future projections. Our analyses illustrate that the combined use of gridded datasets developed from station observations and satellite measurements can help estimate the uncertainty introduced by the choice of baseline climate information to

Does boldness explain vulnerability to angling in Eurasian perch Perca fluviatilis?

PubMed

Vainikka, Anssi; Tammela, Ilkka; Hyvärinen, Pekka

2016-04-01

Consistent individual differences (CIDs) in behavior are of interest to both basic and applied research, because any selection acting on them could induce evolution of animal behavior. It has been suggested that CIDs in the behavior of fish might explain individual differences in vulnerability to fishing. If so, fishing could impose selection on fish behavior. In this study, we assessed boldness-indicating behaviors of Eurasian perch Perca fluviatilis using individually conducted experiments measuring the time taken to explore a novel arena containing predator (burbot, Lota lota ) cues. We studied if individual differences in boldness would explain vulnerability of individually tagged perch to experimental angling in outdoor ponds, or if fishing would impose selection on boldness-indicating behavior. Perch expressed repeatable individual differences in boldness-indicating behavior but the individual boldness-score (the first principal component) obtained using principal component analysis combining all the measured behavioral responses did not explain vulnerability to experimental angling. Instead, large body size appeared as the only statistically significant predictor of capture probability. Our results suggest that angling is selective for large size, but not always selective for high boldness.

Does boldness explain vulnerability to angling in Eurasian perch Perca fluviatilis?

PubMed Central

Vainikka, Anssi; Tammela, Ilkka; Hyvärinen, Pekka

2016-01-01

Abstract Consistent individual differences (CIDs) in behavior are of interest to both basic and applied research, because any selection acting on them could induce evolution of animal behavior. It has been suggested that CIDs in the behavior of fish might explain individual differences in vulnerability to fishing. If so, fishing could impose selection on fish behavior. In this study, we assessed boldness-indicating behaviors of Eurasian perch Perca fluviatilis using individually conducted experiments measuring the time taken to explore a novel arena containing predator (burbot, Lota lota) cues. We studied if individual differences in boldness would explain vulnerability of individually tagged perch to experimental angling in outdoor ponds, or if fishing would impose selection on boldness-indicating behavior. Perch expressed repeatable individual differences in boldness-indicating behavior but the individual boldness-score (the first principal component) obtained using principal component analysis combining all the measured behavioral responses did not explain vulnerability to experimental angling. Instead, large body size appeared as the only statistically significant predictor of capture probability. Our results suggest that angling is selective for large size, but not always selective for high boldness. PMID:29491897

Validation of SCT Methylation as a Hallmark Biomarker for Lung Cancers.

PubMed

Zhang, Yu-An; Ma, Xiaotu; Sathe, Adwait; Fujimoto, Junya; Wistuba, Ignacio; Lam, Stephen; Yatabe, Yasushi; Wang, Yi-Wei; Stastny, Victor; Gao, Boning; Larsen, Jill E; Girard, Luc; Liu, Xiaoyun; Song, Kai; Behrens, Carmen; Kalhor, Neda; Xie, Yang; Zhang, Michael Q; Minna, John D; Gazdar, Adi F

2016-03-01

The human secretin gene (SCT) encodes secretin, a hormone with limited tissue distribution. Analysis of the 450k methylation array data in The Cancer Genome Atlas (TCGA) indicated that the SCT promoter region is differentially hypermethylated in lung cancer. Our purpose was to validate SCT methylation as a potential biomarker for lung cancer. We analyzed data from TCGA and developed and applied SCT-specific bisulfite DNA sequencing and quantitative methylation-specific polymerase chain reaction assays. The analyses of TCGA 450K data for 801 samples showed that SCT hypermethylation has an area under the curve (AUC) value greater than 0.98 that can be used to distinguish lung adenocarcinomas or squamous cell carcinomas from nonmalignant lung tissue. Bisulfite sequencing of lung cancer cell lines and normal blood cells allowed us to confirm that SCT methylation is highly discriminative. By applying a quantitative methylation-specific polymerase chain reaction assay, we found that SCT hypermethylation is frequently detected in all major subtypes of malignant non-small cell lung cancer (AUC = 0.92, n = 108) and small cell lung cancer (AUC = 0.93, n = 40) but is less frequent in lung carcinoids (AUC = 0.54, n = 20). SCT hypermethylation appeared in samples of lung carcinoma in situ during multistage pathogenesis and increased in invasive samples. Further analyses of TCGA 450k data showed that SCT hypermethylation is highly discriminative in most other types of malignant tumors but less frequent in low-grade malignant tumors. The only normal tissue with a high level of methylation was the placenta. Our findings demonstrated that SCT methylation is a highly discriminative biomarker for lung and other malignant tumors, is less frequent in low-grade malignant tumors (including lung carcinoids), and appears at the carcinoma in situ stage. Copyright © 2015 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

TET2 binds the androgen receptor and loss is associated with prostate cancer

PubMed Central

Nickerson, ML; Das, S; Im, KM; Turan, S; Berndt, SI; Li, H; Lou, H; Brodie, SA; Billaud, JN; Zhang, T; Bouk, AJ; Butcher, D; Wang, Z; Sun, L; Misner, K; Tan, W; Esnakula, A; Esposito, D; Huang, WY; Hoover, RN; Tucker, MA; Keller, JR; Boland, J; Brown, K; Anderson, SK; Moore, LE; Isaacs, WB; Chanock, SJ; Yeager, M; Dean, M; Andresson, T

2016-01-01

Genetic alterations associated with prostate cancer (PCa) may be identified by sequencing metastatic tumor genomes to identify molecular markers at this lethal stage of disease. Previously, we characterized somatic alterations in metastatic tumors in the methylcytosine dioxygenase ten-eleven translocation 2 (TET2), which is altered in 5–15% of myeloid, kidney, colon and prostate cancers. Genome-wide association studies previously identified non-coding risk variants associated with PCa and melanoma. We performed fine-mapping of PCa risk across TET2 using genotypes from the PEGASUS case-control cohort and identified six new risk variants in introns 1 and 2. Oligonucleotides containing two risk variants were bound by the transcription factor octamer-binding protein 1 (Oct1/POU2F1) and TET2 and Oct1 expression were positively correlated in prostate tumors. TET2 is expressed in normal prostate tissue and reduced in a subset of tumors from the Cancer Genome Atlas (TCGA). Small interfering RNA (siRNA)-mediated TET2 knockdown (KD) increases LNCaP cell proliferation, migration, and wound healing, verifying loss drives a cancer phenotype. Endogenous TET2 bound the androgen receptor (AR) and AR-coactivator proteins in LNCaP cell extracts, and TET2 KD increases prostate-specific antigen (KLK3/PSA) expression. Published data reveal TET2 binding sites and hydroxymethylcytosine (hmC) proximal to KLK3. A gene co-expression network identified using TCGA prostate tumor RNA-sequencing identifies co-regulated cancer genes associated with 2-oxoglutarate (2-OG) and succinate metabolism, including TET2, lysine demethylase (KDM) KDM6A, BRCA1-associated BAP1, and citric acid cycle enzymes IDH1/2, SDHA/B, and FH. The co-expression signature is conserved across 31 TCGA cancers suggesting a putative role for TET2 as an energy sensor (of 2-OG) that modifies aspects of androgen-AR signaling. Decreased TET2 mRNA expression in TCGA PCa tumors is strongly associated with reduced patient survival

Concentrating Solar Power Projects - Power Tower Projects | Concentrating

Science.gov Websites

(CSP) projects that use power tower systems are listed below-alphabetically by project name. You can browse a project profile by clicking on the project name. You can also find related information on power Aurora Solar Energy Project Copiapó Crescent Dunes Solar Energy Project (Tonopah) Dahan Power Plant DEWA

Teaching children with autism to explain how: A case for problem solving?

PubMed

Frampton, Sarah E; Alice Shillingsburg, M

2018-04-01

Few studies have applied Skinner's (1953) conceptualization of problem solving to teach socially significant behaviors to individuals with developmental disabilities. The current study used a multiple probe design across behavior (sets) to evaluate the effects of problem-solving strategy training (PSST) on the target behavior of explaining how to complete familiar activities. During baseline, none of the three participants with autism spectrum disorder (ASD) could respond to the problems presented to them (i.e., explain how to do the activities). Tact training of the actions in each activity alone was ineffective; however, all participants demonstrated independent explaining-how following PSST. Further, following PSST with Set 1, tact training alone was sufficient for at least one scenario in sets 2 and 3 for all 3 participants. Results have implications for generative responding for individuals with ASD and further the discussion regarding the role of problem solving in complex verbal behavior. © 2018 Society for the Experimental Analysis of Behavior.

EEG: Elements of English Grammar: Rules Explained Simply. Workbook.

ERIC Educational Resources Information Center

Ratti, Marianne

This workbook is a supplement to Harold Van Winkle's "Elements of English Grammar: Rules Explained Simply," a book intended for self-instruction which presents the basic rules of standard English grammar in an easy-to-understand manner. The workbook's six chapters correspond to those in the book and contain exercises on: (1) The…

Creating Indices from the Control Structure Interview Through Data Collapsing and Multidimensional Scaling: Approaches to Data Analysis in Project MITT.

ERIC Educational Resources Information Center

Jovick, Thomas D.

This paper discribes the analysis of data in the Management Implications of Team Teaching Project (MITT). It touches on the interviews conducted with teachers and principals, presents the breadth of information obtained in the questionnaire, and explains how the data were aggregated and how issues were grouped. Information collected in the…

Ace Project as a Project Management Tool

ERIC Educational Resources Information Center

Cline, Melinda; Guynes, Carl S.; Simard, Karine

2010-01-01

The primary challenge of project management is to achieve the project goals and objectives while adhering to project constraints--usually scope, quality, time and budget. The secondary challenge is to optimize the allocation and integration of resources necessary to meet pre-defined objectives. Project management software provides an active…

UCSC Xena | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

UCSC Xena securely analyzes and visualizes your private functional genomics data set in the context of public and shared genomic/phenotypic data sets such as TCGA, ICGC, TARGET, GTEx, and GA4GH (TOIL).

Endometrial and acute myeloid leukemia cancer genomes characterized

Cancer.gov

Two studies from The Cancer Genome Atlas (TCGA) program reveal details about the genomic landscapes of acute myeloid leukemia (AML) and endometrial cancer. Both provide new insights into the molecular underpinnings of these cancers.

P06.19 TERT promoter mutation is an independent prognostic factor in 1p/19q co-deleted oligodendrogliomas: a POLA network study

PubMed Central

Alentorn, A.; Carpentier, C.; Labreche, K.; Ducray, F.; Dehais, C.; Mokhtari, K.; Uro-Coste, E.; Figarella-Branger, D.; Delattre, J.; Idbaih, A.

2016-01-01

Abstract Background: Overall, gliomas harboring 1p19q co-deletion (oligodendrogliomas in the future WHO classification) have better prognosis and better response to treatments compared to their non 1p/19q co-deleted counterparts. However, some of these tumors have disconcerting poor outcome. We have recently shown that chromosome arm 9p loss of heterozygosity (9pLOH) participates to identify some but not all oligodendrogliomas with an aggressive clinical behavior. In parallel, TERT promoter (TERTp) mutations have been recently described as the most frequent mutations in oligodendrogliomas. Objectives: We sought to study the potential clinical significance of TERTp mutational status in oligodendrogliomas. Material and methods: 224 anaplastic oligodendrogliomas (AO) from the POLA network, were included in the present study. TERT mutational status was obtained using Sanger sequencing and SNP-array. 121 lower grade gliomas exhibiting 1p/19q co-deletion, from the TCGA dataset, were used as the validation cohort. In this latter series, level of TERT expression, obtained by RNA-sequencing, was used as a surrogate marker of TERTp mutation. 1p/19q co-deletion was defined as loss of whole-chromosome arms 1p and 19q using allelic-specific copy number analysis. Overall survivals (OS) were compared using log-rank test in univariate analysis. All covariates with p-value < 0.2 were included in a Cox’s proportional hazard ratio model for multivariate analysis. Statistical tests were two-sided and p-values < 0.05 were interpreted as statistically significant. Results: TERTp was wild-type (wt) in 14/224 AO (6.25%) in POLA cohort and in 8/121 (6.6%) in TCGA dataset. TERTp wt is associated with poor OS in univariate analysis in POLA and TCGA cohorts (p=0.032 and p=0.035, respectively). Interestingly, after adjusting for allelic 9p LOH, age (<50 vs. ≥ 50 years), treatment (chemotherapy and radiotherapy versus other treatments) and WHO grade (II vs III), TERTp mutation was an

Decreased expression of serine protease inhibitor family G1 (SERPING1) in prostate cancer can help distinguish high-risk prostate cancer and predicts malignant progression.

PubMed

Peng, Shengmeng; Du, Tao; Wu, Wanhua; Chen, Xianju; Lai, Yiming; Zhu, Dingjun; Wang, Qiong; Ma, Xiaoming; Lin, Chunhao; Li, Zean; Guo, Zhenghui; Huang, Hai

2018-06-11

The aim of this study was to investigate the associations of serine proteinase inhibitor family G1 (SERPING1) down-regulation with poor prognosis in patients with prostate cancer (PCa). Furthermore, we aim to find more novel and effective PCa molecular markers to provide an early screening of PCa, distinguish patients with aggressive PCa, predict the prognosis, or reduce the economic burden of PCa. SERPING1 protein expression in both human PCa and normal prostate tissues was detected by immunohistochemical staining, which intensity was analyzed in association with clinical pathological parameters such Gleason score, pathological grade, clinical stage, tumor stage, lymph node metastasis, and distant metastasis. Moreover, we used The Cancer Genome Atlas (TCGA) Database, Taylor Database, and Oncomine dataset to validate our immunohistochemical results and investigated the value of SERPING1 in PCa at mRNA level. Kaplan-Meier analysis and Cox regression analysis were performed to evaluate the relationship between SERPING1 and prognosis of patients with PCa. The outcome showed that SERPING1 was expressed mainly in cytoplasm of grand cells of prostate tissue and was significantly expressed less in PCa (P<0.001). Furthermore, in the tissue microarray of our samples, decreasing expression of SERPING1 was correlated with the higher Gleason score (P = 0.004), the higher pathological grade (P = 0.01) and the advanced tumor stage (P = 0.005) at protein level. In TCGA dataset and Taylor Dataset, low-expressed SERPING1 was correlated with the younger patient (P = 0.02 in TCGA, P = 0.044 in Taylor) and the higher Gleason score (P = 0.019 in TCGA, P<0.001 in Taylor) at mRNA level. Kaplan-Meier analysis revealed that the lower mRNA of SERPING1 predicted lower overall survivals (P = 0.027 in TCGA), lower disease-free survival (P = 0.029) and lower biochemical recurrence-free survival (P = 0.011 in Taylor). Data from Oncomine database shown that SERPING1 low expression implying higher

The Impact of the Cancer Genome Atlas on Lung Cancer

PubMed Central

Chang, Jeremy Tzu-Huai; Lee, Yee-Ming; Huang, R. Stephanie

2015-01-01

The Cancer Genome Atlas (TCGA) has profiled over 10,000 samples derived from 33 types of cancer to date, with the goal of improving our understanding of the molecular basis of cancer and advancing our ability to diagnose, treat, and prevent cancer. This review focuses on lung cancer as it is the leading cause of cancer-related mortality worldwide in both men and women. Particularly, non-small cell lung cancers (including lung adenocarcinoma and lung squamous cell carcinoma) were evaluated. Our goal is to demonstrate the impact of TCGA on lung cancer research under four themes: namely, diagnostic markers, disease progression markers, novel therapeutic targets, and novel tools. Examples were given related to DNA mutation, copy number variation, mRNA, and microRNA expression along with methylation profiling. PMID:26318634

Explaining socioeconomic inequalities in exclusive breast feeding in Norway.

PubMed

Bærug, Anne; Laake, Petter; Løland, Beate Fossum; Tylleskär, Thorkild; Tufte, Elisabeth; Fretheim, Atle

2017-08-01

In high-income countries, lower socioeconomic position is associated with lower rates of breast feeding, but it is unclear what factors explain this inequality. Our objective was to examine the association between socioeconomic position and exclusive breast feeding, and to explore whether socioeconomic inequality in exclusive breast feeding could be explained by other sociodemographic characteristics, for example, maternal age and parity, smoking habits, birth characteristics, quality of counselling and breastfeeding difficulties. We used data from a questionnaire sent to mothers when their infants were five completed months as part of a trial of a breastfeeding intervention in Norway. We used maternal education as an indicator of socioeconomic position. Analyses of 1598 mother-infant pairs were conducted using logistic regression to assess explanatory factors of educational inequalities in breast feeding. Socioeconomic inequalities in exclusive breast feeding were present from the beginning and persisted for five completed months, when 22% of the most educated mothers exclusively breast fed compared with 7% of the least educated mothers: OR 3.39 (95% CI 1.74 to 6.61). After adjustment for all potentially explanatory factors, the OR was reduced to 1.49 (95% CI 0.70 to 3.14). This decrease in educational inequality seemed to be mainly driven by sociodemographic factors, smoking habits and breastfeeding difficulties, in particular perceived milk insufficiency. Socioeconomic inequalities in exclusive breast feeding at 5 months were largely explained by sociodemographic factors, but also by modifiable factors, such as smoking habits and breastfeeding difficulties, which can be amenable to public health interventions. NCT01025362. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Explaining the forest product selling behavior of private woodland owners

Treesearch

David N. Larsen; David A. Gansner; David A. Gansner

1973-01-01

A multiple-variable screening technique, AID, was used to explain the forest-product-sales behavior of private woodland owners. Results provide a basis for policy-related inferences and suggest an optimal strategy for encouraging sales of forest products.

Understanding Electrochemistry Concepts Using the Predict-Observe-Explain Strategy

ERIC Educational Resources Information Center

Karamustafaoglu, Sevilay; Mamlok-Naaman, Rachel

2015-01-01

The current study deals with freshman students who study at the Department of Science at the Faculty of Education. The aim of the study was to investigate the effect of teaching electrochemistry concepts using Predict-Observe-Explain (POE) strategy. The study was quasi-experimental design using 20 students each in the experimental group (EG) and…

Project Success in Agile Development Software Projects

ERIC Educational Resources Information Center

Farlik, John T.

2016-01-01

Project success has multiple definitions in the scholarly literature. Research has shown that some scholars and practitioners define project success as the completion of a project within schedule and within budget. Others consider a successful project as one in which the customer is satisfied with the product. This quantitative study was conducted…

An IS Project Management Course Project

ERIC Educational Resources Information Center

Frank, Ronald L.

2010-01-01

Information Systems curricula should provide project management (PM) theory, current practice, and hands-on experience. The schedule usually does not allow time in Analysis and Design courses for development oriented project management instruction other than a short introduction. Similarly, networking courses usually don't put project management…

Project Panama: An International Service Project

ERIC Educational Resources Information Center

Aydlett, Lydia; Randolph, Mickey; Wells, Gayle

2010-01-01

Participation in service learning projects is a growing phenomenon at universities and colleges. Research indicates service projects are beneficial for college students and adults. There is little data investigating developmental differences in how younger versus older participants perceive the service learning process. In this project, older…

Phase retrieval with the reverse projection method in the presence of object's scattering

NASA Astrophysics Data System (ADS)

Wang, Zhili; Gao, Kun; Wang, Dajiang

2017-08-01

X-ray grating interferometry can provide substantially increased contrast over traditional attenuation-based techniques in biomedical applications, and therefore novel and complementary information. Recently, special attention has been paid to quantitative phase retrieval in X-ray grating interferometry, which is mandatory to perform phase tomography, to achieve material identification, etc. An innovative approach, dubbed ;Reverse Projection; (RP), has been developed for quantitative phase retrieval. The RP method abandons grating scanning completely, and is thus advantageous in terms of higher efficiency and reduced radiation damage. Therefore, it is expected that this novel method would find its potential in preclinical and clinical implementations. Strictly speaking, the reverse projection method is applicable for objects exhibiting only absorption and refraction. In this contribution, we discuss the phase retrieval with the reverse projection method for general objects with absorption, refraction and scattering simultaneously. Especially, we investigate the influence of the object's scattering on the retrieved refraction signal. Both theoretical analysis and numerical experiments are performed. The results show that the retrieved refraction signal is the product of object's refraction and scattering signals for small values. In the case of a strong scattering, the reverse projection method cannot provide reliable phase retrieval. Those presented results will guide the use of the reverse projection method for future practical applications, and help to explain some possible artifacts in the retrieved images and/or reconstructed slices.

Explaining transgression in respiratory rate observation methods in the emergency department: A classic grounded theory analysis.

PubMed

Flenady, Tracy; Dwyer, Trudy; Applegarth, Judith

2017-09-01

Abnormal respiratory rates are one of the first indicators of clinical deterioration in emergency department(ED) patients. Despite the importance of respiratory rate observations, this vital sign is often inaccurately recorded on ED observation charts, compromising patient safety. Concurrently, there is a paucity of research reporting why this phenomenon occurs. To develop a substantive theory explaining ED registered nurses' reasoning when they miss or misreport respiratory rate observations. This research project employed a classic grounded theory analysis of qualitative data. Seventy-nine registered nurses currently working in EDs within Australia. Data collected included detailed responses from individual interviews and open-ended responses from an online questionnaire. Classic grounded theory (CGT) research methods were utilised, therefore coding was central to the abstraction of data and its reintegration as theory. Constant comparison synonymous with CGT methods were employed to code data. This approach facilitated the identification of the main concern of the participants and aided in the generation of theory explaining how the participants processed this issue. The main concern identified is that ED registered nurses do not believe that collecting an accurate respiratory rate for ALL patients at EVERY round of observations is a requirement, and yet organizational requirements often dictate that a value for the respiratory rate be included each time vital signs are collected. The theory 'Rationalising Transgression', explains how participants continually resolve this problem. The study found that despite feeling professionally conflicted, nurses often erroneously record respiratory rate observations, and then rationalise this behaviour by employing strategies that adjust the significance of the organisational requirement. These strategies include; Compensating, when nurses believe they are compensating for errant behaviour by enhancing the patient's outcome

Understanding Differences in Chemistry Climate Model Projections of Stratospheric Ozone

NASA Technical Reports Server (NTRS)

Douglass, A. R.; Strahan, S. E.; Oman, L. D.; Stolarski, R. S.

2014-01-01

Chemistry climate models (CCMs) are used to project future evolution of stratospheric ozone as concentrations of ozone-depleting substances (ODSs) decrease and greenhouse gases increase, cooling the stratosphere. CCM projections exhibit not only many common features but also a broad range of values for quantities such as year of ozone return to 1980 and global ozone level at the end of the 21st century. Multiple linear regression is applied to each of 14 CCMs to separate ozone response to ODS concentration change from that due to climate change. We show that the sensitivity of lower stratospheric ozone to chlorine change Delta Ozone/Delta inorganic chlorine is a near-linear function of partitioning of total inorganic chlorine into its reservoirs; both inorganic chlorine and its partitioning are largely controlled by lower stratospheric transport. CCMs with best performance on transport diagnostics agree with observations for chlorine reservoirs and produce similar ozone responses to chlorine change. After 2035, differences in Delta Ozone/Delta inorganic chlorine contribute little to the spread in CCM projections as the anthropogenic contribution to inorganic chlorine becomes unimportant. Differences among upper stratospheric ozone increases due to temperature decreases are explained by differences in ozone sensitivity to temperature change Delta Ozone/Delta T due to different contributions from various ozone loss processes, each with its own temperature dependence. Ozone decrease in the tropical lower stratosphere caused by a projected speedup in the Brewer-Dobson circulation may or may not be balanced by ozone increases in the middle- and high-latitude lower stratosphere and upper troposphere. This balance, or lack thereof, contributes most to the spread in late 21st century projections.

Body composition explains sex differential in physical performance among older adults.

PubMed

Tseng, Lisa A; Delmonico, Matthew J; Visser, Marjolein; Boudreau, Robert M; Goodpaster, Bret H; Schwartz, Ann V; Simonsick, Eleanor M; Satterfield, Suzanne; Harris, Tamara; Newman, Anne B

2014-01-01

Older women have higher percent body fat, poorer physical function, lower strength, and higher rates of nonfatal chronic conditions than men. We sought to determine whether these differences explained physical performance differences between men and women. Physical performance was assessed in the Health, Aging and Body Composition study in 2,863 men and women aged 70-79 with a composite 0-4 point score consisting of chair stands, standing balance including one-leg stand, and 6-m usual and narrow walk tests. Total body composition was measured by dual x-ray absorptiometry, thigh composition by computed tomography, and knee extensor strength by isokinetic dynamometer. Analysis of covariance estimated least square mean performance scores for men and women. Men had higher performance scores than women (least square means: 2.33±0.02 vs 2.03±0.02, p < .0001), adjusted for race, study site, age, and height. Body composition measures (total body fat and thigh muscle area, muscle density, subcutaneous fat, and intermuscular fat) accounted for differences between men and women (least square means: 2.15±0.02 vs 2.17±0.02, p = .53). Higher strength in men partly explained the sex difference (least square means: 2.28±0.02 vs 2.12±0.02, p < .0001). Strength attenuated the association of thigh muscle mass with performance. Chronic health conditions did not explain the sex difference. In a well-functioning cohort, poorer physical function in women compared with men can be explained predominantly by their higher fat mass, but also by other body composition differences. The higher proportion of body fat in women may put them at significant biomechanical disadvantage for greater disability in old age.

Potential targets for lung squamous cell carcinoma

Cancer.gov

Researchers have identified potential therapeutic targets in lung squamous cell carcinoma, the second most common form of lung cancer. The Cancer Genome Atlas (TCGA) Research Network study comprehensively characterized the lung squamous cell carcinoma gen

Concentrating Solar Power Projects - Godawari Solar Project | Concentrating

Science.gov Websites

Solar Power | NREL Godawari Solar Project This page provides information on Godawari Solar Project, a concentrating solar power (CSP) project, with data organized by background, participants, and power plant configuration. Status Date: February 13, 2014 Project Overview Project Name: Godawari Solar

Using Culture to Explain Behavior: An Integrative Cultural Approach

ERIC Educational Resources Information Center

Shepherd, Hana R.; Stephens, Nicole M.

2010-01-01

While savings rates among low-income families vary greatly, a 2008 National Poverty Center report finds that over 40 percent of low-income families fail to save any money. For decades policy makers and social scientists have sought to explain this phenomenon. Even after accounting for the fact that low-income families have less money to save, why…

Explaining Global Women's Empowerment Using Geographic Inquiry

ERIC Educational Resources Information Center

Grubbs, Melanie R.

2018-01-01

It is difficult for students who are just being introduced to major geographical concepts to understand how relatively free countries like India or Mali can have such high levels of human rights abuses as child brides, dowry deaths, and domestic violence. Textbooks explain it and video clips show examples, but it still seems surreal to teenagers…

Learning by Teaching: Implementation of a Multimedia Project in Astro 101

NASA Astrophysics Data System (ADS)

Perrodin, D.; Lommen, A.

2011-09-01

Astro 101 students have deep-seated pre-conceptions regarding such topics as the cause of moon phases or the seasons. Beyond exploring the topics in a learner-centered fashion, the "learning by teaching" philosophy enables students to truly master concepts. In order to make students teach the cause of moon phases, we created a multimedia project where groups of students taught other students and filmed the session. They were to produce a 10-minute final movie highlighting their teaching techniques and showing students in the process of learning the concepts. This "experiment" turned out to be a great success for a few reasons. First, students gained experience explaining conceptually-challenging topics, making them learn the material better. Additionally, they learned to apply learner-centered techniques, most likely learning to teach for the first time. Finally, this project provided the students a connection between the classroom and the rest of the college, making them responsible for applying and sharing their knowledge with their peers.

Variability in Temperature-Related Mortality Projections under Climate Change

PubMed Central

Benmarhnia, Tarik; Sottile, Marie-France; Plante, Céline; Brand, Allan; Casati, Barbara; Fournier, Michel

2014-01-01

Background: Most studies that have assessed impacts on mortality of future temperature increases have relied on a small number of simulations and have not addressed the variability and sources of uncertainty in their mortality projections. Objectives: We assessed the variability of temperature projections and dependent future mortality distributions, using a large panel of temperature simulations based on different climate models and emission scenarios. Methods: We used historical data from 1990 through 2007 for Montreal, Quebec, Canada, and Poisson regression models to estimate relative risks (RR) for daily nonaccidental mortality in association with three different daily temperature metrics (mean, minimum, and maximum temperature) during June through August. To estimate future numbers of deaths attributable to ambient temperatures and the uncertainty of the estimates, we used 32 different simulations of daily temperatures for June–August 2020–2037 derived from three global climate models (GCMs) and a Canadian regional climate model with three sets of RRs (one based on the observed historical data, and two on bootstrap samples that generated the 95% CI of the attributable number (AN) of deaths). We then used analysis of covariance to evaluate the influence of the simulation, the projected year, and the sets of RRs used to derive the attributable numbers of deaths. Results: We found that < 1% of the variability in the distributions of simulated temperature for June–August of 2020–2037 was explained by differences among the simulations. Estimated ANs for 2020–2037 ranged from 34 to 174 per summer (i.e., June–August). Most of the variability in mortality projections (38%) was related to the temperature–mortality RR used to estimate the ANs. Conclusions: The choice of the RR estimate for the association between temperature and mortality may be important to reduce uncertainty in mortality projections. Citation: Benmarhnia T, Sottile MF, Plante C, Brand A

Explaining Differences between Retrospective and Traditional Pretest Self-Assessments: Competing Theories and Empirical Evidence

ERIC Educational Resources Information Center

Nimon, Kim

2014-01-01

Summarizing theory and results of empirical research, this article serves to illustrate why effects measured with retrospective pretests may be subject to bias and may not always be explained by response shift theory. It presents three contending theories to explain the difference between retrospective and traditional pretest results and considers…

Interactive Explanations: The Functional Role of Gestural and Bodily Action for Explaining and Learning Scientific Concepts in Face-to-Face Arrangements

NASA Astrophysics Data System (ADS)

Scopelitis, Stephanie A.

As human beings, we live in, live with, and live through our bodies. And because of this it is no wonder that our hands and bodies are in motion as we interact with others in our world. Hands and body move as we give directions to another, anticipate which way to turn the screwdriver, and direct our friend to come sit next to us. Gestures, indeed, fill our everyday lives. The purpose of this study is to investigate the functional role of the body in the parts of our lives where we teach and learn with another. This project is an investigation into, what I call, "interactive explanations". I explore how the hands and body work toward the joint achievement of explanation and learning in face-to-face arrangements. The study aims to uncover how the body participates in teaching and learning in and across events as it slides between the multiple, interdependent roles of (1) a communicative entity, (2) a tool for thinking, and (3) a resource to shape interaction. Understanding gestures functional roles as flexible and diverse better explains how the body participates in teaching and learning interactions. The study further aims to show that these roles and functions are dynamic and changeable based on the interests, goals and contingencies of participants' changing roles and aims in interactions, and within and across events. I employed the methodology of comparative microanalysis of pairs of videotaped conversations in which, first, experts in STEM fields (Science, Technology, Engineering and Mathematics) explained concepts to non-experts, and second, these non-experts re-explained the concept to other non-experts. The principle finding is that people strategically, creatively and collaboratively employ the hands and body as vital and flexible resources for the joint achievement of explanation and understanding. Findings further show that gestures used to explain complex STEM concepts travel across time with the non-expert into re-explanations of the concept. My

Alterations of immune response of non-small cell lung cancer with Azacytidine

PubMed Central

Easwaran, Hariharan; Mohammad, Helai P.; Vendetti, Frank; VanCriekinge, Wim; DeMeyer, Tim; Du, Zhengzong; Parsana, Princy; Rodgers, Kristen; Yen, Ray-Whay; Zahnow, Cynthia A.; Taube, Janis M.; Brahmer, Julie R.; Tykodi, Scott S.; Easton, Keith; Carvajal, Richard D.; Jones, Peter A.; Laird, Peter W.; Weisenberger, Daniel J.; Tsai, Salina; Juergens, Rosalyn A.; Topalian, Suzanne L.; Rudin, Charles M.; Brock, Malcolm V.; Pardoll, Drew; Baylin, Stephen B.

2013-01-01

Innovative therapies are needed for advanced Non-Small Cell Lung Cancer (NSCLC). We have undertaken a genomics based, hypothesis driving, approach to query an emerging potential that epigenetic therapy may sensitize to immune checkpoint therapy targeting PD-L1/PD-1 interaction. NSCLC cell lines were treated with the DNA hypomethylating agent azacytidine (AZA – Vidaza) and genes and pathways altered were mapped by genome-wide expression and DNA methylation analyses. AZA-induced pathways were analyzed in The Cancer Genome Atlas (TCGA) project by mapping the derived gene signatures in hundreds of lung adeno (LUAD) and squamous cell carcinoma (LUSC) samples. AZA up-regulates genes and pathways related to both innate and adaptive immunity and genes related to immune evasion in a several NSCLC lines. DNA hypermethylation and low expression of IRF7, an interferon transcription factor, tracks with this signature particularly in LUSC. In concert with these events, AZA up-regulates PD-L1 transcripts and protein, a key ligand-mediator of immune tolerance. Analysis of TCGA samples demonstrates that a significant proportion of primary NSCLC have low expression of AZA-induced immune genes, including PD-L1. We hypothesize that epigenetic therapy combined with blockade of immune checkpoints – in particular the PD-1/PD-L1 pathway – may augment response of NSCLC by shifting the balance between immune activation and immune inhibition, particularly in a subset of NSCLC with low expression of these pathways. Our studies define a biomarker strategy for response in a recently initiated trial to examine the potential of epigenetic therapy to sensitize patients with NSCLC to PD-1 immune checkpoint blockade. PMID:24162015

Similar Squamous Cell Carcinoma Epithelium microRNA Expression in Never Smokers and Ever Smokers

PubMed Central

Kolokythas, Antonia; Zhou, Yalu; Schwartz, Joel L.; Adami, Guy R.

2015-01-01

The incidence of oral tumors in patients who never used mutagenic agents such as tobacco is increasing. In an effort to better understand these tumors we studied microRNA (miRNA) expression in tumor epithelium of never tobacco users, tumor epithelium of ever tobacco users, and nonpathological control oral epithelium. A comparison of levels among 372 miRNAs in 12 never tobacco users with oral squamous cell carcinoma (OSCC) versus 10 healthy controls was made using the reverse transcription quantitative polymerase chain reaction. A similar analysis was done with 8 ever tobacco users with OSCC. These comparisons revealed miR-10b-5p, miR-196a-5p, and miR-31-5p as enriched in the tumor epithelium in OSCC of both never and ever tobacco users. Examination of The Cancer Genome Atlas (TCGA) project miRNA data on 305 OSCCs and 30 controls revealed 100% of those miRNAs enriched in never smoker OSCCs in this patient group were also enriched in ever smoker OSCCs. Nonsupervised clustering of TCGA OSCCs was suggestive of two or four subgroups of tumors based on miRNA levels with limited evidence for differences in tobacco exposure among the groups. Results from both patient groups together stress the importance of miR196a-5p in OSCC malignancy in both never and ever smokers, and emphasize the overall similarity of miRNA expression in OSCCs in these two risk groups. It implies that there may be great similarity in etiology of OSCC in never and ever smokers and that classifying OSCC based on tobacco exposure may not be helpful in the clinic. PMID:26544609

Quality Assurance Project Plan for Citizen Science Projects

EPA Pesticide Factsheets

The Quality Assurance Project Plan is necessary for every project that collects or uses environmental data. It documents the project planning process and serves as a blueprint for how your project will run.

Do executive functions explain the covariance between internalizing and externalizing behaviors?

PubMed

Hatoum, Alexander S; Rhee, Soo Hyun; Corley, Robin P; Hewitt, John K; Friedman, Naomi P

2017-11-16

This study examined whether executive functions (EFs) might be common features of internalizing and externalizing behavior problems across development. We examined relations between three EF latent variables (a common EF factor and factors specific to updating working memory and shifting sets), constructed from nine laboratory tasks administered at age 17, to latent growth intercept (capturing stability) and slope (capturing change) factors of teacher- and parent-reported internalizing and externalizing behaviors in 885 individual twins aged 7 to 16 years. We then estimated the proportion of intercept-intercept and slope-slope correlations predicted by EF as well as the association between EFs and a common psychopathology factor (P factor) estimated from all 9 years of internalizing and externalizing measures. Common EF was negatively associated with the intercepts of teacher-rated internalizing and externalizing behavior in males, and explained 32% of their covariance; in the P factor model, common EF was associated with the P factor in males. Shifting-specific was positively associated with the externalizing slope across sex. EFs did not explain covariation between parent-rated behaviors. These results suggest that EFs are associated with stable problem behavior variation, explain small proportions of covariance, and are a risk factor that that may depend on gender.

Projective-anticipating, projective, and projective-lag synchronization of time-delayed chaotic systems on random networks.

PubMed

Feng, Cun-Fang; Xu, Xin-Jian; Wang, Sheng-Jun; Wang, Ying-Hai

2008-06-01

We study projective-anticipating, projective, and projective-lag synchronization of time-delayed chaotic systems on random networks. We relax some limitations of previous work, where projective-anticipating and projective-lag synchronization can be achieved only on two coupled chaotic systems. In this paper, we realize projective-anticipating and projective-lag synchronization on complex dynamical networks composed of a large number of interconnected components. At the same time, although previous work studied projective synchronization on complex dynamical networks, the dynamics of the nodes are coupled partially linear chaotic systems. In this paper, the dynamics of the nodes of the complex networks are time-delayed chaotic systems without the limitation of the partial linearity. Based on the Lyapunov stability theory, we suggest a generic method to achieve the projective-anticipating, projective, and projective-lag synchronization of time-delayed chaotic systems on random dynamical networks, and we find both its existence and sufficient stability conditions. The validity of the proposed method is demonstrated and verified by examining specific examples using Ikeda and Mackey-Glass systems on Erdos-Renyi networks.

Properties of glass, oil's formation...how to explain it? The secret is to amaze!

NASA Astrophysics Data System (ADS)

Merlino, Silvia; Evangelista, Rosaria; Bianucci, Marco; Mantovani, Carlo; Gambarelli, Licia

2013-04-01

The design and testing of numerous routes for teaching and dissemination of topics in physics, biology, geology and energy is born from a collaboration between teachers and researchers that lasted for many years in Parma, Italy. These projects are implemented by the association "Parma Casa della Scienza", which promotes the dissemination of scientific culture in schools and among the public. The main purpose of the association is to create a science center in Parma, offering also training opportunities on techniques for teaching science. The funds for the projects come from European competitions and Cariparma Foundation. Currently the association is proposing laboratory activities, with the widespread diffusion of 20 educational programs, included in school curricula. The approach is informal and aims at the stimulation of curiosity and surprise. Students who participate arise so spontaneously in an attitude of research - action, working directly on the phenomena under study. This avoids the clichés of standard passive listening. Our work is a constant search for ideas, ways and means to demonstrate, for the purposes of school education, how useful is the game and the interaction with the phenomena, many of which are usually only seen in books and not lived with awareness. Two in particular are the educational proposals that we would like to present , relating to content of great importance that are rarely addressed in the context of schooling completed First Path: explains the physico-chemical properties and structural properties of glassy materials; enters the details of the molecular structure of "amorphous solid" contrasting it with that of crystalline solid; llustrates the process of formation; gives reason for its peculiar properties from which derive extreme flexibility of working and the many optical properties. This is achieved through the actual processing of a fluid "pseudo glassy" realized at low temperatures, which simulates the processes described

Network image data bank prototype: the RSI project (Resume de Sortie Images)

NASA Astrophysics Data System (ADS)

Abouchi, Nacer; Jourlin, Michel; Bohbot, Oriana; Faurie, Catherine; Grisel, Richard

1995-02-01

The Hospital Edouard Herriot in Lyon and 3M company, associated with the Electronic Department of Physics Chimics and Electronic Engineering School (CPE), decided in 1993 to begin a study on a project of image network. This project is composed of many practical applications to be checked one by one. The purpose of this paper is to discuss the context, which is kind of small picture archiving and communication system (PACS), to explain the methodology which has been used related to hardware and software implementation, and to give examples of the first results obtained. One of the main interests of the results is the possibility to obtain on the same support, 3M laser imager, a film including images from different modalities and abstract summing up the patient stay in the hospital. The framework used is built around Omnis7 and C++ language on a PC computer.

Communicating mega-projects in the face of uncertainties: Israeli mass media treatment of the Dead Sea Water Canal.

PubMed

Fischhendler, Itay; Cohen-Blankshtain, Galit; Shuali, Yoav; Boykoff, Max

2015-10-01

Given the potential for uncertainties to influence mega-projects, this study examines how mega-projects are deliberated in the public arena. The paper traces the strategies used to promote the Dead Sea Water Canal. Findings show that the Dead Sea mega-project was encumbered by ample uncertainties. Treatment of uncertainties in early coverage was dominated by economics and raised primarily by politicians, while more contemporary media discourses have been dominated by ecological uncertainties voiced by environmental non-governmental organizations. This change in uncertainty type is explained by the changing nature of the project and by shifts in societal values over time. The study also reveals that 'uncertainty reduction' and to a lesser degree, 'project cancellation', are still the strategies most often used to address uncertainties. Statistical analysis indicates that although uncertainties and strategies are significantly correlated, there may be other intervening variables that affect this correlation. This research also therefore contributes to wider and ongoing considerations of uncertainty in the public arena through various media representational practices. © The Author(s) 2013.

A common stochastic accumulator with effector-dependent noise can explain eye-hand coordination

PubMed Central

Gopal, Atul; Viswanathan, Pooja

2015-01-01

The computational architecture that enables the flexible coupling between otherwise independent eye and hand effector systems is not understood. By using a drift diffusion framework, in which variability of the reaction time (RT) distribution scales with mean RT, we tested the ability of a common stochastic accumulator to explain eye-hand coordination. Using a combination of behavior, computational modeling and electromyography, we show how a single stochastic accumulator to threshold, followed by noisy effector-dependent delays, explains eye-hand RT distributions and their correlation, while an alternate independent, interactive eye and hand accumulator model does not. Interestingly, the common accumulator model did not explain the RT distributions of the same subjects when they made eye and hand movements in isolation. Taken together, these data suggest that a dedicated circuit underlies coordinated eye-hand planning. PMID:25568161

The BioMedical Evidence Graph (BMEG) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The BMEG is a Cancer Data integration Platform that utilizes methods collected from DREAM challenges and applied to large datasets, such as the TCGA, and makes them avalible for analysis using a high performance graph database

Distinction of Concept and Discussion on Construction Idea of Smart Water Grid Project

NASA Astrophysics Data System (ADS)

Ye, Y.; Yizi, S., Sr.; Lili, L., Sr.; Sang, X.; Zhai, J.

2016-12-01

Smart water grid project includes construction of water physical grid consisting of various flow regulating infrastructures, construction of water information grid in line with the trend of intelligent technology and construction of water management grid featured by system & mechanism construction and systemization of regulation decision-making. It is the integrated platform and comprehensive carrier for water conservancy practices. Currently, there still is dispute over engineering construction idea of smart water grid which, however, represents the future development trend of water management and is increasingly emphasized. The paper, based on distinction of concept of water grid and water grid engineering, explains the concept of water grid intelligentization, actively probes into construction idea of Smart water grid project in our country and presents scientific problems to be solved as well as core technologies to be mastered for smart water grid construction.

Factors that Explain the Cancer-Related Insomnia.

PubMed

Galiano-Castillo, Noelia; Arroyo-Morales, Manuel; Ariza-Garcia, Angélica; Fernández-Lao, Carolina; Fernández-Fernández, Andrés J; Cantarero-Villanueva, Irene

2017-07-01

A better understanding of cancer related insomnia and its relationship with other associated factors is necessary to improve its management. To clarify the relationship between insomnia and treatment related variables, sociodemographic data, health related fitness, pain, anxiety, and depression in breast cancer patients. One hundred twenty-three patients participated in this cross-sectional study. As a primary variable was insomnia using The European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core 30 version. Other variables included: stage of treatment, type of treatment, multiple sit to stand test, trunk curl test, 6-min walk test, back muscle strength test, the Brief Pain Inventory short form and the Hospital Anxiety and Depression Scale. Insomnia was negatively associated with the treatment stage (p = 0.01), the 6-min walk test (p = 0.01) and the back muscle strength test (p = 0.01), while it was positively associated with the type of treatment (p = 0.01) and the multiple sit-to-stand test (p = 0.05). In addition, higher levels of insomnia were associated with higher scores on the Brief Pain Inventory short form (p = 0.01) and the Hospital Anxiety and Depression Scale (p = 0.01). Anxiety, type of treatment, back muscle strength, pain severity and stage of treatment were predictors of insomnia, and when they were combined they explained 51.2% of insomnia in our sample. The variability in insomnia related breast cancer is explained by anxiety, type of treatment, pain, treatment stage, and back muscle strength. Clinicians should take these results into account when generating cancer care programs to control pain and health-related-fitness (Registration of Trials NCT01801527). © 2017 Wiley Periodicals, Inc.

Explaining the R_K and R_{K^*} anomalies

NASA Astrophysics Data System (ADS)

Ghosh, Diptimoy

2017-10-01

Recent LHCb results on R_{K^*}, the ratio of the branching fractions of B → K^* μ ^+ μ ^- to that of B → K^* e^+ e^-, for the dilepton invariant mass bins q^2 ≡ m_{ℓ ℓ }^2 = [0.045-1.1] GeV^2 and [1.1-6] GeV^2 show approximately 2.5 σ deviations from the corresponding Standard Model prediction in each of the bins. This, when combined with the measurement of R_K (q^2=[1-6] GeV^2), a similar ratio for the decay to a pseudo-scalar meson, highly suggests lepton non-universal new physics in semi-leptonic B meson decays. In this work, we perform a model independent analysis of these potential new physics signals and identify the operators that do the best job in satisfying all these measurements. We show that heavy new physics, giving rise to q^2 independent local 4-Fermi operators of scalar, pseudo-scalar, vector or axial-vector type, is unable to explain all the three measurements simultaneously, in particular R_{K^*} in the bin [0.045-1.1], within their experimental 1σ regions. We point out the possibility to explain R_{K^*} in the low bin by an additional light (≲ 20 {MeV}) vector boson with appropriate coupling strengths to (\\bar{b} s) and (\\bar{e} e).

Organ Donation European Quality System: ODEQUS project methodology.

PubMed

Manyalich, M; Guasch, X; Gomez, M P; Páez, G; Teixeira, L

2013-01-01

Differences in the number of organ donors among hospitals cannot be explained only by the number of intensive care unit beds used or neurologic patients treated. The figures obtained are influenced by the organizational structure of the donation process and how efficient it is. The Organ Donation European Quality System (ODEQUS) is a 3-year project (from October 2010 to September 2013) co-financed by the European Agency for Health and Consumers (EAHC20091108) which aims to define a methodology to evaluate organ procurement performance at the hospital level. ODEQUS's specific objectives are to identify quality criteria and to develop quality indicators in three types of organ donation (after brain death, after cardiac death, and living donation). Those tools will be useful for hospitals' self-assessment as well as for developing an international auditing model. A consortium has been established involving 14 associated partners from Austria, Croatia, France, Germany, Italy, Poland, Portugal, Romania, Spain, Sweden, and the United Kingdom, as well as five collaborating partners from Greece, Hungary, Malta, Slovenia, and Turkey. The project has been established in three steps: 1) Design of a survey about the use of quality tools in a wide sample of European hospitals; 2) Development of quality criteria and quality indicators by the project experts. The main fields considered have been organizational structures, clinical procedures, and outcomes; and 3) Elaboration of an evaluation system to test the quality indicators in 11 European hospitals. Two types of training have been designed and performed: one concerns the development of quality criteria and quality indicators, whereas another is focused on how to use evaluation tools. Following this methodology, the project has so far identified 131 quality criteria and developed 31 quality indicators. Currently, the quality indicators are being tested in 11 selected hospitals. Copyright © 2013 Elsevier Inc. All rights

A balanced motor primitive framework can simultaneously explain motor learning in unimanual and bimanual movements.

PubMed

Takiyama, Ken; Sakai, Yutaka

2017-02-01

Certain theoretical frameworks have successfully explained motor learning in either unimanual or bimanual movements. However, no single theoretical framework can comprehensively explain motor learning in both types of movement because the relationship between these two types of movement remains unclear. Although our recent model of a balanced motor primitive framework attempted to simultaneously explain motor learning in unimanual and bimanual movements, this model focused only on a limited subset of bimanual movements and therefore did not elucidate the relationships between unimanual movements and various bimanual movements. Here, we extend the balanced motor primitive framework to simultaneously explain motor learning in unimanual and various bimanual movements as well as the transfer of learning effects between unimanual and various bimanual movements; these phenomena can be simultaneously explained if the mean activity of each primitive for various unimanual movements is balanced with the corresponding mean activity for various bimanual movements. Using this balanced condition, we can reproduce the results of prior behavioral and neurophysiological experiments. Furthermore, we demonstrate that the balanced condition can be implemented in a simple neural network model. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Synchronous population dynamics in California butterflies explained by climatic forcing

PubMed Central

Shapiro, Arthur M.

2017-01-01

A long-standing challenge for population biology has been to understand why some species are characterized by populations that fluctuate in size independently, while populations of other species fluctuate synchronously across space. The effects of climatic variation and dispersal have been invoked to explain synchronous population dynamics, however an understanding of the relative influence of these drivers in natural populations is lacking. Here we compare support for dispersal- versus climate-driven models of interspecific variation in synchrony using 27 years of observations of 65 butterfly species at 10 sites spanning 2750 m of elevation in Northern California. The degree of spatial synchrony exhibited by each butterfly species was used as a response in a unique approach that allowed us to investigate whether interspecific variation in response to climate or dispersal propensity was most predictive of interspecific variation in synchrony. We report that variation in sensitivity to climate explained 50% of interspecific variation in synchrony, whereas variation in dispersal propensity explained 23%. Sensitivity to the El Niño Southern Oscillation, a primary driver of regional climate, was the best predictor of synchrony. Combining sensitivity to climate and dispersal propensity into a single model did not greatly increase model performance, confirming the primacy of climatic sensitivity for driving spatial synchrony in butterflies. Finally, we uncovered a relationship between spatial synchrony and population decline that is consistent with theory, but small in magnitude, which suggests that the degree to which populations fluctuate in synchrony is of limited use for understanding the ongoing decline of the Northern California butterfly fauna. PMID:28791146

[Quality analysis of the statistical used resources (material and methods section) in thesis projects of a university department].

PubMed

Regojo Zapata, O; Lamata Hernández, F; Sánchez Zalabardo, J M; Elizalde Benito, A; Navarro Gil, J; Valdivia Uría, J G

2004-09-01

Studies about quality in thesis and investigation projects in biomedical sciences are unusual, but very important in university teaching because is necessary to improve the quality elaboration of the thesis. The objectives the study were to determine the project's quality of thesis in our department, according to the fulfillment of the scientific methodology and to establish, if it exists, a relation between the global quality of the project and the statistical used resources. Descriptive study of 273 thesis projects performed between 1995-2002 in surgery department of the Zaragoza University. The review realized for 15 observers that they analyzed 28 indicators of every project. Giving a value to each of the indicators, the projects qualified in a scale from 1 to 10 according to the quality in the fulfillment of the scientific methodology. The mean of the project's quality was 5.53 (D.E: 1.77). In 13.9% the thesis projects was concluded with the reading of the work. The three indicators of statistical used resources had a significant difference with the value of the quality projects. The quality of the statistical resources is very important when a project of thesis wants to be realized by good methodology, because it assures to come to certain conclusions. In our study we have thought that more of the third part of the variability in the quality of the project of thesis explains for three statistical above-mentioned articles.

Project-Based Teaching: Helping Students Make Project Connections

NASA Astrophysics Data System (ADS)

Johnson, Heather Jo Pusich

Project-based curriculum materials are designed to support students in engaging with scientific content and practices in meaningful ways, with the goal of improving students' science learning. However, students need to understand the connections between what they are doing on a day-to-day basis with respect to the goals of the overall project for students to get the motivational and cognitive benefits of a project-based approach. In this dissertation, I looked at the challenges that four ninth grade science teachers faced as they helped students to make these connections using a project-based environmental science curriculum. The analysis revealed that in general when the curriculum materials made connections explicit, teachers were better able to articulate the relationship between the lesson and the project during enactment. However, whether the connections were explicit or implicit in the materials, enactments of the same lesson across teachers revealed that teachers leveraged different aspects of the project context in different ways depending on their knowledge, beliefs, and goals about project-based teaching. The quantitative analysis of student data indicated that when teacher enactments supported project goals explicitly, students made stronger connections between a lesson and the project goal. Therefore, a teacher's ability to make clear connections during classroom instruction is essential. Furthermore, when students made connections between each lesson and the larger project goals their attitudes toward the lesson were more positive and they performed better on the final assessment. These findings suggest that connections between individual lessons and the goals of the project are critical to the effectiveness of project-based learning. This study highlights that while some teachers were able to forge these connections successfully as a result of leveraging cognitive resources, teachers' beliefs, knowledge and goals about project-based teaching are

Explaining ethnic disparities in lung function among young adults: A pilot investigation

PubMed Central

Patel, Jaymini; Minelli, Cosetta; Burney, Peter G. J.

2017-01-01

Background Ethnic disparities in lung function have been linked mainly to anthropometric factors but have not been fully explained. We conducted a cross-sectional pilot study to investigate how best to study ethnic differences in lung function in young adults and evaluate whether these could be explained by birth weight and socio-economic factors. Methods We recruited 112 university students of White and South Asian British ethnicity, measured post-bronchodilator lung function, obtained information on respiratory symptoms and socio-economic factors through questionnaires, and acquired birth weight through data linkage. We regressed lung function against ethnicity and candidate predictors defined a priori using linear regression, and used penalised regression to examine a wider range of factors. We reviewed the implications of our findings for the feasibility of a larger study. Results There was a similar parental socio-economic environment and no difference in birth weight between the two ethnic groups, but the ethnic difference in FVC adjusted for sex, age, height, demi-span, father’s occupation, birth weight, maternal educational attainment and maternal upbringing was 0.81L (95%CI: -1.01 to -0.54L). Difference in body proportions did not explain the ethnic differences although parental immigration was an important predictor of FVC independent of ethnic group. Participants were comfortable with study procedures and we were able to link birth weight data to clinical measurements. Conclusion Studies of ethnic disparities in lung function among young adults are feasible. Future studies should recruit a socially more diverse sample and investigate the role of markers of acculturation in explaining such differences. PMID:28575113

Mediating Factors Explaining the Association Between Sexual Minority Status and Dating Violence.

PubMed

Martin-Storey, Alexa; Fromme, Kim

2017-08-01

Dating violence presents a serious threat for individual health and well-being. A growing body of literature suggests that starting in adolescence, individuals with sexual minority identities (e.g., individuals who identify as gay, lesbian, or bisexual) may be at an increased risk for dating violence compared with heterosexuals. Research has not, however, identified the mechanisms that explain this vulnerability. Using a diverse sample of young adults ( n = 2,474), the current study explored how minority stress theory, revictimization theory, sex of sexual partners, and risky sexual behavior explained differences in dating violence between sexual minority and heterosexual young adults. Initial analyses suggested higher rates of dating violence among individuals who identified as bisexual, and individuals who identified as gay or lesbian when compared with heterosexuals, and further found that these associations failed to differ across gender. When mediating and control variables were included in the analyses, however, the association between both sexual minority identities and higher levels of dating violence became nonsignificant. Of particular interest was the role of discrimination, which mediated the association between bisexual identity and dating violence. Other factors, including sex and number of sexual partners, alcohol use, and childhood maltreatment, were associated with higher rates of dating violence but did not significantly explain vulnerability among sexual minority individuals compared with their heterosexual peers. These findings suggest the importance of minority stress theory in explaining vulnerability to dating violence victimization among bisexuals in particular, and generally support the importance of sexual-minority specific variables in understanding risk for dating violence within this vulnerable population.

Concentrating Solar Power Projects - Parabolic Trough Projects |

Science.gov Websites

Project Godawari Solar Project Gujarat Solar One Gulang 100MW Thermal Oil Parabolic Trough project Guzmán Kuraymat (ISCC Kuraymat) Kathu Solar Park KaXu Solar One KVK Energy Solar Project La Africana La Dehesa La Power Facility Nevada Solar One (NSO) NOOR I NOOR II Olivenza 1 Orellana Palma del Río I Palma del Río

An improved optimization algorithm and Bayes factor termination criterion for sequential projection pursuit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Webb-Robertson, Bobbie-Jo M.; Jarman, Kristin H.; Harvey, Scott D.

2005-05-28

A fundamental problem in analysis of highly multivariate spectral or chromatographic data is reduction of dimensionality. Principal components analysis (PCA), concerned with explaining the variance-covariance structure of the data, is a commonly used approach to dimension reduction. Recently an attractive alternative to PCA, sequential projection pursuit (SPP), has been introduced. Designed to elicit clustering tendencies in the data, SPP may be more appropriate when performing clustering or classification analysis. However, the existing genetic algorithm (GA) implementation of SPP has two shortcomings, computation time and inability to determine the number of factors necessary to explain the majority of the structure inmore » the data. We address both these shortcomings. First, we introduce a new SPP algorithm, a random scan sampling algorithm (RSSA), that significantly reduces computation time. We compare the computational burden of the RSS and GA implementation for SPP on a dataset containing Raman spectra of twelve organic compounds. Second, we propose a Bayes factor criterion, BFC, as an effective measure for selecting the number of factors needed to explain the majority of the structure in the data. We compare SPP to PCA on two datasets varying in type, size, and difficulty; in both cases SPP achieves a higher accuracy with a lower number of latent variables.« less

PISA and High-Performing Education Systems: Explaining Singapore's Education Success

ERIC Educational Resources Information Center

Deng, Zongyi; Gopinathan, S.

2016-01-01

Singapore's remarkable performance in Programme for International Student Assessment (PISA) has placed it among the world's high-performing education systems (HPES). In the literature on HPES, its "secret formula" for education success is explained in terms of teacher quality, school leadership, system characteristics and educational…

Adapting Project Management Practices to Research-Based Projects

NASA Technical Reports Server (NTRS)

Bahr, P.; Baker, T.; Corbin, B.; Keith, L.; Loerch, L.; Mullenax, C.; Myers, R.; Rhodes, B.; Skytland, N.

2007-01-01

From dealing with the inherent uncertainties in outcomes of scientific research to the lack of applicability of current NASA Procedural Requirements guidance documentation, research-based projects present challenges that require unique application of classical project management techniques. If additionally challenged by the creation of a new program transitioning from basic to applied research in a technical environment often unfamiliar with the cost and schedule constraints addressed by project management practices, such projects can find themselves struggling throughout their life cycles. Finally, supplying deliverables to a prime vehicle customer, also in the formative stage, adds further complexity to the development and management of research-based projects. The Biomedical Research and Countermeasures Projects Branch at NASA Johnson Space Center encompasses several diverse applied research-based or research-enabling projects within the newly-formed Human Research Program. This presentation will provide a brief overview of the organizational structure and environment in which these projects operate and how the projects coordinate to address and manage technical requirements. We will identify several of the challenges (cost, technical, schedule, and personnel) encountered by projects across the Branch, present case reports of actions taken and techniques implemented to deal with these challenges, and then close the session with an open forum discussion of remaining challenges and potential mitigations.

Uncertainty in Arctic hydrology projections and the permafrost-carbon feedback

NASA Astrophysics Data System (ADS)

Andresen, C. G.; Lawrence, D. M.; Wilson, C. J.; McGuire, D.

2017-12-01

Projected warming is expected to thaw permafrost soils and deepen the permafrost active layer. These changes will affect surface hydrological conditions. Since the soil hydrologic state exerts a strong influence on the rate and pathway of soil organic matter decomposition into CO2 or CH4, there is a strong need to examine and better understand model projections of hydrologic change and how differences in process representation affect projections of wetting and/or drying of changing permafrost landscapes. This study aims to advance understanding of where, when and why arctic will become wetter or drier. We assessed simulations from 8 "permafrost enabled" land models that were run in offline mode from 1960 to 2299 forced with the same projected climate for a high-emissions scenario. Climate models project increased precipitation (P) across most of the Arctic domain and the land models indicate that runoff and evapotranspiration (ET) will also both increase. In general, the water input to the soil (P-ET) also increases, but the models project a contradicting long-term drying of the surface soil. The surface drying in the models can generally be explained by filtration of moisture to deeper soil layers as the active layer deepens or by increased sub-surface drainage where permafrost in a grid cell thaws completely. Though, there is a qualitative agreement in this type of response across the models, the projections vary dramatically in magnitude. Variability among simulations is largely attributed to parameterization and structural differences across the participating models, particularly the diverse representations of evapotranspiration, water table and soil water storage and transmission. A limited set of results from single forcing experiments suggests that the warming effect in the sensitivity analysis was the principal driver of soil drying while CO2 and precipitation effects had a small wetting influence. When compared to observational data, simulations tend to

The CHPRC Columbia River Protection Project Quality Assurance Project Plan

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fix, N. J.

Pacific Northwest National Laboratory researchers are working on the CHPRC Columbia River Protection Project (hereafter referred to as the Columbia River Project). This is a follow-on project, funded by CH2M Hill Plateau Remediation Company, LLC (CHPRC), to the Fluor Hanford, Inc. Columbia River Protection Project. The work scope consists of a number of CHPRC funded, related projects that are managed under a master project (project number 55109). All contract releases associated with the Fluor Hanford Columbia River Project (Fluor Hanford, Inc. Contract 27647) and the CHPRC Columbia River Project (Contract 36402) will be collected under this master project. Each projectmore » within the master project is authorized by a CHPRC contract release that contains the project-specific statement of work. This Quality Assurance Project Plan provides the quality assurance requirements and processes that will be followed by the Columbia River Project staff.« less

How to explain variations in sea cliff erosion rate?

NASA Astrophysics Data System (ADS)

Prémaillon, Melody; Regard, Vincent; Dewez, Thomas

2017-04-01

Every rocky coast of the world is eroding at different rate (cliff retreat rates). Erosion is caused by a complex interaction of multiple sea weather factors. While numerous local studies exist and explain erosion processes on specific sites, global studies lack. We started to compile many of those local studies and analyse their results with a global point of view in order to quantify the various parameters influencing erosion rates. In other words: is erosion more important in energetic seas? Are chalk cliff eroding faster in rainy environment? etc. In order to do this, we built a database based on literature and national erosion databases. It now contains 80 publications which represents 2500 cliffs studied and more than 3500 erosion rate estimates. A statistical analysis was conducted on this database. On a first approximation, cliff lithology is the only clear signal explaining erosion rate variation: hard lithologies are eroding at 1cm/y or less, whereas unconsolidated lithologies commonly erode faster than 10cm/y. No clear statistical relation were found between erosion rate and external parameters such as sea energy (swell, tide) or weather condition, even on cliff with similar lithology.

Epigenetics and obesity: a relationship waiting to be explained.

PubMed

Symonds, Michael E; Budge, Helen; Frazier-Wood, Alexis C

2013-01-01

Obesity can have multifactorial causes that may change with development and are not simply attributable to one's genetic constitution. To date, expensive and laborious genome-wide association studies have only ascribed a small contribution of genetic variants to obesity. The emergence of the field of epigenetics now offers a new paradigm with which to study excess fat mass. Currently, however, there are no compelling epigenetic studies to explain the role of epigenetics in obesity, especially from a developmental perspective. It is clear that until there are advances in the understanding of the main mechanisms by which different fat types, i.e. brown, beige, and white, are established and how these differ between depots and species, population-based studies designed to determine specific aspects of epigenetics will be potentially limited. Obesity is a slowly evolving condition that is not simply explained by changes in the intake of one macronutrient. The latest advances in epigenetics, coupled with the establishment of relevant longitudinal models of obesity, which incorporate functionally relevant end points, may now permit the precise contribution of epigenetic modifications to excess fat mass to be effectively studied. © 2013 S. Karger AG, Basel.

Explaining the footsteps, belly dancer, Wenceslas, and kickback illusions.

PubMed

Howe, Piers D L; Thompson, Peter G; Anstis, Stuart M; Sagreiya, Hersh; Livingstone, Margaret S

2006-12-12

The footsteps illusion (FI) demonstrates that an object's background can have a profound effect on the object's perceived speed. This illusion consists of a yellow bar and a blue bar that move over a black-and-white, striped background. Although the bars move at a constant rate, they appear to repeatedly accelerate and decelerate in antiphase with each other. Previously, this illusion has been explained in terms of the variations in contrast at the leading and trailing edges of the bars that occur as the bars traverse the striped background. Here, we show that this explanation is inadequate and instead propose that for each bar, the bar's leading edge, trailing edge, lateral edges, and the surrounding background edges all contribute to the bar's perceived speed and that the degree to which each edge contributes to the motion percept is determined by that edge's contrast. We show that this theory can explain all the data on the FI as well as the belly dancer and Wenceslas illusions. We conclude by presenting a new illusion, the kickback illusion, which, although geometrically similar to the FI, is mediated by a different mechanism, namely, reverse phi motion.

Uncertainties in Navigation of Elderly People in Towns - the Assistant Project

NASA Astrophysics Data System (ADS)

Kainz, W.; Kalian, K.

2013-05-01

The ASSISTANT project contributes to maintaining the mobility of older people in Europe, in order to safeguard their social and economic participation in an increasingly ageing society. It does this by helping them to travel safely and independently by public transport. This three-year project develops an application for the home PC and smartphone that designed to help older travelers to plan their public transport journeys and then receive guidance during their journey. This guidance will help them to find the vehicle they need, warn them when to get off, when and where to change to another route, and will provide assistance if something goes wrong. There are several stages in the guidance where uncertainties play a major role and have an effect on the quality of the trip. The major uncertainty is with the location services when GPS reception in poor or impossible due to urban canyons or the user being under ground or in a tunnel. In addition, when waiting at a stop where for instance several buses might arrive at the same time, it could be difficult to identify the correct bus to board. This paper explains the overall design of the ASSISTANT project and addresses some of the issues related to positional uncertainties.

Climate variation explains a third of global crop yield variability

PubMed Central

Ray, Deepak K.; Gerber, James S.; MacDonald, Graham K.; West, Paul C.

2015-01-01

Many studies have examined the role of mean climate change in agriculture, but an understanding of the influence of inter-annual climate variations on crop yields in different regions remains elusive. We use detailed crop statistics time series for ~13,500 political units to examine how recent climate variability led to variations in maize, rice, wheat and soybean crop yields worldwide. While some areas show no significant influence of climate variability, in substantial areas of the global breadbaskets, >60% of the yield variability can be explained by climate variability. Globally, climate variability accounts for roughly a third (~32–39%) of the observed yield variability. Our study uniquely illustrates spatial patterns in the relationship between climate variability and crop yield variability, highlighting where variations in temperature, precipitation or their interaction explain yield variability. We discuss key drivers for the observed variations to target further research and policy interventions geared towards buffering future crop production from climate variability. PMID:25609225

Explaining pathological changes in axonal excitability through dynamical analysis of conductance-based models

NASA Astrophysics Data System (ADS)

Coggan, Jay S.; Ocker, Gabriel K.; Sejnowski, Terrence J.; Prescott, Steven A.

2011-10-01

Neurons rely on action potentials, or spikes, to relay information. Pathological changes in spike generation likely contribute to certain enigmatic features of neurological disease, like paroxysmal attacks of pain and muscle spasm. Paroxysmal symptoms are characterized by abrupt onset and short duration, and are associated with abnormal spiking although the exact pathophysiology remains unclear. To help decipher the biophysical basis for 'paroxysmal' spiking, we replicated afterdischarge (i.e. continued spiking after a brief stimulus) in a minimal conductance-based axon model. We then applied nonlinear dynamical analysis to explain the dynamical basis for initiation and termination of afterdischarge. A perturbation could abruptly switch the system between two (quasi-)stable attractor states: rest and repetitive spiking. This bistability was a consequence of slow positive feedback mediated by persistent inward current. Initiation of afterdischarge was explained by activation of the persistent inward current forcing the system to cross a saddle point that separates the basins of attraction associated with each attractor. Termination of afterdischarge was explained by the attractor associated with repetitive spiking being destroyed. This occurred when ultra-slow negative feedback, such as intracellular sodium accumulation, caused the saddle point and stable limit cycle to collide; in that regard, the active attractor is not truly stable when the slowest dynamics are taken into account. The model also explains other features of paroxysmal symptoms, including temporal summation and refractoriness.

Downregulated CDKN1C/p57kip2 drives tumorigenesis and associates with poor overall survival in breast cancer.

PubMed

Qiu, Zhu; Li, Yunhai; Zeng, Beilei; Guan, Xiaoqin; Li, Hongzhong

2018-02-26

CDKN1C, also known as p57 kip2 , is considered to be a potential tumor suppressor implicated in several kinds of human cancers. However, the current knowledge of CDKN1C in breast cancer remains obscure. In the present study, we demonstrated that CDKN1C was dramatically downregulated in breast cancer compared with normal tissues by using real-time quantitative polymerase chain reaction, western blot and two public data portals: The Cancer Genome Atlas (TCGA) and Oncomine datasets. Moreover, the expression of CDKN1C was correlated with age and tumor size in the TCGA cohort containing 708 cases of breast cancer. Low expression of CDKN1C was significantly associated with poor overall survival (OS) in the TCGA cohort and validated cohort composed of 1402 patients. Multivariate Cox regression analysis indicated that CDKN1C was an independent prognostic factor for worse OS (HR = 1.78, 95% CI: 1.09-2.89, p = 0.020). Furthermore, gene set enrichment analysis (GSEA) revealed that CDKN1C was significantly correlated with gene signatures involving DNA repair, cell cycle, glycolysis, adipogenesis, and two critical signaling pathways mTORC1 and PI3K/Akt/mTOR. In conclusion, our data suggested an essential role of CDKN1C in the tumorgenesis of breast cancer. Targeting CDKN1C may be a promising strategy for anticancer therapeutics. Copyright © 2018 Elsevier Inc. All rights reserved.