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Sample records for genomic context reflect

  1. A reflective approach to HE language provision : integrating context and language through semistructured reflection

    NARCIS (Netherlands)

    Haines, Kevin; Ashworth - Kadwell, Angela; Wilkinson, Robert; Zegers, Vera

    2008-01-01

    Taking a sociocultural perspective to second language acquisition, this paper describes the implementation in an HE curriculum of an approach that encourages students to reflect on language learning in its wider context. Students are provided with tools for reflection through which they can make cle

  2. A reflective approach to HE language provision : integrating context and language through semistructured reflection

    NARCIS (Netherlands)

    Haines, Kevin; Ashworth - Kadwell, Angela; Wilkinson, Robert; Zegers, Vera

    2008-01-01

    Taking a sociocultural perspective to second language acquisition, this paper describes the implementation in an HE curriculum of an approach that encourages students to reflect on language learning in its wider context. Students are provided with tools for reflection through which they can make

  3. Glucocorticoid signature in a neuronal genomic context

    NARCIS (Netherlands)

    Polman, J.A.E.

    2016-01-01

    During this research we wanted to gain more insight into the potential gene repertoire that is involved in the hippocampus when coping with stress and regulating learning and memory processes. To investigate this further we aimed to answer the question:""What are the primary genomic binding sites of

  4. Improving microbial genome annotations in an integrated database context.

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    I-Min A Chen

    Full Text Available Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.

  5. The Genome Organization of Thermotoga maritima Reflects Its Lifestyle

    Energy Technology Data Exchange (ETDEWEB)

    Latif, Haythem; Lerman, Joshua A.; Portnoy, Vasiliy A.; Tarasova, Yekaterina; Nagarajan, Harish; Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua N.; Lee, Dae-Hee; Qiu, Yu; Zengler, Karsten

    2013-04-25

    Recent studies have revealed that microbial genomes have many more organizational features than previously thought. Here, an integrated approach utilizing multiple ‘omics’ datasets and bioinformatics tools is established that elucidates genomic features spanning various levels of cellular organization. This methodology produces gene annotation improvements and includes the definition of transcription units. These enhancements to the annotation enable identification of a set of genetic elements instrumental to gene expression and regulation including promoters, ribosome binding sites (RBSs) and untranslated regions (UTRs). This was applied to characterize the genome organization of Thermotoga maritima—a phylogenetically deep-branching, hyperthermophilic bacterium with a small 1.86 Mb genome. Analysis derived from this multiomics approach in combination with bioinformatics tools demonstrate that the genome organization of T. maritima reflects its lifestyle, both with respect to its extreme growth temperature and compact genome. Comparative analysis of genome features suggests that thermodynamic limitations on binding kinetics for RNA polymerase and the ribosome necessitate increased sequence conservation of promoters and RBSs. Thus, restricting the sequences capable of initiating transcription and translation. Furthermore, this organism has uncharacteristically short 5’UTRs (11-17 nucleotides), which reduce the potential for 5’UTR regulatory interactions. The short intergenic distances in the T. maritima genome (5 bp on average) leave little space for regulation through transcription factor binding. The net effect of these constraints, temperature and genomic space, is a reduced ability to tune gene expression. This effect is readily apparent in global gene expression patterns, which show a high fraction of genes expressed independent of growth state with a tight, linear mRNA/protein correlation (Pearson r = 0.62, p < 2.2 x 10-16 t-test). This methodology

  6. Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits

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    Nylander Johan AA

    2011-06-01

    Full Text Available Abstract Background Cyanobacteria belong to an ancient group of photosynthetic prokaryotes with pronounced variations in their cellular differentiation strategies, physiological capacities and choice of habitat. Sequencing efforts have shown that genomes within this phylum are equally diverse in terms of size and protein-coding capacity. To increase our understanding of genomic changes in the lineage, the genomes of 58 contemporary cyanobacteria were analysed for shared and unique orthologs. Results A total of 404 protein families, present in all cyanobacterial genomes, were identified. Two of these are unique to the phylum, corresponding to an AbrB family transcriptional regulator and a gene that escapes functional annotation although its genomic neighbourhood is conserved among the organisms examined. The evolution of cyanobacterial genome sizes involves a mix of gains and losses in the clade encompassing complex cyanobacteria, while a single event of reduction is evident in a clade dominated by unicellular cyanobacteria. Genome sizes and gene family copy numbers evolve at a higher rate in the former clade, and multi-copy genes were predominant in large genomes. Orthologs unique to cyanobacteria exhibiting specific characteristics, such as filament formation, heterocyst differentiation, diazotrophy and symbiotic competence, were also identified. An ancestral character reconstruction suggests that the most recent common ancestor of cyanobacteria had a genome size of approx. 4.5 Mbp and 1678 to 3291 protein-coding genes, 4%-6% of which are unique to cyanobacteria today. Conclusions The different rates of genome-size evolution and multi-copy gene abundance suggest two routes of genome development in the history of cyanobacteria. The expansion strategy is driven by gene-family enlargment and generates a broad adaptive potential; while the genome streamlining strategy imposes adaptations to highly specific niches, also reflected in their different

  7. Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits

    Science.gov (United States)

    2011-01-01

    Background Cyanobacteria belong to an ancient group of photosynthetic prokaryotes with pronounced variations in their cellular differentiation strategies, physiological capacities and choice of habitat. Sequencing efforts have shown that genomes within this phylum are equally diverse in terms of size and protein-coding capacity. To increase our understanding of genomic changes in the lineage, the genomes of 58 contemporary cyanobacteria were analysed for shared and unique orthologs. Results A total of 404 protein families, present in all cyanobacterial genomes, were identified. Two of these are unique to the phylum, corresponding to an AbrB family transcriptional regulator and a gene that escapes functional annotation although its genomic neighbourhood is conserved among the organisms examined. The evolution of cyanobacterial genome sizes involves a mix of gains and losses in the clade encompassing complex cyanobacteria, while a single event of reduction is evident in a clade dominated by unicellular cyanobacteria. Genome sizes and gene family copy numbers evolve at a higher rate in the former clade, and multi-copy genes were predominant in large genomes. Orthologs unique to cyanobacteria exhibiting specific characteristics, such as filament formation, heterocyst differentiation, diazotrophy and symbiotic competence, were also identified. An ancestral character reconstruction suggests that the most recent common ancestor of cyanobacteria had a genome size of approx. 4.5 Mbp and 1678 to 3291 protein-coding genes, 4%-6% of which are unique to cyanobacteria today. Conclusions The different rates of genome-size evolution and multi-copy gene abundance suggest two routes of genome development in the history of cyanobacteria. The expansion strategy is driven by gene-family enlargment and generates a broad adaptive potential; while the genome streamlining strategy imposes adaptations to highly specific niches, also reflected in their different functional capacities. A few

  8. Selvamicin, an atypical antifungal polyene from two alternative genomic contexts.

    Science.gov (United States)

    Van Arnam, Ethan B; Ruzzini, Antonio C; Sit, Clarissa S; Horn, Heidi; Pinto-Tomás, Adrián A; Currie, Cameron R; Clardy, Jon

    2016-11-15

    The bacteria harbored by fungus-growing ants produce a variety of small molecules that help maintain a complex multilateral symbiosis. In a survey of antifungal compounds from these bacteria, we discovered selvamicin, an unusual antifungal polyene macrolide, in bacterial isolates from two neighboring ant nests. Selvamicin resembles the clinically important antifungals nystatin A1 and amphotericin B, but it has several distinctive structural features: a noncationic 6-deoxymannose sugar at the canonical glycosylation site and a second sugar, an unusual 4-O-methyldigitoxose, at the opposite end of selvamicin's shortened polyene macrolide. It also lacks some of the pharmacokinetic liabilities of the clinical agents and appears to have a different target. Whole genome sequencing revealed the putative type I polyketide gene cluster responsible for selvamicin's biosynthesis including a subcluster of genes consistent with selvamicin's 4-O-methyldigitoxose sugar. Although the selvamicin biosynthetic cluster is virtually identical in both bacterial producers, in one it is on the chromosome, in the other it is on a plasmid. These alternative genomic contexts illustrate the biosynthetic gene cluster mobility that underlies the diversity and distribution of chemical defenses by the specialized bacteria in this multilateral symbiosis.

  9. Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates

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    Adams Josephine C

    2006-04-01

    Full Text Available Abstract Background The syndecans are the major family of transmembrane proteoglycans in animals and are known for multiple roles in cell interactions and growth factor signalling during development, inflammatory response, wound-repair and tumorigenesis. Although syndecans have been cloned from several invertebrate and vertebrate species, the extent of conservation of the family across the animal kingdom is unknown and there are gaps in our knowledge of chordate syndecans. Here, we develop a new level of knowledge for the whole syndecan family, by combining molecular phylogeny of syndecan protein sequences with analysis of the genomic contexts of syndecan genes in multiple vertebrate organisms. Results We identified syndecan-encoding sequences in representative Cnidaria and throughout the Bilateria. The C1 and C2 regions of the cytoplasmic domain are highly conserved throughout the animal kingdom. We identified in the variable region a universally-conserved leucine residue and a tyrosine residue that is conserved throughout the Bilateria. Of all the genomes examined, only tetrapod and fish genomes encode multiple syndecans. No syndecan-1 was identified in fish. The genomic context of each vertebrate syndecan gene is syntenic between human, mouse and chicken, and this conservation clearly extends to syndecan-2 and -3 in T. nigroviridis. In addition, tetrapod syndecans were found to be encoded from paralogous chromosomal regions that also contain the four members of the matrilin family. Whereas the matrilin-3 and syndecan-1 genes are adjacent in tetrapods, this chromosomal region appears to have undergone extensive lineage-specific rearrangements in fish. Conclusion Throughout the animal kingdom, syndecan extracellular domains have undergone rapid change and elements of the cytoplasmic domains have been very conserved. The four syndecan genes of vertebrates are syntenic across tetrapods, and synteny of the syndecan-2 and -3 genes is apparent

  10. Some reflections upon Internet TV in the Brazilian context

    Science.gov (United States)

    de Lima-Lopes, Rodrigo

    2016-10-01

    Negroponte [1996. Being digital (1st ed.). New York, NY: Vintage Books] discusses the migration television might take from its air-based broadcasting to the digital environment. This paper takes into consideration the exercise in futurology made by Negroponte [1996. Being digital (1st ed.). New York, NY: Vintage Books] as an inspiration to discuss which Internet TV models are currently adopted in Brazil. They are studied in terms of the platforms used and the nature of the channels available. Results show that a number of devices can be used for Internet TV; some channels are redundant, since they are present in more than one context. There are a number of foreign (broadcasting in their own language) and Brazilian channels that seem to be exclusive in each device. Due to the price of some devices, as well as some issues regarding connectivity in Brazil, some platforms seem to lack local production.

  11. Education through Fiction: Acquiring Opinion-Forming Skills in the Context of Genomics

    Science.gov (United States)

    Knippels, Marie-Christine P. J.; Severiens, Sabine E.; Klop, Tanja

    2009-01-01

    The present study examined the outcomes of a newly designed four-lesson science module on opinion-forming in the context of genomics in upper secondary education. The lesson plan aims to foster 16-year-old students' opinion-forming skills in the context of genomics and to test the effect of the use of fiction in the module. The basic hypothesis…

  12. Education through fiction: acquiring opinion-forming skills in the context of genomics

    NARCIS (Netherlands)

    Knippels, M.C.P.J.; Severiens, S.E.; Klop, T.

    2009-01-01

    The present study examined the outcomes of a newly designed four-lesson science module on opinion-forming in the context of genomics in upper secondary education. The lesson plan aims to foster 16-year-old students’ opinion-forming skills in the context of genomics and to test the effect of the use

  13. Caryoscope: An Open Source Java application for viewing microarray data in a genomic context

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    Ball Catherine A

    2004-10-01

    Full Text Available Abstract Background Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context. Results We have developed Caryoscope, which is an open source Java application for visualizing microarray data from array comparative genome hybridization experiments in a genomic context. Caryoscope can read General Feature Format files (GFF files, as well as comma- and tab-delimited files, that define the genomic positions of the microarray reporters for which data are obtained. The microarray data can be browsed using an interactive, zoomable interface, which helps users identify regions of chromosomal deletion or amplification. The graphical representation of the data can be exported in a number of graphic formats, including publication-quality formats such as PostScript. Conclusion Caryoscope is a useful tool that can aid in the visualization, exploration and interpretation of microarray data in a genomic context.

  14. Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits

    OpenAIRE

    Nylander Johan AA; Larsson John; Bergman Birgitta

    2011-01-01

    Background Cyanobacteria belong to an ancient group of photosynthetic prokaryotes with pronounced variations in their cellular differentiation strategies, physiological capacities and choice of habitat. Sequencing efforts have shown that genomes within this phylum are equally diverse in terms of size and protein-coding capacity. To increase our understanding of genomic changes in the lineage, the genomes of 58 contemporary cyanobacteria were analysed for shared and unique o...

  15. Socio-Cultural Context of Drug Use with Reflections to Cannabis Use in Croatia

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    Niksa Dubreta

    2013-01-01

    Full Text Available Socio-cultural context of drug use is reflected as the constitutive part of interpretation of its effects and corresponding meanings, both at macro and micro-societal level of sociological analysis. In the first part of the article some more influential social-theoretical approaches to drug use are considered. Most of them consider drug use in terms of sociology of subculture and deviance. In second part, Croatian socio-cultural context is analysed, with reflections on questioning key terms that are addressed in the first part of the article. The concluding part indicates the ability for critical reflection of part of theories with regard to specificities of Croatian socio-cultural context. Furthermore, it is indicated that is necessary to overcome existing focus on the war, transition and after-war period as still dominant interpretative model in actual Croatian social research on drug use.

  16. Use of the Repertory Grid for collaboration and reflection in a research context

    CSIR Research Space (South Africa)

    Alexander, P

    2010-09-01

    Full Text Available for collaboration and reflection in a research context Patricia Alexander1, Johan van Loggerenberg2, Hugo Lotriet3, Jackie Phahlamohlaka4 1,2,3 Department of Informatics, University of Pretoria, Hatfield, PRETORIA, 0083, South Africa Patricia....Alexander@up.ac.za 4 Department of Informatics, University of Pretoria and Council for Scientific and Industrial Research (CSIR), Pretoria, South Africa JPhahlamohlaka@csir.co.za Running head: Repertory Grid for collaboration & reflection ABSTRACT...

  17. 3D Genome Tuner: Compare Multiple Circular Genomes in a 3D Context

    Institute of Scientific and Technical Information of China (English)

    Qi Wang; Qun Liang; Xiuqing Zhang

    2009-01-01

    Circular genomes, being the largest proportion of sequenced genomes, play an important role in genome analysis. However, traditional 2D circular map only provides an overview and annotations of genome but does not offer feature-based comparison. For remedying these shortcomings, we developed 3D Genome Tuner, a hybrid of circular map and comparative map tools. Its capability of viewing comparisons between multiple circular maps in a 3D space offers great benefits to the study of comparative genomics. The program is freely available(under an LGPL licence)at http://sourceforge.net/projects/dgenometuner.

  18. Primary Teachers' Reflections on Inquiry- and Context-Based Science Education

    Science.gov (United States)

    Walan, Susanne; Mc Ewen, Birgitta

    2017-01-01

    Inquiry- and context-based teaching strategies have been proven to stimulate and motivate students' interests in learning science. In this study, 12 teachers reflected on these strategies after using them in primary schools. The teachers participated in a continuous professional development (CPD) programme. During the programme, they were also…

  19. A New Theory-to-Practice Model for Student Affairs: Integrating Scholarship, Context, and Reflection

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    Reason, Robert D.; Kimball, Ezekiel W.

    2012-01-01

    In this article, we synthesize existing theory-to-practice approaches within the student affairs literature to arrive at a new model that incorporates formal and informal theory, institutional context, and reflective practice. The new model arrives at a balance between the rigor necessary for scholarly theory development and the adaptability…

  20. Mathematics teachers’ reflective practice within the context of adapted lesson study

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    Barbara Posthuma

    2012-10-01

    Full Text Available There seems to be paucity of research in South Africa on mathematics teachers’ reflective practice. In order to study this phenomenon, the context of lesson study (in an adapted form was introduced to five mathematics teachers in a rural school in the Free State. The purpose was to investigate their reflective practice whilst they collaboratively planned mathematics lessons and reflected on the teaching of the lessons. Data were obtained through interviews, video-recorded lesson observations, field notes taken during the lesson study group meetings and document analyses (lesson plans and reflective writings. The adapted lesson study context provided a safe space for teachers to reflect on their teaching and they reported an increase in self-knowledge and finding new ways of teaching mathematics to learners. This finding has some potential value for planning professional learning programmes in which teachers are encouraged to talk about their classroom experiences, share their joys and challenges with one another and strive to build a community of reflective practitioners to enhance their learners’ understanding of mathematics.

  1. Female Teachers’ Perception of Reflective Teaching as a Teacher Development Tool in the Saudi Context

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    Nadia Shukri

    2014-10-01

    Full Text Available Teacher development in the EFL context has been well-established in Western educational institutions. However, although there are some limited studies in the Middle East, it is still under-researched in Saudi Arabia. This study investigates the EFL teachers’ perceptions of reflective teaching as a tool for teacher development and its challenges in higher education in Saudi Arabia. It also aims to raise teachers’ awareness of the importance of teacher development and its empowering impact in meeting their students’ needs. Based on a review of previous studies, the present study hypothesized a significant relevance between reflective teaching practice and the promotion of professional development. A structured questionnaire is used as a quantitative methodology followed by qualitative analysis of the findings. The findings support the hypothesis in which the participants’ views revealed a strong relationship between reflective teaching and professionalism in teaching. Finally, further recommendations that suggest methods of reflective teaching are proposed. 

  2. Integrative Genomics with Mediation Analysis in a Survival Context

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    Szilárd Nemes

    2013-01-01

    Full Text Available DNA copy number aberrations (DCNA and subsequent altered gene expression profiles may have a major impact on tumor initiation, on development, and eventually on recurrence and cancer-specific mortality. However, most methods employed in integrative genomic analysis of the two biological levels, DNA and RNA, do not consider survival time. In the present note, we propose the adoption of a survival analysis-based framework for the integrative analysis of DCNA and mRNA levels to reveal their implication on patient clinical outcome with the prerequisite that the effect of DCNA on survival is mediated by mRNA levels. The specific aim of the paper is to offer a feasible framework to test the DCNA-mRNA-survival pathway. We provide statistical inference algorithms for mediation based on asymptotic results. Furthermore, we illustrate the applicability of the method in an integrative genomic analysis setting by using a breast cancer data set consisting of 141 invasive breast tumors. In addition, we provide implementation in R.

  3. Reflections and perspectives of African-American community leaders regarding genetics and genomics research: sentiment and wisdom of Sankofa.

    Science.gov (United States)

    Underwood, Sandra Millon; Buseh, Aaron G; Stevens, Patricia E; Townsend, Leolia; Kelber, Sheryl T

    2013-07-01

    Advances in genetic and genomic research are shifting the typical disease timeline. For those afflicted by disease and for population groups known to experience excess disease-related morbidity and mortality, the ability to use genetics and genomics to predict an individuals' predisposition for developing a disease and/or to anticipate an individual's response to treatments holds tremendous promise. Over the past two decades several public and private institutions within the United States have been established for the purpose of collecting and storing biological specimens for the purpose of conducting genetic/genomic research. Multiple reports indicate that the involvement of racial/ethnic minority participants in these bio-repositories is limited. Little is known about the willingness of African-Americans, one of the largest and most vulnerable racial/ethnic population groups, to participate in genetic research, genomic research, and to contribute biological specimens to bio-repositories. An exploratory study was undertaken using principles of community engagement and community-based participatory research to examine the perspectives of leaders within the African-American community about participation in genetics research, genomics research, and bio-banking. Semi-structured focus groups with twenty-one African-American community leaders were the primary means of gathering the study data. Reflections and commentary of the community leaders were interspersed with sentiments of "Sankofa." The emergent themes, health-related disparities, historical injustices in medical research, the promise of genetic and genomic research, and genetics/genomic research engagement, implicated the importance of conducting genetics/genomics research in the context of the community interdependent with efforts to address determinants of health and health disparities.

  4. TraV: a genome context sensitive transcriptome browser.

    Science.gov (United States)

    Dietrich, Sascha; Wiegand, Sandra; Liesegang, Heiko

    2014-01-01

    Next-generation sequencing (NGS) technologies like Illumina and ABI Solid enable the investigation of transcriptional activities of genomes. While read mapping tools have been continually improved to enable the processing of the increasing number of reads generated by NGS technologies, analysis and visualization tools are struggling with the amount of data they are presented with. Current tools are capable of handling at most two to three datasets simultaneously before they are limited by available memory or due to processing overhead. In order to process fifteen transcriptome sequencing experiments of Bacillus licheniformis DSM13 obtained in a previous study, we developed TraV, a RNA-Seq analysis and visualization tool. The analytical methods are designed for prokaryotic RNA-seq experiments. TraV calculates single nucleotide activities from the mapping information to visualize and analyze multiple transcriptome sequencing experiments. The use of nucleotide activities instead of single read mapping information is highly memory efficient without incurring a processing overhead. TraV is available at http://appmibio.uni-goettingen.de/index.php?sec=serv.

  5. Genomic diversification of giant enteric symbionts reflects host dietary lifestyles

    KAUST Repository

    Ngugi, David

    2017-08-24

    Herbivorous surgeonfishes are an ecologically successful group of reef fish that rely on marine algae as their principal food source. Here, we elucidated the significance of giant enteric symbionts colonizing these fishes regarding their roles in the digestive processes of hosts feeding predominantly on polysiphonous red algae and brown Turbinaria algae, which contain different polysaccharide constituents. Using metagenomics, single-cell genomics, and metatranscriptomic analyses, we provide evidence of metabolic diversification of enteric microbiota involved in the degradation of algal biomass in these fishes. The enteric microbiota is also phylogenetically and functionally simple relative to the complex lignocellulose-degrading microbiota of terrestrial herbivores. Over 90% of the enzymes for deconstructing algal polysaccharides emanate from members of a single bacterial lineage,

  6. Comparative analysis of codon usage bias and codon context patterns between dipteran and hymenopteran sequenced genomes.

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    Susanta K Behura

    Full Text Available BACKGROUND: Codon bias is a phenomenon of non-uniform usage of codons whereas codon context generally refers to sequential pair of codons in a gene. Although genome sequencing of multiple species of dipteran and hymenopteran insects have been completed only a few of these species have been analyzed for codon usage bias. METHODS AND PRINCIPAL FINDINGS: Here, we use bioinformatics approaches to analyze codon usage bias and codon context patterns in a genome-wide manner among 15 dipteran and 7 hymenopteran insect species. Results show that GAA is the most frequent codon in the dipteran species whereas GAG is the most frequent codon in the hymenopteran species. Data reveals that codons ending with C or G are frequently used in the dipteran genomes whereas codons ending with A or T are frequently used in the hymenopteran genomes. Synonymous codon usage orders (SCUO vary within genomes in a pattern that seems to be distinct for each species. Based on comparison of 30 one-to-one orthologous genes among 17 species, the fruit fly Drosophila willistoni shows the least codon usage bias whereas the honey bee (Apis mellifera shows the highest bias. Analysis of codon context patterns of these insects shows that specific codons are frequently used as the 3'- and 5'-context of start and stop codons, respectively. CONCLUSIONS: Codon bias pattern is distinct between dipteran and hymenopteran insects. While codon bias is favored by high GC content of dipteran genomes, high AT content of genes favors biased usage of synonymous codons in the hymenopteran insects. Also, codon context patterns vary among these species largely according to their phylogeny.

  7. Integration and visualization of systems biology data in context of the genome

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    Tenenbaum Dan

    2010-07-01

    Full Text Available Abstract Background High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

  8. Feature context-dependency and complexity-reduction in probability landscapes for integrative genomics

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    Benecke Arndt

    2008-09-01

    Full Text Available Abstract Background The question of how to integrate heterogeneous sources of biological information into a coherent framework that allows the gene regulatory code in eukaryotes to be systematically investigated is one of the major challenges faced by systems biology. Probability landscapes, which include as reference set the probabilistic representation of the genomic sequence, have been proposed as a possible approach to the systematic discovery and analysis of correlations amongst initially heterogeneous and un-relatable descriptions and genome-wide measurements. Much of the available experimental sequence and genome activity information is de facto, but not necessarily obviously, context dependent. Furthermore, the context dependency of the relevant information is itself dependent on the biological question addressed. It is hence necessary to develop a systematic way of discovering the context-dependency of functional genomics information in a flexible, question-dependent manner. Results We demonstrate here how feature context-dependency can be systematically investigated using probability landscapes. Furthermore, we show how different feature probability profiles can be conditionally collapsed to reduce the computational and formal, mathematical complexity of probability landscapes. Interestingly, the possibility of complexity reduction can be linked directly to the analysis of context-dependency. Conclusion These two advances in our understanding of the properties of probability landscapes not only simplify subsequent cross-correlation analysis in hypothesis-driven model building and testing, but also provide additional insights into the biological gene regulatory problems studied. Furthermore, insights into the nature of individual features and a classification of features according to their minimal context-dependency are achieved. The formal structure proposed contributes to a concrete and tangible basis for attempting to formulate novel

  9. A systematic study of genome context methods: calibration, normalization and combination

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    Dale Joseph M

    2010-10-01

    Full Text Available Abstract Background Genome context methods have been introduced in the last decade as automatic methods to predict functional relatedness between genes in a target genome using the patterns of existence and relative locations of the homologs of those genes in a set of reference genomes. Much work has been done in the application of these methods to different bioinformatics tasks, but few papers present a systematic study of the methods and their combination necessary for their optimal use. Results We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor. We find that for most organisms the gene neighbor method outperforms the phylogenetic profile method by as much as 40% in sensitivity, being competitive with the gene cluster method at low sensitivities. Gene fusion is generally the worst performing of the four methods. A thorough exploration of the parameter space for each method is performed and results across different target organisms are presented. We propose the use of normalization procedures as those used on microarray data for the genome context scores. We show that substantial gains can be achieved from the use of a simple normalization technique. In particular, the sensitivity of the phylogenetic profile method is improved by around 25% after normalization, resulting, to our knowledge, on the best-performing phylogenetic profile system in the literature. Finally, we show results from combining the various genome context methods into a single score. When using a cross-validation procedure to train the combiners, with both original and normalized scores as input, a decision tree combiner results in gains of up to 20% with respect to the gene neighbor method. Overall, this represents a gain of around 15% over what can be considered the state of the art in this area: the four original genome context methods combined using a

  10. Primary Teachers' Reflections on Inquiry- and Context-Based Science Education

    Science.gov (United States)

    Walan, Susanne; Mc Ewen, Birgitta

    2016-03-01

    Inquiry- and context-based teaching strategies have been proven to stimulate and motivate students' interests in learning science. In this study, 12 teachers reflected on these strategies after using them in primary schools. The teachers participated in a continuous professional development (CPD) programme. During the programme, they were also introduced to a teaching model from a European project, where inquiry- and context-based education (IC-BaSE) strategies were fused. The research question related to teachers' reflections on these teaching strategies, and whether they found the model to be useful in primary schools after testing it with their students. Data collection was performed during the CPD programme and consisted of audio-recorded group discussions, individual portfolios and field notes collected by researchers. Results showed that compared with using only one instructional strategy, teachers found the new teaching model to be a useful complement. However, their discussions also showed that they did not reflect on choices of strategies or purposes and aims relating to students' understanding, or the content to be taught. Before the CPD programme, teachers discussed the use of inquiry mainly from the aspect that students enjoy practical work. After the programme, they identified additional reasons for using inquiry and discussed the importance of knowing why inquiry is performed. However, to develop teachers' knowledge of instructional strategies as well as purposes for using certain strategies, there is need for further investigations among primary school teachers.

  11. Primary Teachers' Reflections on Inquiry- and Context-Based Science Education

    Science.gov (United States)

    Walan, Susanne; Mc Ewen, Birgitta

    2017-04-01

    Inquiry- and context-based teaching strategies have been proven to stimulate and motivate students' interests in learning science. In this study, 12 teachers reflected on these strategies after using them in primary schools. The teachers participated in a continuous professional development (CPD) programme. During the programme, they were also introduced to a teaching model from a European project, where inquiry- and context-based education (IC-BaSE) strategies were fused. The research question related to teachers' reflections on these teaching strategies, and whether they found the model to be useful in primary schools after testing it with their students. Data collection was performed during the CPD programme and consisted of audio-recorded group discussions, individual portfolios and field notes collected by researchers. Results showed that compared with using only one instructional strategy, teachers found the new teaching model to be a useful complement. However, their discussions also showed that they did not reflect on choices of strategies or purposes and aims relating to students' understanding, or the content to be taught. Before the CPD programme, teachers discussed the use of inquiry mainly from the aspect that students enjoy practical work. After the programme, they identified additional reasons for using inquiry and discussed the importance of knowing why inquiry is performed. However, to develop teachers' knowledge of instructional strategies as well as purposes for using certain strategies, there is need for further investigations among primary school teachers.

  12. Narrative thematic analysis of baccalaureate nursing students' reflections: critical thinking in the clinical education context.

    Science.gov (United States)

    Naber, Jessica L; Hall, Joanne; Schadler, Craig Matthew

    2014-09-01

    This study sought to identify characteristics of clinically situated critical thinking in nursing students' reflections, originally part of a study guided by Richard Paul's model of critical thinking. Nurses are expected to apply critical thinking in all practice situations to improve health outcomes, including patient safety and satisfaction. In a previous study, Paul's model of critical thinking was used to develop questions for reflective writing assignments. Within that study, 30 nursing students completed six open-ended narratives of nurse-patient clinical encounters during an 8-week period. Improvements were seen in critical thinking scores after the intervention. This article reports the qualitative analysis of the content of six open-ended narratives. Six overarching themes were identified and combined into a tentative conceptual model. Faculty's understanding of the characteristics of critical thinking in the context of clinical education will help them to teach and evaluate students' progress and competencies for future practice.

  13. Personality-dependent differences in problem-solving performance in a social context reflect foraging strategies.

    Science.gov (United States)

    Zandberg, Lies; Quinn, John L; Naguib, Marc; van Oers, Kees

    2017-01-01

    Individuals develop innovative behaviours to solve foraging challenges in the face of changing environmental conditions. Little is known about how individuals differ in their tendency to solve problems and in their subsequent use of this solving behaviour in social contexts. Here we investigated whether individual variation in problem-solving performance could be explained by differences in the likelihood of solving the task, or if they reflect differences in foraging strategy. We tested this by studying the use of a novel foraging skill in groups of great tits (Parus major), consisting of three naive individuals with different personality, and one knowledgeable tutor. We presented them with multiple, identical foraging devices over eight trials. Though birds of different personality type did not differ in solving latency; fast and slow explorers showed a steeper increase over time in their solving rate, compared to intermediate explorers. Despite equal solving potential, personality influenced the subsequent use of the skill, as well as the pay-off received from solving. Thus, variation in the tendency to solve the task reflected differences in foraging strategy among individuals linked to their personality. These results emphasize the importance of considering the social context to fully understand the implications of learning novel skills. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing.

    Science.gov (United States)

    Abdolrasouli, Alireza; Rhodes, Johanna; Beale, Mathew A; Hagen, Ferry; Rogers, Thomas R; Chowdhary, Anuradha; Meis, Jacques F; Armstrong-James, Darius; Fisher, Matthew C

    2015-06-02

    A rapid and global emergence of azole resistance has been observed in the pathogenic fungus Aspergillus fumigatus over the past decade. The dominant resistance mechanism appears to be of environmental origin and involves mutations in the cyp51A gene, which encodes a protein targeted by triazole antifungal drugs. Whole-genome sequencing (WGS) was performed for high-resolution single-nucleotide polymorphism (SNP) analysis of 24 A. fumigatus isolates, including azole-resistant and susceptible clinical and environmental strains obtained from India, the Netherlands, and the United Kingdom, in order to assess the utility of WGS for characterizing the alleles causing resistance. WGS analysis confirmed that TR34/L98H (a mutation comprising a tandem repeat [TR] of 34 bases in the promoter of the cyp51A gene and a leucine-to-histidine change at codon 98) is the sole mechanism of azole resistance among the isolates tested in this panel of isolates. We used population genomic analysis and showed that A. fumigatus was panmictic, with as much genetic diversity found within a country as is found between continents. A striking exception to this was shown in India, where isolates are highly related despite being isolated from both clinical and environmental sources across >1,000 km; this broad occurrence suggests a recent selective sweep of a highly fit genotype that is associated with the TR34/L98H allele. We found that these sequenced isolates are all recombining, showing that azole-resistant alleles are segregating into diverse genetic backgrounds. Our analysis delineates the fundamental population genetic parameters that are needed to enable the use of genome-wide association studies to identify the contribution of SNP diversity to the generation and spread of azole resistance in this medically important fungus. Resistance to azoles in the ubiquitous ascomycete fungus A. fumigatus was first reported from clinical isolates collected in the United States during the late 1980s

  15. Reflections on the cost of "low-cost" whole genome sequencing: framing the health policy debate.

    Directory of Open Access Journals (Sweden)

    Timothy Caulfield

    2013-11-01

    Full Text Available The cost of whole genome sequencing is dropping rapidly. There has been a great deal of enthusiasm about the potential for this technological advance to transform clinical care. Given the interest and significant investment in genomics, this seems an ideal time to consider what the evidence tells us about potential benefits and harms, particularly in the context of health care policy. The scale and pace of adoption of this powerful new technology should be driven by clinical need, clinical evidence, and a commitment to put patients at the centre of health care policy.

  16. Reflective Practice in Developing World Contexts: A General Review of Literature and a Specific Consideration of an Iranian Experience

    Science.gov (United States)

    Sangani, Hamid Rahmani; Stelma, Juup

    2012-01-01

    This paper begins with a review of an emerging set of studies, combining a critical focus on reflective teacher development in developing educational contexts, and a greater level of authorial identification (as compared with previous studies) with the contexts being researched. Next, the paper adds to this emerging literature an analysis of a…

  17. DNA barcoding in the media: does coverage of cool science reflect its social context?

    Science.gov (United States)

    Geary, Janis; Camicioli, Emma; Bubela, Tania

    2016-09-01

    Paul Hebert and colleagues first described DNA barcoding in 2003, which led to international efforts to promote and coordinate its use. Since its inception, DNA barcoding has generated considerable media coverage. We analysed whether this coverage reflected both the scientific and social mandates of international barcoding organizations. We searched newspaper databases to identify 900 English-language articles from 2003 to 2013. Coverage of the science of DNA barcoding was highly positive but lacked context for key topics. Coverage omissions pose challenges for public understanding of the science and applications of DNA barcoding; these included coverage of governance structures and issues related to the sharing of genetic resources across national borders. Our analysis provided insight into how barcoding communication efforts have translated into media coverage; more targeted communication efforts may focus media attention on previously omitted, but important topics. Our analysis is timely as the DNA barcoding community works to establish the International Society for the Barcode of Life.

  18. THE IMPORTANCE OF THIS AND THAT: REFLECTIONS ON CONTEXT IN EARLY ISLAMIC PHILOSOPHY

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    Phil Enns

    2011-02-01

    Full Text Available The discussion over the relationship between what is true globally and what is true locally is not new. It might be helpful, therefore, to consider issues surrounding the relationship between globalization and local values in light of previous forms of this discussion. To this end, I would like to reflect on the discussion of context in the writings of al-Farabi, Ibn Sina and al-Ghazali. To focus this paper, I will consider only three issues, namely that of history, science and the role of reason in religion. I will argue that al-Farabi and Ibn Sina present an account of context that begins with experience as a foundation and then moves to the universal, emphasizing the importance of tradition, demonstration and rationality. Against these two, al-Ghazali argues for the importance of leaving behind experience in order to reach that which is certain, emphasizing the supernatural, intuition and mystical. My goal is to draw out some implications these writers recognized followed from their often dense and esoteric discussions of the nature of particulars and universals, and conclude with some suggestions for our contemporary situation. Keywords: Knowledge, al-Ghazali, al-Farabi, Ibn Sina

  19. The influence of genomic context on mutation patterns in the human genome inferred from rare variants.

    Science.gov (United States)

    Schaibley, Valerie M; Zawistowski, Matthew; Wegmann, Daniel; Ehm, Margaret G; Nelson, Matthew R; St Jean, Pamela L; Abecasis, Gonçalo R; Novembre, John; Zöllner, Sebastian; Li, Jun Z

    2013-12-01

    Understanding patterns of spontaneous mutations is of fundamental interest in studies of human genome evolution and genetic disease. Here, we used extremely rare variants in humans to model the molecular spectrum of single-nucleotide mutations. Compared to common variants in humans and human-chimpanzee fixed differences (substitutions), rare variants, on average, arose more recently in the human lineage and are less affected by the potentially confounding effects of natural selection, population demographic history, and biased gene conversion. We analyzed variants obtained from a population-based sequencing study of 202 genes in >14,000 individuals. We observed considerable variability in the per-gene mutation rate, which was correlated with local GC content, but not recombination rate. Using >20,000 variants with a derived allele frequency ≤ 10(-4), we examined the effect of local GC content and recombination rate on individual variant subtypes and performed comparisons with common variants and substitutions. The influence of local GC content on rare variants differed from that on common variants or substitutions, and the differences varied by variant subtype. Furthermore, recombination rate and recombination hotspots have little effect on rare variants of any subtype, yet both have a relatively strong impact on multiple variant subtypes in common variants and substitutions. This observation is consistent with the effect of biased gene conversion or selection-dependent processes. Our results highlight the distinct biases inherent in the initial mutation patterns and subsequent evolutionary processes that affect segregating variants.

  20. Reflection on College English Vocabulary Teaching from Non-linguistic Context Perspective

    Institute of Scientific and Technical Information of China (English)

    LIU Fang

    2013-01-01

    Vocabulary understanding is very important in English study; however, there exist some problems in the present college English vocabulary teaching, so it is necessary to propose some suggestions for it from the non-linguistic context perspectives to im⁃prove the students’vocabulary capacity. Based on the three non-linguistic contexts (situational context, cultural context and cogni⁃tive context), the passage suggests teachers pay much attention to the non-linguistic context while teaching.

  1. A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.

    Directory of Open Access Journals (Sweden)

    Hojung Nam

    2014-09-01

    Full Text Available Altered metabolism in cancer cells has been viewed as a passive response required for a malignant transformation. However, this view has changed through the recently described metabolic oncogenic factors: mutated isocitrate dehydrogenases (IDH, succinate dehydrogenase (SDH, and fumarate hydratase (FH that produce oncometabolites that competitively inhibit epigenetic regulation. In this study, we demonstrate in silico predictions of oncometabolites that have the potential to dysregulate epigenetic controls in nine types of cancer by incorporating massive scale genetic mutation information (collected from more than 1,700 cancer genomes, expression profiling data, and deploying Recon 2 to reconstruct context-specific genome-scale metabolic models. Our analysis predicted 15 compounds and 24 substructures of potential oncometabolites that could result from the loss-of-function and gain-of-function mutations of metabolic enzymes, respectively. These results suggest a substantial potential for discovering unidentified oncometabolites in various forms of cancers.

  2. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

    Science.gov (United States)

    Normand, Philippe; Lapierre, Pascal; Tisa, Louis S.; Gogarten, Johann Peter; Alloisio, Nicole; Bagnarol, Emilie; Bassi, Carla A.; Berry, Alison M.; Bickhart, Derek M.; Choisne, Nathalie; Couloux, Arnaud; Cournoyer, Benoit; Cruveiller, Stephane; Daubin, Vincent; Demange, Nadia; Francino, Maria Pilar; Goltsman, Eugene; Huang, Ying; Kopp, Olga R.; Labarre, Laurent; Lapidus, Alla; Lavire, Celine; Marechal, Joelle; Martinez, Michele; Mastronunzio, Juliana E.; Mullin, Beth C.; Niemann, James; Pujic, Pierre; Rawnsley, Tania; Rouy, Zoe; Schenowitz, Chantal; Sellstedt, Anita; Tavares, Fernando; Tomkins, Jeffrey P.; Vallenet, David; Valverde, Claudio; Wall, Luis G.; Wang, Ying; Medigue, Claudine; Benson, David R.

    2007-01-01

    Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the “actinorhizal” symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses. PMID:17151343

  3. Supporting Use of Evidence in Argumentation through Practice in Argumentation and Reflection in the Context of SOCRATES Learning Environment

    Science.gov (United States)

    Iordanou, Kalypso; Constantinou, Costas P.

    2015-01-01

    The aim of this study was to examine how students used evidence in argumentation while they engaged in argumentive and reflective activities in the context of a designed learning environment. A Web-based learning environment, SOCRATES, was developed, which included a rich data base on the topic of climate change. Sixteen 11th graders, working with…

  4. Ministering effectively in the context of Pentecostalism in Africa: A reformed missional reflection

    Directory of Open Access Journals (Sweden)

    T. Derrick Mashau

    2013-11-01

    Full Text Available Pentecostalism is a global phenomenon with a large following in North America, Latin America, Asia, Africa and other parts of the world. The rise, growth and influence of Pentecostalism in Africa are enormous and have, without fear of contradiction, become one of the dominant expressions of Christianity on the continent. A contextual analysis of Christianity in Africa showed that the African soil is more fertile for this movement. Its manifestation ranges from classical Pentecostalism (first wave, to the charismatic movement (second wave and the charismatic renewal movements (third wave. Its growth in Africa came with a fair number of missiological challenges to evangelical reformed churches, and therefore this article sought to sketch this movement by providing a historical perspective on Pentecostalism, a contextual analysis of Pentecostalism in Africa, issues and challenges in Pentecostalism, and concludes by looking closely at a reformed missional reflection, thereby providing some nuances as to how best one can minister effectively in the context of Pentecostalism. This article called for evangelical reformed churches to exercise the spirit of discernment whilst dealing with the influence of Pentecostalism, but at the same time to learn from this movement the zeal for mission and the role of the Holy Spirit in mission.Reformatoriese missionale nadenke oor effektiewe bediening in the konteks van Afrika Pentekostalisme. Pentekostalisme is 'n globale fenomeen met ‘n groot aanhang in Noord-Amerika, Latyns Amerika, Asië, Afrika en ander wêrelddele. Die opkoms, groei en invloed van Pentekostalisme in Afrika was geweldig en het een van die dominante gedaantes van Christenskap op die kontinent geword. ‘n Kontekstuele analise van Christenskap in Afrika wys dat Afrika meer vatbaar was vir hierdie tendens. Die manifestasie daarvan reik van klassieke Pentekostalisme (eerste golf, tot die charismatiese beweging (tweede golf en die charismatiese

  5. On the representability of complete genomes by multiple competing finite-context (Markov models.

    Directory of Open Access Journals (Sweden)

    Armando J Pinho

    Full Text Available A finite-context (Markov model of order k yields the probability distribution of the next symbol in a sequence of symbols, given the recent past up to depth k. Markov modeling has long been applied to DNA sequences, for example to find gene-coding regions. With the first studies came the discovery that DNA sequences are non-stationary: distinct regions require distinct model orders. Since then, Markov and hidden Markov models have been extensively used to describe the gene structure of prokaryotes and eukaryotes. However, to our knowledge, a comprehensive study about the potential of Markov models to describe complete genomes is still lacking. We address this gap in this paper. Our approach relies on (i multiple competing Markov models of different orders (ii careful programming techniques that allow orders as large as sixteen (iii adequate inverted repeat handling (iv probability estimates suited to the wide range of context depths used. To measure how well a model fits the data at a particular position in the sequence we use the negative logarithm of the probability estimate at that position. The measure yields information profiles of the sequence, which are of independent interest. The average over the entire sequence, which amounts to the average number of bits per base needed to describe the sequence, is used as a global performance measure. Our main conclusion is that, from the probabilistic or information theoretic point of view and according to this performance measure, multiple competing Markov models explain entire genomes almost as well or even better than state-of-the-art DNA compression methods, such as XM, which rely on very different statistical models. This is surprising, because Markov models are local (short-range, contrasting with the statistical models underlying other methods, where the extensive data repetitions in DNA sequences is explored, and therefore have a non-local character.

  6. The Colonial Context of Violence: Reflections on Violence in the Lives of Native American Women

    Science.gov (United States)

    Weaver, Hilary N.

    2009-01-01

    This article presents an overview of the ongoing colonial context that perpetuates and supports violence against First Nations women. This context must be recognized and changed as a prerequisite to eliminating or reducing this violence. The article includes a discussion of how gender roles have changed under colonization, the extent of violence,…

  7. Bootstrapping reflection on classroom interactions: discourse contexts of novice teachers' thinking

    NARCIS (Netherlands)

    Bannink, A.; Van Dam, J.

    2007-01-01

    The powerful role of prior experiences and cultural schemata in guiding novice teachers' conceptions of how to teach is hardly contested. We report on a ‘reflective practicum’ at the very beginning of a pre-service teacher education course that interconnects prior beliefs, reflection-in-action and

  8. Bootstrapping reflection on classroom interactions: discourse contexts of novice teachers' thinking

    NARCIS (Netherlands)

    A. Bannink; J. Van Dam

    2007-01-01

    The powerful role of prior experiences and cultural schemata in guiding novice teachers' conceptions of how to teach is hardly contested. We report on a ‘reflective practicum’ at the very beginning of a pre-service teacher education course that interconnects prior beliefs, reflection-in-action and r

  9. An Exploration of Reflection: Expression of Learning Style in an International Experiential Learning Context

    Science.gov (United States)

    Lamm, Alexa J.; Cannon, Karen J.; Roberts, T. Grady; Irani, Tracy A.; Snyder, Lori J. Unruh; Brendemuhl, Joel; Rodriguez, Mary T.

    2011-01-01

    Experiential learning techniques have been used in agricultural education programs for decades. An essential part of this experiential learning process is reflection. Kolb (1984) stated "knowledge results from the combination of grasping experience and transforming it" (p. 41) in a process that involves using reflection. Few researchers…

  10. Discovery of new enzymes and metabolic pathways by using structure and genome context.

    Science.gov (United States)

    Zhao, Suwen; Kumar, Ritesh; Sakai, Ayano; Vetting, Matthew W; Wood, B McKay; Brown, Shoshana; Bonanno, Jeffery B; Hillerich, Brandan S; Seidel, Ronald D; Babbitt, Patricia C; Almo, Steven C; Sweedler, Jonathan V; Gerlt, John A; Cronan, John E; Jacobson, Matthew P

    2013-10-31

    Assigning valid functions to proteins identified in genome projects is challenging: overprediction and database annotation errors are the principal concerns. We and others are developing computation-guided strategies for functional discovery with 'metabolite docking' to experimentally derived or homology-based three-dimensional structures. Bacterial metabolic pathways often are encoded by 'genome neighbourhoods' (gene clusters and/or operons), which can provide important clues for functional assignment. We recently demonstrated the synergy of docking and pathway context by 'predicting' the intermediates in the glycolytic pathway in Escherichia coli. Metabolite docking to multiple binding proteins and enzymes in the same pathway increases the reliability of in silico predictions of substrate specificities because the pathway intermediates are structurally similar. Here we report that structure-guided approaches for predicting the substrate specificities of several enzymes encoded by a bacterial gene cluster allowed the correct prediction of the in vitro activity of a structurally characterized enzyme of unknown function (PDB 2PMQ), 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) and cis-4-hydroxy-D-proline betaine (cHyp-B), and also the correct identification of the catabolic pathway in which Hyp-B 2-epimerase participates. The substrate-liganded pose predicted by virtual library screening (docking) was confirmed experimentally. The enzymatic activities in the predicted pathway were confirmed by in vitro assays and genetic analyses; the intermediates were identified by metabolomics; and repression of the genes encoding the pathway by high salt concentrations was established by transcriptomics, confirming the osmolyte role of tHyp-B. This study establishes the utility of structure-guided functional predictions to enable the discovery of new metabolic pathways.

  11. Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases.

    Science.gov (United States)

    Daboussi, Fayza; Zaslavskiy, Mikhail; Poirot, Laurent; Loperfido, Mariana; Gouble, Agnès; Guyot, Valerie; Leduc, Sophie; Galetto, Roman; Grizot, Sylvestre; Oficjalska, Danusia; Perez, Christophe; Delacôte, Fabien; Dupuy, Aurélie; Chion-Sotinel, Isabelle; Le Clerre, Diane; Lebuhotel, Céline; Danos, Olivier; Lemaire, Frédéric; Oussedik, Kahina; Cédrone, Frédéric; Epinat, Jean-Charles; Smith, Julianne; Yáñez-Muñoz, Rafael J; Dickson, George; Popplewell, Linda; Koo, Taeyoung; VandenDriessche, Thierry; Chuah, Marinee K; Duclert, Aymeric; Duchateau, Philippe; Pâques, Frédéric

    2012-07-01

    The ability to specifically engineer the genome of living cells at precise locations using rare-cutting designer endonucleases has broad implications for biotechnology and medicine, particularly for functional genomics, transgenics and gene therapy. However, the potential impact of chromosomal context and epigenetics on designer endonuclease-mediated genome editing is poorly understood. To address this question, we conducted a comprehensive analysis on the efficacy of 37 endonucleases derived from the quintessential I-CreI meganuclease that were specifically designed to cleave 39 different genomic targets. The analysis revealed that the efficiency of targeted mutagenesis at a given chromosomal locus is predictive of that of homologous gene targeting. Consequently, a strong genome-wide correlation was apparent between the efficiency of targeted mutagenesis (≤ 0.1% to ≈ 6%) with that of homologous gene targeting (≤ 0.1% to ≈ 15%). In contrast, the efficiency of targeted mutagenesis or homologous gene targeting at a given chromosomal locus does not correlate with the activity of individual endonucleases on transiently transfected substrates. Finally, we demonstrate that chromatin accessibility modulates the efficacy of rare-cutting endonucleases, accounting for strong position effects. Thus, chromosomal context and epigenetic mechanisms may play a major role in the efficiency rare-cutting endonuclease-induced genome engineering.

  12. Mind and Inferiority: Reflections on "English" as a University Discipline in a Black Context.

    Science.gov (United States)

    Aitken, Richard

    1987-01-01

    The social/political issues facing university English departments in South Africa include problems of identity and definition, the need for instruction within the context of social and political history, the problems of cultural relativism, the corrosive implications of Black subordination, and the complex alternatives of private and public…

  13. Personality-dependent differences in problem-solving performance in a social context reflect foraging strategies

    NARCIS (Netherlands)

    Zandberg, Lies; Quinn, John L.; Naguib, Marc; van Oers, Kees

    2016-01-01

    Abstract Individuals develop innovative behaviours to solve foraging challenges in the face of changing environmental conditions. Little is known about how individuals differ in their tendency to solve problems and in their subsequent use of this solving behaviour in social contexts. Here we

  14. Personality-dependent differences in problem-solving performance in a social context reflect foraging strategies

    NARCIS (Netherlands)

    Zandberg, Lies; Quinn, John L.; Naguib, Marc; Oers, Van Kees

    2016-01-01

    Individuals develop innovative behaviours to solve foraging challenges in the face of changing environmental conditions. Little is known about how individuals differ in their tendency to solve problems and in their subsequent use of this solving behaviour in social contexts. Here we investigated

  15. Pain ratings reflect cognitive context: a range frequency model of pain perception.

    Science.gov (United States)

    Watkinson, Pat; Wood, Alex M; Lloyd, Donna M; Brown, Gordon D A

    2013-05-01

    When painful stimuli are evaluated at the time they are experienced, judgments are made not in isolation but with reference to other experienced stimuli. We tested a specific quantitative model of how such context effects occur. Participants experienced 3 blocks of 11 different pressure pain stimuli, and rated each stimulus on a 0-10 scale of intensity. Stimulus distribution was varied between participants. Study 1 found that that the rating of a stimulus of a particular pressure was higher in the context in which it ranked highest. Study 2 found that pain ratings were higher in a context where most stimuli were relatively intense, even when the mean stimulus was constant. It is suggested that pain judgments are relative, involve the same cognitive processes as are used in other psychophysical and socioemotional judgments, and are well described by range frequency theory. This approach can further inform the existing body of research on context-dependent pain evaluation. Copyright © 2013 International Association for the Study of Pain. Published by Elsevier B.V. All rights reserved.

  16. Empirical Reflections on Academic Training Programs in Counseling Psychology: Contexts and Commitments

    Science.gov (United States)

    Neimeyer, Greg J.; Goodyear, Rodney K.

    2005-01-01

    The three main articles in the Major Contribution of the September issue of "The Counseling Psychologist" address academic training programs in counseling psychology, focusing on their institutional contexts and commitments. Each article examines one key issue, provides empirical data concerning this issue, and traces the practical implications of…

  17. AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context.

    Science.gov (United States)

    Martin, Olivier; Valsesia, Armand; Telenti, Amalio; Xenarios, Ioannis; Stevenson, Brian J

    2009-03-01

    We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in genomic context. Gene annotations can be retrieved from Ensembl, linkage disequilibrium data downloaded from HapMap and custom data imported in BED or WIG format. AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It implements an efficient cache system and allows the display of several, very large-scale genomic datasets. The Java code for AssociationViewer is distributed under the GNU General Public Licence and has been tested on Microsoft Windows XP, MacOSX and GNU/Linux operating systems. It is available from the SourceForge repository. This also includes Java webstart, documentation and example datafiles.

  18. A Corpus-Based Investigation of Critical Reflective Practice and Context in Early Career Teacher Settings

    Science.gov (United States)

    Murphy, Bróna

    2015-01-01

    Reflective practice is at the core of teacher education programmes and is highly regarded as an essential component in the education of new and experienced teachers. Given the recent interest in language use and the role of discourse in articulating knowledge of one's practice, this paper focuses on how two groups of early career teachers from…

  19. Educational Change in Post-Conflict Contexts: Reflections on the South African Experience 20 Years Later

    Science.gov (United States)

    Christie, Pam

    2016-01-01

    Reflecting on South African experience, this paper develops an analytical framework using the work of Henri Lefebvre and Nancy Fraser to understand why socially just arrangements may be so difficult to achieve in post-conflict reconstruction. The paper uses Lefebvre's analytic to trace three sets of entangled practices…

  20. Goal-Setting and Self-Reflection to Enhance Learners' Interaction in an ESP Context

    Science.gov (United States)

    Lozano Velandia, Sergio Andrés

    2015-01-01

    This qualitative action research study explored the interactions of young-adult learners carrying out self-reflection on their learning processes in an ESP (English for special purposes) course at an airline training-center in Bogotá, Colombia. Needs analysis revealed that learners had poor knowledge of technical English, and lacked strong…

  1. Arts practices in unreasonable doubt? Reflections on understandings of arts practices in healthcare contexts

    Science.gov (United States)

    Broderick, Sheelagh

    2011-01-01

    This article suggests that the discourse on arts and health encompass contemporary arts practices as an active and engaged analytical activity. Distinctions between arts therapy and arts practice are made to suggest that clinical evidence-based evaluation, while appropriate for arts therapy, is not appropriate for arts practice and in effect cast them in unreasonable doubt. Themes in current discourse on “arts” and “health” are broadly sketched to provide a context for discussion of arts practices. Approaches to knowledge validation in relation to each domain are discussed. These discourses are applied to the Irish healthcare context, offering a reading of three different art projects; it suggests a multiplicity of analyses beyond causal positive health gains. It is suggested that the social turn in medicine and the social turn in arts practices share some similar pre-occupations that warrant further attention. PMID:22675403

  2. Writing context-dependent item sets that reflect critical thinking learning outcomes.

    Science.gov (United States)

    Su, Whei Ming

    2007-01-01

    Faculty in a medical-surgical nursing course developed learning outcomes to foster critical thinking skills involved in clinical reasoning. To facilitate students' abilities to make effective clinical judgments, direct teaching of thinking skills was incorporated into nursing content instruction. This instructional design challenged faculty to develop test items that would permit direct observation of students' thought processes. The author describes how context-dependent item sets were developed to meet this evaluation need.

  3. Gender and Multiculturalism: Reflections on the Research in Poland after 1989 Year in the Context of Multicultural Communication

    Directory of Open Access Journals (Sweden)

    Małgorzata Bieńkowska

    2016-09-01

    Full Text Available The aim of the paper is to reflect on the condition of the research concerning gender issues in a culturally diverse society in Poland. After the political breakthrough in 1989, Poland emerged as a democratic state, where various categories of the Other came back to life. At the same time, new social minorities appeared. In the context of talking about issues of multiculturalism in Poland is a new aspect of gender, have not so much ignored, which overlooked in general discussions about the relationship between minority and dominant group.

  4. Reflections

    OpenAIRE

    Kennedy, Mary B

    2008-01-01

    In the two decades after the founding of Neuron, we witnessed the unfolding of the “molecular biology revolution” and its culmination in the sequencing of individual genomes. Cloning of cDNAs and rapid nucleotide sequencing were invented in the early 1970s. By the mid-1980s, “cDNA-cloning” was all the rage. A new breed of “molecular neuroscientists” began cloning and sequencing transcripts encoding neuronal receptors, ion channels, and signaling enzymes. The wealth of molecular data they gene...

  5. Mirroring Tirana Reflections on Tirana’s Urban Context and Perspectives

    Directory of Open Access Journals (Sweden)

    Dorina Pllumbi

    2013-04-01

    Full Text Available The crisis of the city is long been recognized worldwide, and the discussion about findinga form of sustainable urban development continues among professionals. Despite effortsto make simplistic classifications the difficulty to provide prescriptions is directly relatedto the complexity of each different reality, where the creation and development history,the climate and terrain characteristics, the economic situation, and in particular the cultureand the way of living makes it impossible to create prototypes.The paper reviews current debates on principles of the theoretical urban formsproposed to achieve sustainability of a city. Related to the Albanian context in general andthe metropolitan area of Tirana in particular, it analyses the problems and trends of therecent territorial development of this city and the potentialities to apply certain forms ofsustainable urban development that may be acceptable and feasible in the local context.Concluding, it’s given a new approach to achieving an urban sustainability, arguing thatthe efforts to this purpose are connected not only to its urban form. Instead, perceivingthe city in terms of process gives much more prospect in attaining the goal of asustainable city.

  6. DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history

    Energy Technology Data Exchange (ETDEWEB)

    Yuhki, Naoya; O' Brien, S.J. (National Cancer Institute, Frederick, MD (USA))

    1990-01-01

    The major histocompatibility complex (MHC) is a multigene complex of tightly linked homologous genes that encode cell surface antigens that play a key role in immune regulation and response to foreign antigens. In most species, MHC gene products display extreme antigenic polymorphism, and their variability has been interpreted to reflect an adaptive strategy for accommodating rapidly evolving infectious agents that periodically afflict natural populations. Determination of the extent of MHC variation has been limited to populations in which skin grafting is feasible or for which serological reagents have been developed. The authors present here a quantitative analysis of restriction fragment length polymorphism of MHC class I genes in several mammalian species (cats, rodents, humans) known to have very different levels of genetic diversity based on functional MHC assays and on allozyme surveys. When homologous class I probes were employed, a notable concordance was observed between the extent of MHC restriction fragment variation and functional MHC variation detected by skin grafts or genome-wide diversity estimated by allozyme screens. These results confirm the genetically depauperate character of the African cheetah, Acinonyx jubatus, and the Asiatic lion, Panthera leo persica; further, they support the use of class I MHC molecular reagents in estimating the extent and character of genetic diversity in natural populations.

  7. Reflections On Music Therapy Training Within E-learning Education Contexts

    Directory of Open Access Journals (Sweden)

    Imogen Nicola Clark

    2016-03-01

    Full Text Available The rapid expansion of e-learning technology is transforming the availability and delivery of university education. In Australia, e-learning offers opportunities for students to study music therapy while living in remote locations across a vast country. Students enrolled in the Masters of Music Therapy at the University of Melbourne may choose traditional on-campus learning or blended learning, which involves a combination of face-to-face intensives and e-learning. This article focuses on blended learning with reflections from music therapy students and teachers at the University of Melbourne. A description of the music therapy program is provided with a detailed explanation of one subject to illustrate how e-learning is managed. Our experiences of teaching blended learning students are discussed, and we identify key challenges including teacher-student rapport, regular communication, student-to-student engagement, and user friendly on line learning tools. We then reflect on student feedback from an informal evaluation, and explain students’ experiences of collaborative learning, interaction with teaching staff, and staying on track with learning. In conclusion, we discuss the future of music therapy education over an online forum, taking into consideration challenges and advantages for students, teaching academics and learning institutions, and offer ideas from which future research projects might be developed.

  8. Context-based FISH localization of genomic rearrangements within chromosome 15q11.2q13 duplicons

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    Knoll Joan HM

    2011-08-01

    Full Text Available Abstract Background Segmental duplicons (SDs predispose to an increased frequency of chromosomal rearrangements. These rearrangements can cause a diverse range of phenotypes due to haploinsufficiency, in cis positional effects or gene interruption. Genomic microarray analysis has revealed gene dosage changes adjacent to duplicons, but the high degree of similarity between duplicon sequences has confounded unequivocal assignment of chromosome breakpoints within these intervals. In this study, we localize rearrangements within duplicon-enriched regions of Angelman/Prader-Willi (AS/PWS syndrome chromosomal deletions with fluorescence in situ hybridization (FISH. Results Breakage intervals in AS deletions were localized recursively with short, coordinate-defined, single copy (SC and low copy (LC genomic FISH probes. These probes were initially coincident with duplicons and regions of previously reported breakage in AS/PWS. Subsequently, probes developed from adjacent genomic intervals more precisely delineated deletion breakage intervals involving genes, pseudogenes and duplicons in 15q11.2q13. The observed variability in the deletion boundaries within previously described Class I and Class II deletion AS samples is related to the local genomic architecture in this chromosomal region. Conclusions Chromosome 15 abnormalities associated with SDs were precisely delineated at a resolution equivalent to genomic Southern analysis. This context-dependent approach can define the boundaries of chromosome rearrangements for other genomic disorders associated with SDs.

  9. Comparative Education and Research Capacity Building: Reflections on International Transfer and the Significance of Context

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    Michael Crossley

    2012-04-01

    Full Text Available Recent years have seen a resurgence of interest in comparative and international education, along with a fundamental reconceptualisation of this distinctive multidisciplinary field of study. The nature and significance of these developments are explored with particular reference to their implications for broader research capacity building initiatives worldwide. In doing so, a critique of the international transfer of globally dominant research modalities and strategies is presented--along with arguments for increased attention to context sensitivity in both international development cooperation and educational research in general. Illustrative examples that support these arguments are drawn from the author's own research, from an analysis of emergent educational policy debates in the UK, and from related studies being carried out in Malaysia. In concluding, the strategic role of comparative research traditions and perspectives in a rapidly globalizing world is highlighted, while supporting the promotion of new initiative and research centres for comparative and international education.

  10. The Incorporation of Entrepreneurship in the Public Sector: reflections based on brazilian context

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    Josiel Valadares

    2015-04-01

    Full Text Available This essay aims seeks to broaden the debate on the incorporation of the theme Entrepreneurship in the Public Sector (EPS through the literature review on the reflective character to be taken to transpose concepts from the private sector to the public sector. It was understood that needs a critical discussion on the process of appropriating that theme in Brazil. It was observed that the Brazilian Public Administration is marked by a hybrid model of administration, in which patrimonial practices, bureaucratic and managerial coexist, making the complex adaptation of entrepreneurship. Therefore, we must be wary of exaggerated expectations regarding this theme in Brazilian Public Administration, as have several limitations that meet the sustainability of democratic governments.

  11. Putting evaluation capacity building in context: Reflections on the Ontario Brain Institute's Evaluation Support Program.

    Science.gov (United States)

    King, Jean A

    2017-05-13

    This article, in three parts, reflects on the content of the six articles included in the forum. It begins with a description of the Evaluation Support Program, emphasizing its key attributes. Next, it raises two points regarding ECB theory: (1) the need to become clearer about the concepts and terms used to describe and study this phenomenon, and (2) the potential value of social science theory to understand ECB and improve its practice. The article concludes with practical ideas for improving ECB: (1) framing it as an educative act, which assigns the evaluator the critical role of evaluation teacher/coach; and (2) the importance of never assuming that an ECB effort begins in unchartered territory, but rather that it builds on people's knowledge, skills, attitudes, and previous experiences. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context.

    Science.gov (United States)

    Kel, Alexander E; Niehof, Monika; Matys, Volker; Zemlin, Rüdiger; Borlak, Jürgen

    2008-01-01

    We report an application of machine learning algorithms that enables prediction of the functional context of transcription factor binding sites in the human genome. We demonstrate that our method allowed de novo identification of hepatic nuclear factor (HNF)4alpha binding sites and significantly improved an overall recognition of faithful HNF4alpha targets. When applied to published findings, an unprecedented high number of false positives were identified. The technique can be applied to any transcription factor.

  13. Intrapopulation Genome Size Variation in D. melanogaster Reflects Life History Variation and Plasticity

    Science.gov (United States)

    Ellis, Lisa L.; Huang, Wen; Quinn, Andrew M.; Ahuja, Astha; Alfrejd, Ben; Gomez, Francisco E.; Hjelmen, Carl E.; Moore, Kristi L.; Mackay, Trudy F. C.; Johnston, J. Spencer; Tarone, Aaron M.

    2014-01-01

    We determined female genome sizes using flow cytometry for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel, and found significant conspecific and intrapopulation variation in genome size. We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Expression data implicate differences in metabolism that correspond to genome size variation. These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species. Genome size variation accounts for a significant portion of life history variation in an environmentally dependent manner, suggesting that potential fitness effects associated with genome size variation also depend on environmental conditions. PMID:25057905

  14. Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity.

    Directory of Open Access Journals (Sweden)

    Lisa L Ellis

    2014-07-01

    Full Text Available We determined female genome sizes using flow cytometry for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel, and found significant conspecific and intrapopulation variation in genome size. We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Expression data implicate differences in metabolism that correspond to genome size variation. These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species. Genome size variation accounts for a significant portion of life history variation in an environmentally dependent manner, suggesting that potential fitness effects associated with genome size variation also depend on environmental conditions.

  15. How evolution of genomes is reflected in exact DNA sequence match statistics.

    Science.gov (United States)

    Massip, Florian; Sheinman, Michael; Schbath, Sophie; Arndt, Peter F

    2015-02-01

    Genome evolution is shaped by a multitude of mutational processes, including point mutations, insertions, and deletions of DNA sequences, as well as segmental duplications. These mutational processes can leave distinctive qualitative marks in the statistical features of genomic DNA sequences. One such feature is the match length distribution (MLD) of exactly matching sequence segments within an individual genome or between the genomes of related species. These have been observed to exhibit characteristic power law decays in many species. Here, we show that simple dynamical models consisting solely of duplication and mutation processes can already explain the characteristic features of MLDs observed in genomic sequences. Surprisingly, we find that these features are largely insensitive to details of the underlying mutational processes and do not necessarily rely on the action of natural selection. Our results demonstrate how analyzing statistical features of DNA sequences can help us reveal and quantify the different mutational processes that underlie genome evolution.

  16. Interprofessional collaboration - a matter of differentiation and integration? Theoretical reflections based in the context of Norwegian childcare.

    Science.gov (United States)

    Willumsen, Elisabeth

    2008-08-01

    This paper presents a selection of theoretical approaches illuminating some aspects of interprofessional collaboration, which will be related to theory of contingency as well as to the concepts of differentiation and integration. Theories that describe collaboration on an interpersonal as well as inter-organizational level are outlined and related to dynamic and contextual factors. Implications for the organization of welfare services are elucidated and a categorization of internal and external collaborative forms is proposed. A reflection model is presented in order to analyse the degree of integration in collaborative work and may serve as an analytical tool for addressing the linkage between different levels of collaboration and identifying opportunities and limitations. Some implications related to the legal mandate(s) given to childcare agencies are discussed in relation to the context of childcare in Norway.

  17. Public–Private Partnerships in Cloud-Computing Services in the Context of Genomic Research

    Science.gov (United States)

    Granados Moreno, Palmira; Joly, Yann; Knoppers, Bartha Maria

    2017-01-01

    Public–private partnerships (PPPs) have been increasingly used to spur and facilitate innovation in a number of fields. In healthcare, the purpose of using a PPP is commonly to develop and/or provide vaccines and drugs against communicable diseases, mainly in developing or underdeveloped countries. With the advancement of technology and of the area of genomics, these partnerships also focus on large-scale genomic research projects that aim to advance the understanding of diseases that have a genetic component and to develop personalized treatments. This new focus has created new forms of PPPs that involve information technology companies, which provide computing infrastructure and services to store, analyze, and share the massive amounts of data genomic-related projects produce. In this article, we explore models of PPPs proposed to handle, protect, and share the genomic data collected and to further develop genomic-based medical products. We also identify the reasons that make these models suitable and the challenges they have yet to overcome. To achieve this, we describe the details and complexities of MSSNG, International Cancer Genome Consortium, and 100,000 Genomes Project, the three PPPs that focus on large-scale genomic research to better understand the genetic components of autism, cancer, rare diseases, and infectious diseases with the intention to find appropriate treatments. Organized as PPP and employing cloud-computing services, the three projects have advanced quickly and are likely to be important sources of research and development for future personalized medicine. However, there still are unresolved matters relating to conflicts of interest, commercialization, and data control. Learning from the challenges encountered by past PPPs allowed us to establish that developing guidelines to adequately manage personal health information stored in clouds and ensuring the protection of data integrity and privacy would be critical steps in the development

  18. Regulatory hurdles for genome editing: process- vs. product-based approaches in different regulatory contexts

    OpenAIRE

    Sprink, Thorben; Eriksson, Dennis; Schiemann, Joachim; Hartung, Frank

    2016-01-01

    Novel plant genome editing techniques call for an updated legislation regulating the use of plants produced by genetic engineering or genome editing, especially in the European Union. Established more than 25?years ago and based on a clear distinction between transgenic and conventionally bred plants, the current EU Directives fail to accommodate the new continuum between genetic engineering and conventional breeding. Despite the fact that the Directive 2001/18/EC contains both process- and p...

  19. Public-Private Partnerships in Cloud-Computing Services in the Context of Genomic Research.

    Science.gov (United States)

    Granados Moreno, Palmira; Joly, Yann; Knoppers, Bartha Maria

    2017-01-01

    Public-private partnerships (PPPs) have been increasingly used to spur and facilitate innovation in a number of fields. In healthcare, the purpose of using a PPP is commonly to develop and/or provide vaccines and drugs against communicable diseases, mainly in developing or underdeveloped countries. With the advancement of technology and of the area of genomics, these partnerships also focus on large-scale genomic research projects that aim to advance the understanding of diseases that have a genetic component and to develop personalized treatments. This new focus has created new forms of PPPs that involve information technology companies, which provide computing infrastructure and services to store, analyze, and share the massive amounts of data genomic-related projects produce. In this article, we explore models of PPPs proposed to handle, protect, and share the genomic data collected and to further develop genomic-based medical products. We also identify the reasons that make these models suitable and the challenges they have yet to overcome. To achieve this, we describe the details and complexities of MSSNG, International Cancer Genome Consortium, and 100,000 Genomes Project, the three PPPs that focus on large-scale genomic research to better understand the genetic components of autism, cancer, rare diseases, and infectious diseases with the intention to find appropriate treatments. Organized as PPP and employing cloud-computing services, the three projects have advanced quickly and are likely to be important sources of research and development for future personalized medicine. However, there still are unresolved matters relating to conflicts of interest, commercialization, and data control. Learning from the challenges encountered by past PPPs allowed us to establish that developing guidelines to adequately manage personal health information stored in clouds and ensuring the protection of data integrity and privacy would be critical steps in the development of

  20. The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes.

    Directory of Open Access Journals (Sweden)

    Adam Alexander Thil Smith

    2012-05-01

    Full Text Available Of all biochemically characterized metabolic reactions formalized by the IUBMB, over one out of four have yet to be associated with a nucleic or protein sequence, i.e. are sequence-orphan enzymatic activities. Few bioinformatics annotation tools are able to propose candidate genes for such activities by exploiting context-dependent rather than sequence-dependent data, and none are readily accessible and propose result integration across multiple genomes. Here, we present CanOE (Candidate genes for Orphan Enzymes, a four-step bioinformatics strategy that proposes ranked candidate genes for sequence-orphan enzymatic activities (or orphan enzymes for short. The first step locates "genomic metabolons", i.e. groups of co-localized genes coding proteins catalyzing reactions linked by shared metabolites, in one genome at a time. These metabolons can be particularly helpful for aiding bioanalysts to visualize relevant metabolic data. In the second step, they are used to generate candidate associations between un-annotated genes and gene-less reactions. The third step integrates these gene-reaction associations over several genomes using gene families, and summarizes the strength of family-reaction associations by several scores. In the final step, these scores are used to rank members of gene families which are proposed for metabolic reactions. These associations are of particular interest when the metabolic reaction is a sequence-orphan enzymatic activity. Our strategy found over 60,000 genomic metabolons in more than 1,000 prokaryote organisms from the MicroScope platform, generating candidate genes for many metabolic reactions, of which more than 70 distinct orphan reactions. A computational validation of the approach is discussed. Finally, we present a case study on the anaerobic allantoin degradation pathway in Escherichia coli K-12.

  1. Genomic context drives transcription of insertion sequences in the bacterial endosymbiont Wolbachia wVulC.

    Science.gov (United States)

    Cerveau, Nicolas; Gilbert, Clément; Liu, Chao; Garrett, Roger A; Grève, Pierre; Bouchon, Didier; Cordaux, Richard

    2015-06-10

    Transposable elements (TEs) are DNA pieces that are present in almost all the living world at variable genomic density. Due to their mobility and density, TEs are involved in a large array of genomic modifications. In eukaryotes, TE expression has been studied in detail in several species. In prokaryotes, studies of IS expression are generally linked to particular copies that induce a modification of neighboring gene expression. Here we investigated global patterns of IS transcription in the Alphaproteobacterial endosymbiont Wolbachia wVulC, using both RT-PCR and bioinformatic analyses. We detected several transcriptional promoters in all IS groups. Nevertheless, only one of the potentially functional IS groups possesses a promoter located upstream of the transposase gene, that could lead up to the production of a functional protein. We found that the majority of IS groups are expressed whatever their functional status. RT-PCR analyses indicate that the transcription of two IS groups lacking internal promoters upstream of the transposase start codon may be driven by the genomic environment. We confirmed this observation with the transcription analysis of individual copies of one IS group. These results suggest that the genomic environment is important for IS expression and it could explain, at least partly, copy number variability of the various IS groups present in the wVulC genome and, more generally, in bacterial genomes. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Context-dependent individualization of nucleotides and virtual genomic hybridization allow the precise location of human SNPs.

    Science.gov (United States)

    Reyes, José; Gómez-Romero, Laura; Ibarra-Soria, Ximena; Palacios-Flores, Kim; Arriola, Luis R; Wences, Alejandro; García, Delfino; Boege, Margareta; Dávila, Guillermo; Flores, Margarita; Palacios, Rafael

    2011-09-13

    We have entered the era of individual genomic sequencing, and can already see exponential progress in the field. It is of utmost importance to exclude false-positive variants from reported datasets. However, because of the nature of the used algorithms, this task has not been optimized to the required level of precision. This study presents a unique strategy for identifying SNPs, called COIN-VGH, that largely minimizes the presence of false-positives in the generated data. The algorithm was developed using the X-chromosome-specific regions from the previously sequenced genomes of Craig Venter and James Watson. The algorithm is based on the concept that a nucleotide can be individualized if it is analyzed in the context of its surrounding genomic sequence. COIN-VGH consists of defining the most comprehensive set of nucleotide strings of a defined length that map with 100% identity to a unique position within the human reference genome (HRG). Such set is used to retrieve sequence reads from a query genome (QG), allowing the production of a genomic landscape that represents a draft HRG-guided assembly of the QG. This landscape is analyzed for specific signatures that indicate the presence of SNPs. The fidelity of the variation signature was assessed using simulation experiments by virtually altering the HRG at defined positions. Finally, the signature regions identified in the HRG and in the QG reads are aligned and the precise nature and position of the corresponding SNPs are detected. The advantages of COIN-VGH over previous algorithms are discussed.

  3. Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context.

    Science.gov (United States)

    Ha, Misook; Hong, Soondo; Li, Wen-Hsiung

    2013-05-01

    Histone modifications regulate chromatin structure and gene expression. Although nucleosome formation is known to be affected by primary DNA sequence composition, no sequence signature has been identified for histone modifications. It is known that dense H3K4me3 nucleosome sites are accompanied by a low density of other nucleosomes and are associated with gene activation. This observation suggests a different sequence composition of H3K4me3 from other nucleosomes. To understand the relationship between genome sequence and chromatin structure, we studied DNA sequences at histone modification sites in various human cell types. We found sequence specificity for H3K4me3, but not for other histone modifications. Using the sequence specificities of H3 and H3K4me3 nucleosomes, we developed a model that computes the probability of H3K4me3 occupation at each base pair from the genome sequence context. A comparison of our predictions with experimental data suggests a high performance of our method, revealing a strong association between H3K4me3 and specific genomic DNA context. The high probability of H3K4me3 occupation occurs at transcription start and termination sites, exon boundaries and binding sites of transcription regulators involved in chromatin modification activities, including histone acetylases and enhancer- and insulator-associated factors. Thus, the human genome sequence contains signatures for chromatin modifications essential for gene regulation and development. Our method may be applied to find new sequence elements functioning by chromatin modulation. Software and supplementary data are available at Bioinformatics online.

  4. Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context

    Science.gov (United States)

    Ha, Misook; Hong, Soondo; Li, Wen-Hsiung

    2013-01-01

    Motivation: Histone modifications regulate chromatin structure and gene expression. Although nucleosome formation is known to be affected by primary DNA sequence composition, no sequence signature has been identified for histone modifications. It is known that dense H3K4me3 nucleosome sites are accompanied by a low density of other nucleosomes and are associated with gene activation. This observation suggests a different sequence composition of H3K4me3 from other nucleosomes. Approach: To understand the relationship between genome sequence and chromatin structure, we studied DNA sequences at histone modification sites in various human cell types. We found sequence specificity for H3K4me3, but not for other histone modifications. Using the sequence specificities of H3 and H3K4me3 nucleosomes, we developed a model that computes the probability of H3K4me3 occupation at each base pair from the genome sequence context. Results: A comparison of our predictions with experimental data suggests a high performance of our method, revealing a strong association between H3K4me3 and specific genomic DNA context. The high probability of H3K4me3 occupation occurs at transcription start and termination sites, exon boundaries and binding sites of transcription regulators involved in chromatin modification activities, including histone acetylases and enhancer- and insulator-associated factors. Thus, the human genome sequence contains signatures for chromatin modifications essential for gene regulation and development. Our method may be applied to find new sequence elements functioning by chromatin modulation. Availability: Software and supplementary data are available at Bioinformatics online. Contact: misook.ha@samsung.com or wli@uchicago.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23511541

  5. The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

    Directory of Open Access Journals (Sweden)

    Marco Ventura

    2009-12-01

    Full Text Available Bifidobacteria, one of the relatively dominant components of the human intestinal microbiota, are considered one of the key groups of beneficial intestinal bacteria (probiotic bacteria. However, in addition to health-promoting taxa, the genus Bifidobacterium also includes Bifidobacterium dentium, an opportunistic cariogenic pathogen. The genetic basis for the ability of B. dentium to survive in the oral cavity and contribute to caries development is not understood. The genome of B. dentium Bd1, a strain isolated from dental caries, was sequenced to completion to uncover a single circular 2,636,368 base pair chromosome with 2,143 predicted open reading frames. Annotation of the genome sequence revealed multiple ways in which B. dentium has adapted to the oral environment through specialized nutrient acquisition, defences against antimicrobials, and gene products that increase fitness and competitiveness within the oral niche. B. dentium Bd1 was shown to metabolize a wide variety of carbohydrates, consistent with genome-based predictions, while colonization and persistence factors implicated in tissue adhesion, acid tolerance, and the metabolism of human saliva-derived compounds were also identified. Global transcriptome analysis demonstrated that many of the genes encoding these predicted traits are highly expressed under relevant physiological conditions. This is the first report to identify, through various genomic approaches, specific genetic adaptations of a Bifidobacterium taxon, Bifidobacterium dentium Bd1, to a lifestyle as a cariogenic microorganism in the oral cavity. In silico analysis and comparative genomic hybridization experiments clearly reveal a high level of genome conservation among various B. dentium strains. The data indicate that the genome of this opportunistic cariogen has evolved through a very limited number of horizontal gene acquisition events, highlighting the narrow boundaries that separate commensals from

  6. Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species.

    Science.gov (United States)

    West, Claire; James, Stephen A; Davey, Robert P; Dicks, Jo; Roberts, Ian N

    2014-07-01

    The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the internal transcribed spacer region, frequently used in plant phylogenetics, is now recognized as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analyzed data sets from the Saccharomyces Genome Resequencing Project, characterizing rDNA sequence variation within multiple strains of the baker's yeast Saccharomyces cerevisiae and its nearest wild relative Saccharomyces paradoxus in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterization of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intraspecies phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridization events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of

  7. Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted/founder genome

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    Song Hongshuo

    2012-10-01

    Full Text Available Abstract Background A modest change in HIV-1 fitness can have a significant impact on viral quasispecies evolution and viral pathogenesis, transmission and disease progression. To determine the impact of immune escape mutations selected by cytotoxic T lymphocytes (CTL on viral fitness in the context of the cognate transmitted/founder (T/F genome, we developed a new competitive fitness assay using molecular clones of T/F genomes lacking exogenous genetic markers and a highly sensitive and precise parallel allele-specific sequencing (PASS method. Results The T/F and mutant viruses were competed in CD4+ T-cell enriched cultures, relative proportions of viruses were assayed after repeated cell-free passage, and fitness costs were estimated by mathematical modeling. Naturally occurring HLA B57-restricted mutations involving the TW10 epitope in Gag and two epitopes in Tat/Rev and Env were assessed independently and together. Compensatory mutations which restored viral replication fitness were also assessed. A principal TW10 escape mutation, T242N, led to a 42% reduction in replication fitness but V247I and G248A mutations in the same epitope restored fitness to wild-type levels. No fitness difference was observed between the T/F and a naturally selected variant carrying the early CTL escape mutation (R355K in Env and a reversion mutation in the Tat/Rev overlapping region. Conclusions These findings reveal a broad spectrum of fitness costs to CTL escape mutations in T/F viral genomes, similar to recent findings reported for neutralizing antibody escape mutations, and highlight the extraordinary plasticity and adaptive potential of the HIV-1 genome. Analysis of T/F genomes and their evolved progeny is a powerful approach for assessing the impact of composite mutational events on viral fitness.

  8. Maternal and child reflective functioning in the context of child sexual abuse: pathways to depression and externalising difficulties

    Directory of Open Access Journals (Sweden)

    Karin Ensink

    2016-01-01

    Full Text Available Background: Sexual abuse is a well-recognised risk factor for child psychopathology. Little is known regarding whether child and maternal mentalization can be considered a potential resource or protective factor in this context, respectively, mediating or moderating the relationship between sexual abuse and psychopathology. Objective: The aims of this study were (1 to explore the relationships between child and maternal mentalizing, measured as reflective functioning (RF, and child depressive symptoms and externalising difficulties; and (2 to examine whether child mentalizing mediates the relationship between child sexual abuse (CSA and psychopathology. Method: A total of 168 children aged 7–12 years and their mothers participated in the study. The sample included 74 dyads where children had experienced sexual abuse. The Child Attachment Interview was rated by using the Child Reflective Functioning Scale to assess children's mentalization, and the Child Depression Inventory was used to assess depressive symptoms. Mothers completed the Parent Development Interview to assess maternal RF and the Child Behavior Checklist to assess their child's externalising difficulties. A model involving direct and indirect paths from CSA, child and maternal RF to child psychopathology was examined using Mplus software. Results: Child mentalization partially mediated the relationships between CSA and depressive symptoms, as well as the relationship between CSA and externalising difficulties. Maternal mentalization was an independent predictor of child externalising difficulties, with higher maternal RF associated with less externalising difficulties. Discussion: The findings indicate that by ages 7–12, child mentalization is an important inner resource associated with lower depression and externalising. In addition, this study provides new evidence of the importance of the parent's mentalizing stance for the development of self-regulation and externalising

  9. Maternal and child reflective functioning in the context of child sexual abuse: pathways to depression and externalising difficulties

    Science.gov (United States)

    Ensink, Karin; Bégin, Michaël; Normandin, Lina; Fonagy, Peter

    2016-01-01

    Background Sexual abuse is a well-recognised risk factor for child psychopathology. Little is known regarding whether child and maternal mentalization can be considered a potential resource or protective factor in this context, respectively, mediating or moderating the relationship between sexual abuse and psychopathology. Objective The aims of this study were (1) to explore the relationships between child and maternal mentalizing, measured as reflective functioning (RF), and child depressive symptoms and externalising difficulties; and (2) to examine whether child mentalizing mediates the relationship between child sexual abuse (CSA) and psychopathology. Method A total of 168 children aged 7–12 years and their mothers participated in the study. The sample included 74 dyads where children had experienced sexual abuse. The Child Attachment Interview was rated by using the Child Reflective Functioning Scale to assess children's mentalization, and the Child Depression Inventory was used to assess depressive symptoms. Mothers completed the Parent Development Interview to assess maternal RF and the Child Behavior Checklist to assess their child's externalising difficulties. A model involving direct and indirect paths from CSA, child and maternal RF to child psychopathology was examined using Mplus software. Results Child mentalization partially mediated the relationships between CSA and depressive symptoms, as well as the relationship between CSA and externalising difficulties. Maternal mentalization was an independent predictor of child externalising difficulties, with higher maternal RF associated with less externalising difficulties. Discussion The findings indicate that by ages 7–12, child mentalization is an important inner resource associated with lower depression and externalising. In addition, this study provides new evidence of the importance of the parent's mentalizing stance for the development of self-regulation and externalising difficulties in both

  10. Codon-triplet context unveils unique features of the Candida albicans protein coding genome

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    Oliveira José L

    2007-11-01

    Full Text Available Abstract Background The evolutionary forces that determine the arrangement of synonymous codons within open reading frames and fine tune mRNA translation efficiency are not yet understood. In order to tackle this question we have carried out a large scale study of codon-triplet contexts in 11 fungal species to unravel associations or relationships between codons present at the ribosome A-, P- and E-sites during each decoding cycle. Results Our analysis unveiled high bias within the context of codon-triplets, in particular strong preference for triplets of identical codons. We have also identified a surprisingly large number of codon-triplet combinations that vanished from fungal ORFeomes. Candida albicans exacerbated these features, showed an unbalanced tRNA population for decoding its pool of codons and used near-cognate decoding for a large set of codons, suggesting that unique evolutionary forces shaped the evolution of its ORFeome. Conclusion We have developed bioinformatics tools for large-scale analysis of codon-triplet contexts. These algorithms identified codon-triplets context biases, allowed for large scale comparative codon-triplet analysis, and identified rules governing codon-triplet context. They could also detect alterations to the standard genetic code.

  11. The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements.

    Science.gov (United States)

    Staton, S Evan; Bakken, Bradley H; Blackman, Benjamin K; Chapman, Mark A; Kane, Nolan C; Tang, Shunxue; Ungerer, Mark C; Knapp, Steven J; Rieseberg, Loren H; Burke, John M

    2012-10-01

    Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well-documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain-containing Gypsy LTR retrotransposons ('chromoviruses'), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.

  12. Population stratification in the context of diverse epidemiologic surveys sans genome-wide data

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    Matthew T. Oetjens

    2016-05-01

    Full Text Available Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS arrays. While array data is now widespread, these data are not ubiquitous as several large epidemiologic and clinic-based studies lack genome-wide data. One such large epidemiologic-based study lacking genome-wide data accessible to investigators is the National Health and Nutrition Examination Surveys (NHANES, population-based cross-sectional surveys of Americans linked to demographic, health, and lifestyle data conducted by the Centers for Disease Control and Prevention. DNA samples (n=14,998 were extracted from biospecimens from consented NHANES participants between 1991-1994 (NHANES III, phase 2 and 1999-2002 and represent three major self-identified racial/ethnic groups: non-Hispanic whites (n=6,634, non-Hispanic blacks (n=3,458, and Mexican Americans (n=3,950. We as the Epidemiologic Architecture for Genes Linked to Environment (EAGLE study genotyped candidate gene and GWAS-identified index variants in NHANES as part of the larger Population Architecture using Genomics and Epidemiology (PAGE I study for collaborative genetic association studies. To enable basic quality control such as estimation of genetic ancestry to control for population stratification in NHANES san genome-wide data, we outline here strategies that use limited genetic data to identify the markers optimal for characterizing genetic ancestry. From among 411 and 295 autosomal SNPs available in NHANES III and NHANES 1999-2002, we demonstrate that markers with ancestry information can be identified to estimate global ancestry. Despite limited resolution, global genetic ancestry is highly correlated with self-identified race for the majority of participants

  13. Secure Base Scripts are Associated with Maternal Parenting Behavior across Contexts and Reflective Functioning among Trauma-Exposed Mothers

    Science.gov (United States)

    Huth-Bocks, Alissa C.; Muzik, Maria; Beeghly, Marjorie; Earls, Lauren; Stacks, Ann M.

    2015-01-01

    There is growing evidence that ‘secure-base scripts’ (Waters & Waters, 2006) are an important part of the cognitive underpinnings of internal working models of attachment. Recent research in middle class samples has shown that secure-base scripts are linked to maternal attachment-oriented behavior and child outcomes. However, little is known about the correlates of secure base scripts in higher-risk samples. Participants in the current study included 115 mothers who were oversampled for childhood maltreatment and their infants. Results revealed that a higher level of secure base scriptedness was significantly related to more positive and less negative maternal parenting in both unstructured free play and structured teaching contexts, and to higher reflective functioning scores on the Parent Development Interview-Revised Short Form (Slade, Aber, Berger, Bresgi, & Kaplan, 2003). Associations with parent-child secure base scripts, specifically, indicate some level of relationship-specificity in attachment scripts. Many, but not all, significant associations remained after controlling for family income and maternal age. Findings suggest that assessing secure base scripts among mothers known to be at risk for parenting difficulties may be important for interventions aimed at altering problematic parental representations and caregiving behavior. PMID:25319230

  14. Regulatory hurdles for genome editing: process- vs. product-based approaches in different regulatory contexts.

    Science.gov (United States)

    Sprink, Thorben; Eriksson, Dennis; Schiemann, Joachim; Hartung, Frank

    2016-07-01

    Novel plant genome editing techniques call for an updated legislation regulating the use of plants produced by genetic engineering or genome editing, especially in the European Union. Established more than 25 years ago and based on a clear distinction between transgenic and conventionally bred plants, the current EU Directives fail to accommodate the new continuum between genetic engineering and conventional breeding. Despite the fact that the Directive 2001/18/EC contains both process- and product-related terms, it is commonly interpreted as a strictly process-based legislation. In view of several new emerging techniques which are closer to the conventional breeding than common genetic engineering, we argue that it should be actually interpreted more in relation to the resulting product. A legal guidance on how to define plants produced by exploring novel genome editing techniques in relation to the decade-old legislation is urgently needed, as private companies and public researchers are waiting impatiently with products and projects in the pipeline. We here outline the process in the EU to develop a legislation that properly matches the scientific progress. As the process is facing several hurdles, we also compare with existing frameworks in other countries and discuss ideas for an alternative regulatory system.

  15. Reflections on Mental Retardation and Eugenics, Old and New: Mensa and the Human Genome Project.

    Science.gov (United States)

    Smith, J. David

    1994-01-01

    This article addresses the moral and ethical issues of mental retardation and a continuing legacy of belief in eugenics. It discusses the involuntary sterilization of Carrie Buck in 1927, support for legalized killing of subnormal infants by 47% of respondents to a Mensa survey, and implications of the Human Genome Project for the field of mental…

  16. Reflections on Mental Retardation and Eugenics, Old and New: Mensa and the Human Genome Project.

    Science.gov (United States)

    Smith, J. David

    1994-01-01

    This article addresses the moral and ethical issues of mental retardation and a continuing legacy of belief in eugenics. It discusses the involuntary sterilization of Carrie Buck in 1927, support for legalized killing of subnormal infants by 47% of respondents to a Mensa survey, and implications of the Human Genome Project for the field of mental…

  17. Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia

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    Tisa Louis S

    2009-10-01

    Full Text Available Abstract Background Genome analysis of three Frankia sp. strains has revealed a high number of transposable elements in two of the strains. Twelve out of the 20 major families of bacterial Insertion Sequence (IS elements are represented in the 148 annotated transposases of Frankia strain HFPCcI3 (CcI3 comprising 3% of its total coding sequences (CDS. EAN1pec (EAN has 183 transposase ORFs from 13 IS families comprising 2.2% of its CDS. Strain ACN14a (ACN differs significantly from the other strains with only 33 transposase ORFs (0.5% of the total CDS from 9 IS families. Results Insertion sequences in the Frankia genomes were analyzed using BLAST searches, PHYML phylogenies and the IRF (Inverted Repeat Finder algorithms. To identify putative or decaying IS elements, a PSI-TBLASTN search was performed on all three genomes, identifying 36%, 39% and 12% additional putative transposase ORFs than originally annotated in strains CcI3, EAN and ACN, respectively. The distribution of transposase ORFs in each strain was then analysed using a sliding window, revealing significant clustering of elements in regions of the EAN and CcI3 genomes. Lastly the three genomes were aligned with the MAUVE multiple genome alignment tool, revealing several Large Chromosome Rearrangement (LCR events; many of which correlate to transposase clusters. Conclusion Analysis of transposase ORFs in Frankia sp. revealed low inter-strain diversity of transposases, suggesting that the majority of transposase proliferation occurred without recent horizontal transfer of novel mobile elements from outside the genus. Exceptions to this include representatives from the IS3 family in strain EAN and seven IS4 transposases in all three strains that have a lower G+C content, suggesting recent horizontal transfer. The clustering of transposase ORFs near LCRs revealed a tendency for IS elements to be associated with regions of chromosome instability in the three strains. The results of this

  18. The active engagement model of applied ethics as a structure for ethical reflection in the context of course-based service learning.

    Science.gov (United States)

    Nesbit, Kathryn C; Jensen, Gail M; Delany, Clare

    2017-08-30

    The purpose of this case report is to explore the active engagement model as a tool to illuminate the ethical reflections of student physical therapists in the context of service learning in a developing country. The study participants were a convenience sample of six students. The study design is a case report using a phenomenological perspective. Data were collected from students' narrative writing and semi-structured interviews. The steps of the active engagement model provided the structural framework for student responses. The analysis process included open coding, selective coding, and member checking. Results showed the emergence of two main themes: 1) gathering rich detail and 2) developing independent moral identity. Students' descriptions of their relationships were detailed and included explanations about the complexities of the sociocultural context. Independent and deliberate agency was evident by the students' preparedness to be collaborative, to raise ethical questions, to identify ethically important aspects of their practice and to describe their professional roles. The students noted that the use of the model increased their engagement in the ethical decision-making process and their recognition of ethical questions. This case report illustrates attributes of the active engagement model which have implications for teaching ethical reflection: scaffolding for ethical reflection, use of narrative for reflection, reflection in action, and illumination of relevant themes. Each of these attributes leads to the development of meaningful ethical reflection. The attributes of this model shown by this case report have potential applications to teaching ethical reflection.

  19. The influence of micronutrients in cell culture: a reflection on viability and genomic stability.

    Science.gov (United States)

    Arigony, Ana Lúcia Vargas; de Oliveira, Iuri Marques; Machado, Miriana; Bordin, Diana Lilian; Bergter, Lothar; Prá, Daniel; Henriques, João Antonio Pêgas

    2013-01-01

    Micronutrients, including minerals and vitamins, are indispensable to DNA metabolic pathways and thus are as important for life as macronutrients. Without the proper nutrients, genomic instability compromises homeostasis, leading to chronic diseases and certain types of cancer. Cell-culture media try to mimic the in vivo environment, providing in vitro models used to infer cells' responses to different stimuli. This review summarizes and discusses studies of cell-culture supplementation with micronutrients that can increase cell viability and genomic stability, with a particular focus on previous in vitro experiments. In these studies, the cell-culture media include certain vitamins and minerals at concentrations not equal to the physiological levels. In many common culture media, the sole source of micronutrients is fetal bovine serum (FBS), which contributes to only 5-10% of the media composition. Minimal attention has been dedicated to FBS composition, micronutrients in cell cultures as a whole, or the influence of micronutrients on the viability and genetics of cultured cells. Further studies better evaluating micronutrients' roles at a molecular level and influence on the genomic stability of cells are still needed.

  20. The Influence of Micronutrients in Cell Culture: A Reflection on Viability and Genomic Stability

    Science.gov (United States)

    Arigony, Ana Lúcia Vargas; de Oliveira, Iuri Marques; Bordin, Diana Lilian; Prá, Daniel; Pêgas Henriques, João Antonio

    2013-01-01

    Micronutrients, including minerals and vitamins, are indispensable to DNA metabolic pathways and thus are as important for life as macronutrients. Without the proper nutrients, genomic instability compromises homeostasis, leading to chronic diseases and certain types of cancer. Cell-culture media try to mimic the in vivo environment, providing in vitro models used to infer cells' responses to different stimuli. This review summarizes and discusses studies of cell-culture supplementation with micronutrients that can increase cell viability and genomic stability, with a particular focus on previous in vitro experiments. In these studies, the cell-culture media include certain vitamins and minerals at concentrations not equal to the physiological levels. In many common culture media, the sole source of micronutrients is fetal bovine serum (FBS), which contributes to only 5–10% of the media composition. Minimal attention has been dedicated to FBS composition, micronutrients in cell cultures as a whole, or the influence of micronutrients on the viability and genetics of cultured cells. Further studies better evaluating micronutrients' roles at a molecular level and influence on the genomic stability of cells are still needed. PMID:23781504

  1. The Influence of Micronutrients in Cell Culture: A Reflection on Viability and Genomic Stability

    Directory of Open Access Journals (Sweden)

    Ana Lúcia Vargas Arigony

    2013-01-01

    Full Text Available Micronutrients, including minerals and vitamins, are indispensable to DNA metabolic pathways and thus are as important for life as macronutrients. Without the proper nutrients, genomic instability compromises homeostasis, leading to chronic diseases and certain types of cancer. Cell-culture media try to mimic the in vivo environment, providing in vitro models used to infer cells' responses to different stimuli. This review summarizes and discusses studies of cell-culture supplementation with micronutrients that can increase cell viability and genomic stability, with a particular focus on previous in vitro experiments. In these studies, the cell-culture media include certain vitamins and minerals at concentrations not equal to the physiological levels. In many common culture media, the sole source of micronutrients is fetal bovine serum (FBS, which contributes to only 5–10% of the media composition. Minimal attention has been dedicated to FBS composition, micronutrients in cell cultures as a whole, or the influence of micronutrients on the viability and genetics of cultured cells. Further studies better evaluating micronutrients' roles at a molecular level and influence on the genomic stability of cells are still needed.

  2. Environmentally selected aphid variants in clonality context display differential patterns of methylation in the genome.

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    Claude Pasquier

    Full Text Available Heritability of acquired phenotypic traits is an adaptive evolutionary process that appears more complex than the basic allele selection guided by environmental pressure. In insects, the trans-generational transmission of epigenetic marks in clonal and/or sexual species is poorly documented. Aphids were used as a model to explore this feature because their asexual phase generates a stochastic and/or environment-oriented repertoire of variants. The a priori unchanged genome in clonal individuals prompts us to hypothesize whether covalent methyl DNA marks might be associated to the phenotypic variability and fitness selection. The full differential transcriptome between two environmentally selected clonal variants that originated from the same founder mother was mapped on the entire genomic scaffolds, in parallel with the methyl cytosine distribution. Data suggest that the assortments of heavily methylated DNA sites are distinct in these two clonal phenotypes. This might constitute an epigenetic mechanism that confers the robust adaptation of insect species to various environments involving clonal reproduction.

  3. Sequence Similarity of Clostridium difficile Strains by Analysis of Conserved Genes and Genome Content Is Reflected by Their Ribotype Affiliation

    Science.gov (United States)

    Kurka, Hedwig; Ehrenreich, Armin; Ludwig, Wolfgang; Monot, Marc; Rupnik, Maja; Barbut, Frederic; Indra, Alexander; Dupuy, Bruno; Liebl, Wolfgang

    2014-01-01

    PCR-ribotyping is a broadly used method for the classification of isolates of Clostridium difficile, an emerging intestinal pathogen, causing infections with increased disease severity and incidence in several European and North American countries. We have now carried out clustering analysis with selected genes of numerous C. difficile strains as well as gene content comparisons of their genomes in order to broaden our view of the relatedness of strains assigned to different ribotypes. We analyzed the genomic content of 48 C. difficile strains representing 21 different ribotypes. The calculation of distance matrix-based dendrograms using the neighbor joining method for 14 conserved genes (standard phylogenetic marker genes) from the genomes of the C. difficile strains demonstrated that the genes from strains with the same ribotype generally clustered together. Further, certain ribotypes always clustered together and formed ribotype groups, i.e. ribotypes 078, 033 and 126, as well as ribotypes 002 and 017, indicating their relatedness. Comparisons of the gene contents of the genomes of ribotypes that clustered according to the conserved gene analysis revealed that the number of common genes of the ribotypes belonging to each of these three ribotype groups were very similar for the 078/033/126 group (at most 69 specific genes between the different strains with the same ribotype) but less similar for the 002/017 group (86 genes difference). It appears that the ribotype is indicative not only of a specific pattern of the amplified 16S–23S rRNA intergenic spacer but also reflects specific differences in the nucleotide sequences of the conserved genes studied here. It can be anticipated that the sequence deviations of more genes of C. difficile strains are correlated with their PCR-ribotype. In conclusion, the results of this study corroborate and extend the concept of clonal C. difficile lineages, which correlate with ribotypes affiliation. PMID:24482682

  4. Self-Reflecting in Developmental Context: Variations in Level and Patterning during the First 2 University Years

    Science.gov (United States)

    Bell, Nancy J.; Wieling, Elizabeth; Watson, Wendy

    2004-01-01

    Self-reflection, typically operationalized in scales of egocentrism and introspectiveness, is portrayed as problematic in much of the literature on adolescents. Self-reflection has been linked to dysfunctional self-consciousness, symptomatology, and risk behaviors. Yet, self-reflection also is seen as essential for adolescent development,…

  5. Use of genomic tools to improve cattle health in the context of infectious diseases

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    Mikolaj Marek Raszek

    2016-03-01

    Full Text Available Although infectious diseases impose a heavy economic burden on the cattle industry, the etiology of many disorders that affect livestock is not fully elucidated, and effective countermeasures are often lacking. The main tools available until now have been vaccines, antibiotics and antiparasitic drugs. Although these have been very successful in some cases, the appearance of parasite and microbial resistance to these treatments is a cause of concern. This review describes the rapid gains achieved to track disease progression, identify the pathogens involved, and map pathogen interactions with the host. Next-generation sequencing provides important opportunities to tackle problems associated with pathogenic illnesses. Use of novel genomic tools subsequently aids in treatment development, as well as successful creation of breeding programs aimed towards less susceptible livestock. These may be important tools for mitigating the long term effects of combating infection and helping reduce the reliance on antibiotic treatment.

  6. Genome complexity in the coelacanth is reflected in its adaptive immune system.

    Science.gov (United States)

    Saha, Nil Ratan; Ota, Tatsuya; Litman, Gary W; Hansen, John; Parra, Zuly; Hsu, Ellen; Buonocore, Francesco; Canapa, Adriana; Cheng, Jan-Fang; Amemiya, Chris T

    2014-09-01

    We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding α/β and γ/δ T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR α/δ locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations.

  7. Genome complexity in the coelacanth is reflected in its adaptive immune system

    Science.gov (United States)

    Saha, Nil Ratan; Ota, Tatsuya; Litman, Gary W.; Hansen, John; Parra, Zuly; Hsu, Ellen; Buonocore, Francesco; Canapa, Adriana; Cheng, Jan-Fang; Amemiya, Chris T.

    2014-01-01

    We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding α/β and γ/δ T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR α/δ locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations.

  8. Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions.

    Science.gov (United States)

    Martí-Arbona, Ricardo; Mu, Fangping; Nowak-Lovato, Kristy L; Wren, Melinda S; Unkefer, Clifford J; Unkefer, Pat J

    2014-12-18

    The clustering of genes in a pathway and the co-location of functionally related genes is widely recognized in prokaryotes. We used these characteristics to predict the metabolic involvement for a Transcriptional Regulator (TR) of unknown function, identified and confirmed its biological activity. A software tool that identifies the genes encoded within a defined genomic neighborhood for the subject TR and its homologs was developed. The output lists of genes in the genetic neighborhoods, their annotated functions, the reactants/products, and identifies the metabolic pathway in which the encoded-proteins function. When a set of TRs of known function was analyzed, we observed that their homologs frequently had conserved genomic neighborhoods that co-located the metabolically related genes regulated by the subject TR. We postulate that TR effectors are metabolites in the identified pathways; indeed the known effectors were present. We analyzed Bxe_B3018 from Burkholderia xenovorans, a TR of unknown function and predicted that this TR was related to the glycine, threonine and serine degradation. We tested the binding of metabolites in these pathways and for those that bound, their ability to modulate TR binding to its specific DNA operator sequence. Using rtPCR, we confirmed that methylglyoxal was an effector of Bxe_3018. These studies provide the proof of concept and validation of a systematic approach to the discovery of the biological activity for proteins of unknown function, in this case a TR. Bxe_B3018 is a methylglyoxal responsive TR that controls the expression of an operon composed of a putative efflux system.

  9. Transfer of Nature of Science Understandings into Similar Contexts: Promises and Possibilities of an Explicit Reflective Approach

    Science.gov (United States)

    Khishfe, Rola

    2013-11-01

    The purpose of this study was to (a) investigate the effectiveness of explicit nature of science (NOS) instruction in the context of controversial socioscientific issues and (b) explore whether the transfer of acquired NOS understandings, which were explicitly taught in the context of one socioscientific context, into other similar contexts (familiar and unfamiliar) was possible. Participants were 10th grade students in two intact sections at one high school. The treatment involved teaching a six-week unit about genetic engineering. For one group (non-NOS group), there was no explicit instruction about NOS. For the other group (NOS group), explicit instruction about three NOS aspects (subjective, empirical, and tentative) was dispersed across the genetic engineering unit. A questionnaire including two open-ended scenarios, in conjunction with semi-structured interviews, was used to assess the change in participants' understandings of NOS and their ability to transfer their acquired understandings into similar contexts. The first scenario involved a familiar context about genetically modified food and the second one focused on an unfamiliar context about water fluoridation. Results showed no improvement in NOS understandings of participants in the non-NOS group in relation to the familiar and unfamiliar contexts. On the other hand, there was a general improvement in the NOS understandings of participants in the NOS group in relation to both the familiar and unfamiliar contexts. Implications about the transfer of participants' acquired NOS understandings on the basis of the distance between the context of learning and that of application are highlighted and discussed in link with the classroom learning environment.

  10. The multifaceted origin of taurine cattle reflected by the mitochondrial genome.

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    Alessandro Achilli

    Full Text Available A Neolithic domestication of taurine cattle in the Fertile Crescent from local aurochsen (Bos primigenius is generally accepted, but a genetic contribution from European aurochsen has been proposed. Here we performed a survey of a large number of taurine cattle mitochondrial DNA (mtDNA control regions from numerous European breeds confirming the overall clustering within haplogroups (T1, T2 and T3 of Near Eastern ancestry, but also identifying eight mtDNAs (1.3% that did not fit in haplogroup T. Sequencing of the entire mitochondrial genome showed that four mtDNAs formed a novel branch (haplogroup R which, after the deep bifurcation that gave rise to the taurine and zebuine lineages, constitutes the earliest known split in the mtDNA phylogeny of B. primigenius. The remaining four mtDNAs were members of the recently discovered haplogroup Q. Phylogeographic data indicate that R mtDNAs were derived from female European aurochsen, possibly in the Italian Peninsula, and sporadically included in domestic herds. In contrast, the available data suggest that Q mtDNAs and T subclades were involved in the same Neolithic event of domestication in the Near East. Thus, the existence of novel (and rare taurine haplogroups highlights a multifaceted genetic legacy from distinct B. primigenius populations. Taking into account that the maternally transmitted mtDNA tends to underestimate the extent of gene flow from European aurochsen, the detection of the R mtDNAs in autochthonous breeds, some of which are endangered, identifies an unexpected reservoir of genetic variation that should be carefully preserved.

  11. Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication.

    Science.gov (United States)

    Xiang, Yezi; Huang, Chien-Hsun; Hu, Yi; Wen, Jun; Li, Shisheng; Yi, Tingshuang; Chen, Hongyi; Xiang, Jun; Ma, Hong

    2017-02-01

    Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ∼3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ∼101.6 Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.

  12. The Armc10/SVH gene: genome context, regulation of mitochondrial dynamics and protection against Aβ-induced mitochondrial fragmentation

    Science.gov (United States)

    Serrat, R; Mirra, S; Figueiro-Silva, J; Navas-Pérez, E; Quevedo, M; López-Doménech, G; Podlesniy, P; Ulloa, F; Garcia-Fernàndez, J; Trullas, R; Soriano, E

    2014-01-01

    Mitochondrial function and dynamics are essential for neurotransmission, neural function and neuronal viability. Recently, we showed that the eutherian-specific Armcx gene cluster (Armcx1–6 genes), located in the X chromosome, encodes for a new family of proteins that localise to mitochondria, regulating mitochondrial trafficking. The Armcx gene cluster evolved by retrotransposition of the Armc10 gene mRNA, which is present in all vertebrates and is considered to be the ancestor gene. Here we investigate the genomic organisation, mitochondrial functions and putative neuroprotective role of the Armc10 ancestor gene. The genomic context of the Armc10 locus shows considerable syntenic conservation among vertebrates, and sequence comparisons and CHIP-data suggest the presence of at least three conserved enhancers. We also show that the Armc10 protein localises to mitochondria and that it is highly expressed in the brain. Furthermore, we show that Armc10 levels regulate mitochondrial trafficking in neurons, but not mitochondrial aggregation, by controlling the number of moving mitochondria. We further demonstrate that the Armc10 protein interacts with the KIF5/Miro1-2/Trak2 trafficking complex. Finally, we show that overexpression of Armc10 in neurons prevents Aβ-induced mitochondrial fission and neuronal death. Our data suggest both conserved and differential roles of the Armc10/Armcx gene family in regulating mitochondrial dynamics in neurons, and underscore a protective effect of the Armc10 gene against Aβ-induced toxicity. Overall, our findings support a further degree of regulation of mitochondrial dynamics in the brain of more evolved mammals. PMID:24722288

  13. Reflecting the Context of MPA Education in the Time of Economic Crisis in Public Sectors in Britain and the Netherlands

    Science.gov (United States)

    Oldfield, Chrissie; Berg, Mireille van den

    2013-01-01

    The reality of the economic crisis and subsequent cuts in public sector funding in some European countries means that the context for public management education is significantly changing. In a period of economic constraint there is the obvious questioning of the cost of public management education programmes and even more of their relevance and…

  14. Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration

    National Research Council Canada - National Science Library

    Manoj Kannan; Jingfeng Li; Sarah E Fritz; Kathryn E Husarek; Jonathan C Sanford; Teresa L Sullivan; Pawan Kumar Tiwary; Wenfeng An; Jef D Boeke; David E Symer

    2017-01-01

    ... retrotransposon reporter constructs. Results Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human...

  15. Guided Portfolio Writing as a Scaffold for Reflective Learning in In-Service Contexts: A Case Study

    Science.gov (United States)

    Pires Pereira, Íris Susana; Cristo Parente, Maria Cristina; Vieira da Silva, Cristina

    2016-01-01

    Language is widely recognized as an inescapable mediating tool for professional learning, and with this text we want to contribute to a better understanding of the particular role that guided writing can play in in-service professional reflective learning. We analysed one pre-school teacher's written portfolio, the construction of which was guided…

  16. Teaching percussion in a music therapy training context: reflections on different cultures, PBL and ways of teaching

    DEFF Research Database (Denmark)

    Anderson-Ingstrup, Jens; Gattino, Gustavo

    2017-01-01

    This publication deals with reflections on teaching percussion in the music therapy training at Aalborg University (Denmark). Discussions are focused in challenges and characteristics of this teaching as follows: cultural differences, teaching based on Problem Based Methodology (PBL) and the ways...

  17. Taking a long look at Art: Reflections on the context of production and consumption of art in Art Therapy

    OpenAIRE

    Gilroy, Andrea

    2014-01-01

    This paper draws on experiences of looking at art to consider the influence of social context on the production and consumption of art in art therapy. I draw on art historical discourses to explore the experience and relate this to looking at art in art therapy. I suggest that professional socialisation profoundly influences how art therapists look and think about what they see. I propose that attention to our tacit knowledge about art, extending art therapy’s practices of looking to include ...

  18. Taking a long look at Art: Reflections on the context of production and consumption of art in Art Therapy

    OpenAIRE

    Gilroy, Andrea

    2014-01-01

    This paper draws on experiences of looking at art to consider the influence of social context on the production and consumption of art in art therapy. I draw on art historical discourses to explore the experience and relate this to looking at art in art therapy. I suggest that professional socialisation profoundly influences how art therapists look and think about what they see. I propose that attention to our tacit knowledge about art, extending art therapy’s practices of looking to include ...

  19. Reflective Journals of Students Taking a Positive Youth-Development Course in a University Context in Hong Kong

    Directory of Open Access Journals (Sweden)

    Daniel T. L. Shek

    2012-01-01

    Full Text Available To promote the holistic development of university students, a course entitled “Tomorrow's Leaders” was developed and offered at The Hong Kong Polytechnic University. Based on a case study approach, reflective journals of five outstanding students of the course are presented and analyzed (i.e., thick description, with several themes emerging from the reflection. First, the students liked the course, and they identified many positive attributes. Second, the students appreciated the instructors. Third, the students viewed that the course contributed to different aspects of their development. Fourth, some areas of improvements were proposed. In conjunction with other evaluation mechanisms, the present findings strongly suggest that the course is able to promote psychosocial competencies in university students taking this course.

  20. EgoFlecto: stimulating being calm and in control through self-reflection in the context of driving

    DEFF Research Database (Denmark)

    Mosleh, Sara Said; Schmidt, Nele; Teisanu, Tudor

    2015-01-01

    commuting and propose a concept for enhancing this notion. Based on an iterative design process, we have developed a platform to test different ways of enhancing self-reflection in the car. The concept EgoFlecto is based on a seductive design strategy that aims to alter people's behavior simply through self......The car has for a long time been an essential part of a household and has different meanings for the individual. Some experience their car simply as a practicality, while others are far more attached to it. In this project we investigate the notion of being calm and in control in the car while......-reflection and not through a forceful design. The design tries to present the driver with their actions, without requiring different forms of interactions, but by letting the driver interact with the car as usual....

  1. A Feminist Reflection on Ethnographic Research in China: Gender, Sex, and Power in Cross-Cultural Context

    Directory of Open Access Journals (Sweden)

    Arianne M. Gaetano

    2016-03-01

    Full Text Available As a feminist cultural anthropologist specializing in social transformations in contemporary China, my research and teaching necessarily involves exploring the construction of difference, the intersectionality of gender with other social positions, and how difference upholds or challenges power. In this essay, I employ biographical reflection to illustrate how my everyday experiences as a student, foreign English teacher, and scholarly researcher in China have refined my awareness of these important insights of feminist theory. As my attention to these processes increased, I became more mindful of the myriad ways women negotiate cultural configurations of gender and power in their everyday lives. Personal experiences also prompted me to reflect on how my identity and positionality impact the research process and outcomes. Thus experiential knowledge greatly enriched my study and understanding of the changing lives of women in China. I suggest how educators can impart these valuable lessons to students through experiential learning.

  2. Understanding Group-based Learning in an Academic Context : Rwandan Students’ Reflections on Collaborative Writing and Peer Assessment

    OpenAIRE

    Mutwarasibo, Faustin

    2013-01-01

    The overarching aim of the present thesis is to gain knowledge about how Rwandan university students understand and practice group-based learning. Specifically, this research takes a social constructivist perspective when examining how second year students within the area of Modern Languages reflect on collaborative writing and peer assessment as means to promote academic writing and active learning. Four studies make up this research. Thus, Study I examines how students carry out self-direct...

  3. Teachers’ Reflection Process to Improve Learning Assessment Practices in the Context of Education for Youngsters and Adults (EPJA

    Directory of Open Access Journals (Sweden)

    Juan Ariel Muñoz Olivero

    2016-06-01

    Full Text Available Education for youngsters and adults (in Spanish, EPJA has reached prominence in the Chilean educational system. It has had to give a new chance to a large number of young people who, for one reason or another, did not complete their studies in traditional training. In this scenario, it explores pedagogical practices developed by teachers working with youngsters and adults, especially those who refer to learning assessment. Therefore, the purpose of this study is to present the results of a reflection carried out by a group of teachers from a comprehensive adult education center, in order to improve their practices to evaluate their students’ learning. The research model is based on the qualitative approach with a case study design. It makes a comprehensive diagnostic of teaching practices, conducted through discussion groups. The analysis of the results shows that most teachers working at this educational center follow traditional assessment practices. They tend to copy conceptions of assessment centered around products that can be scored in order to check goal achievement, rather than around providing feedback that promotes self-regulated learning. However, the reflection also shows that teachers are willing to participate in pedagogical reflection sessions that guide them to improve their assessment practices.

  4. The Landscapes of the Bosque Rodrigues Alves, Belém (PA: reflections on the conservation of urban patrimony in the amazonian context

    Directory of Open Access Journals (Sweden)

    Flávio Leonel Abreu da Silveira

    2014-12-01

    Full Text Available This paper aims at discussing the importance of the woods Bosque Rodrigues Alves (Belém - PA for the Pará urban context, seeking to reflect on their status as County Heritage, considering the spectrum of patrimonies included there. Based on this, the discussion on the topic of landscapes, sociability and relationships between nature and culture in the field of heritage conservation related to the urban green area, implies the necessity of rethinking the opposition of culture versus nature, and the consequent problematization of the cultural landscape concept as an alternative to surmount it.

  5. [Technology and humanization of the neonatal intensive care unit: reflections in the context of the health-illness process].

    Science.gov (United States)

    da Silva, Laura Johanson; da Silva, Leila Rangel; Christoffel, Marialda Moreira

    2009-09-01

    This article reflects on technology and humanization in care of newborns, having as theoretical premise the health-illness process. Some parallels are established among the several conceptions of health and illness, and their influences in the way we behave and think about the care spaces as subjects of the neonatal care. The Kangaroo Mother Care is presented as a relational technology that proposes to shelter the family-baby unity in the Neonatal Intensive Care Unit, valuing experiences and major needs of affection and comprehension.

  6. Taking the Concept of Citizenship in Mental Health across Countries. Reflections on Transferring Principles and Practice to Different Sociocultural Contexts

    Directory of Open Access Journals (Sweden)

    Francisco José Eiroa-Orosa

    2017-06-01

    Full Text Available Transferring principles and practices to different sociocultural and professional contexts in the field of mental health can be very complex. Previous research on public health policy points to difficulties in different areas such as the understanding the new concepts, their applicability in different health systems, and suitable approaches to its effective implementation. The purpose of this article is to describe and analyze the process of transferring the concept of Citizenship, from its United States origins in mental health outreach work with persons who are homeless to Catalonia, Spain. We define Citizenship as promoting the rights, responsibilities, roles, resources and relationships of persons with mental illnesses, along with a sense of belonging that is validated by other citizens. The process of this transition involves embedding Citizenship in the mental health “first-person” (internationally known as Consumer/Survivor/Peer movement in Catalonia. The paper includes a discussion of the concept of transference, including a case example of the adoption of the concept of mental health recovery in different countries. Following this, we describe the United States Citizenship model and key elements of its development. We then turn to Spain and the evolution of its mental health system, and then to Catalonia for a brief case history of transference of the principles and practices of Citizenship to that region. The “take home message” of this work is that concepts being brought from one sociocultural and national context to another, must focus on contextualization in the ‘adoptee’s’ practices, including the balance between personal involvement and professional rigor, the involvement of key actors, and ongoing evaluation of actions taken.

  7. AFRICAN-STYLE MEDIATION AND WESTERN-STYLE DIVORCE AND FAMILY MEDIATION: REFLECTIONS FOR THE SOUTH AFRICAN CONTEXT

    Directory of Open Access Journals (Sweden)

    AE Boniface

    2012-12-01

    Full Text Available Both Western-styled mediation and African-styled mediation are practised in South Africa. Each of these models is applied in specific social contexts. In this article a brief explanation of what is meant by the term divorce and family mediation is provided. Thereafter the principles and processes of both Western-styled divorce and family mediation and African-styled group mediation are explored. Attention is given to the roles of mediators in both of these models as well as the ubuntu-styled values found in African group mediation. In Africa, there is a tradition of family neighbourhood negotiation facilitated by elders and an attitude of togetherness in the spirit of humanhood. Both of these show a commitment to the community concerned and a comprehensive view of life. In Africa conflicts are viewed as non-isolated events and are viewed in their social contexts. Not only are consequences for the disputing parties taken into account but also consequences for others in their families. These methods can be found in present-day methods, which are either used independently of imported Western structures or used alternatively to such structures. In this article the concept of mediation circles, as currently found in Western-styled mediation are also covered. Additionally, the provisions of the Children’s Act 38 of 2005 referring to mediation as well as the provisions of the Child Justice Act 75 of 2008 and family group conferencing in the realm of restorative justice in South Africa are critiqued. It is suggested that divorce and family mediation can learn from the principles of restorative justice applied during family group conferencing as well as from African-styled group mediation.

  8. Taking the Concept of Citizenship in Mental Health across Countries. Reflections on Transferring Principles and Practice to Different Sociocultural Contexts.

    Science.gov (United States)

    Eiroa-Orosa, Francisco José; Rowe, Michael

    2017-01-01

    Transferring principles and practices to different sociocultural and professional contexts in the field of mental health can be very complex. Previous research on public health policy points to difficulties in different areas such as the understanding the new concepts, their applicability in different health systems, and suitable approaches to its effective implementation. The purpose of this article is to describe and analyze the process of transferring the concept of Citizenship, from its United States origins in mental health outreach work with persons who are homeless to Catalonia, Spain. We define Citizenship as promoting the rights, responsibilities, roles, resources and relationships of persons with mental illnesses, along with a sense of belonging that is validated by other citizens. The process of this transition involves embedding Citizenship in the mental health "first-person" (internationally known as Consumer/Survivor/Peer) movement in Catalonia. The paper includes a discussion of the concept of transference, including a case example of the adoption of the concept of mental health recovery in different countries. Following this, we describe the United States Citizenship model and key elements of its development. We then turn to Spain and the evolution of its mental health system, and then to Catalonia for a brief case history of transference of the principles and practices of Citizenship to that region. The "take home message" of this work is that concepts being brought from one sociocultural and national context to another, must focus on contextualization in the 'adoptee's' practices, including the balance between personal involvement and professional rigor, the involvement of key actors, and ongoing evaluation of actions taken.

  9. Genomics and Bioinformatics in Undergraduate Curricula: Contexts for Hybrid Laboratory/Lecture Courses for Entering and Advanced Science Students

    Science.gov (United States)

    Temple, Louise; Cresawn, Steven G.; Monroe, Jonathan D.

    2010-01-01

    Emerging interest in genomics in the scientific community prompted biologists at James Madison University to create two courses at different levels to modernize the biology curriculum. The courses are hybrids of classroom and laboratory experiences. An upper level class uses raw sequence of a genome (plasmid or virus) as the subject on which to…

  10. Genomics and Bioinformatics in Undergraduate Curricula: Contexts for Hybrid Laboratory/Lecture Courses for Entering and Advanced Science Students

    Science.gov (United States)

    Temple, Louise; Cresawn, Steven G.; Monroe, Jonathan D.

    2010-01-01

    Emerging interest in genomics in the scientific community prompted biologists at James Madison University to create two courses at different levels to modernize the biology curriculum. The courses are hybrids of classroom and laboratory experiences. An upper level class uses raw sequence of a genome (plasmid or virus) as the subject on which to…

  11. Methods to Monitor DNA Repair Defects and Genomic Instability in the Context of a Disrupted Nuclear Lamina

    Science.gov (United States)

    Gonzalo, Susana; Kreienkamp, Ray

    2016-01-01

    The organization of the genome within the nuclear space is viewed as an additional level of regulation of genome function, as well as a means to ensure genome integrity. Structural proteins associated with the nuclear envelope, in particular lamins (A- and B-type) and lamin-associated proteins, play an important role in genome organization. Interestingly, there is a whole body of evidence that links disruptions of the nuclear lamina with DNA repair defects and genomic instability. Here, we describe a few standard techniques that have been successfully utilized to identify mechanisms behind DNA repair defects and genomic instability in cells with an altered nuclear lamina. In particular, we describe protocols to monitor changes in the expression of DNA repair factors (Western blot) and their recruitment to sites of DNA damage (immunofluorescence); kinetics of DNA double-strand break repair after ionizing radiation (neutral comet assays); frequency of chromosomal aberrations (FISH, fluorescence in situ hybridization); and alterations in telomere homeostasis (Quantitative-FISH). These techniques have allowed us to shed some light onto molecular mechanisms by which alterations in A-type lamins induce genomic instability, which could contribute to the pathophysiology of aging and aging-related diseases. PMID:27147057

  12. The Ethical, Legal, and Social Implications Program of the National Human Genome Research Institute: reflections on an ongoing experiment.

    Science.gov (United States)

    McEwen, Jean E; Boyer, Joy T; Sun, Kathie Y; Rothenberg, Karen H; Lockhart, Nicole C; Guyer, Mark S

    2014-01-01

    For more than 20 years, the Ethical, Legal, and Social Implications (ELSI) Program of the National Human Genome Research Institute has supported empirical and conceptual research to anticipate and address the ethical, legal, and social implications of genomics. As a component of the agency that funds much of the underlying science, the program has always been an experiment. The ever-expanding number of issues the program addresses and the relatively low level of commitment on the part of other funding agencies to support such research make setting priorities especially challenging. Program-supported studies have had a significant impact on the conduct of genomics research, the implementation of genomic medicine, and broader public policies. The program's influence is likely to grow as ELSI research, genomics research, and policy development activities become increasingly integrated. Achieving the benefits of increased integration while preserving the autonomy, objectivity, and intellectual independence of ELSI investigators presents ongoing challenges and new opportunities.

  13. Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation

    Directory of Open Access Journals (Sweden)

    Ronne Hans

    2008-11-01

    Full Text Available Abstract Background The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence is important for gene regulation. Results In this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy. Conclusion We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.

  14. Evaluation of MeDIP-chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis

    NARCIS (Netherlands)

    Wardenaar, René; Liu, Haiyin; Colot, Vincent; Colomé-Tatché, Maria; Johannes, Frank

    2013-01-01

    Studies of DNA methylation in Arabidopsis have rapidly advanced from the analysis of a single reference accession to investigations of large populations. The goal of emerging population studies is to detect differentially methylated regions (DMRs) at the genome-wide scale, and to relate this

  15. Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources

    Directory of Open Access Journals (Sweden)

    van Hijum Sacha AFT

    2008-10-01

    Full Text Available Abstract Background Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown. The increasing amount of microarray data for many species allows employing the guilt-by-association principle to predict function on a large scale: genes exhibiting similar expression patterns are more likely to participate in shared biological processes. Results We developed Prosecutor, an application that enables researchers to rapidly infer gene function based on available gene expression data and functional annotations. Our parameter-free functional prediction method uses a sensitive algorithm to achieve a high association rate of linking genes with unknown function to annotated genes. Furthermore, Prosecutor utilizes additional biological information such as genomic context and known regulatory mechanisms that are specific for prokaryotes. We analyzed publicly available transcriptome data sets and used literature sources to validate putative functions suggested by Prosecutor. We supply the complete results of our analysis for 11 prokaryotic organisms on a dedicated website. Conclusion The Prosecutor software and supplementary datasets available at http://www.prosecutor.nl allow researchers working on any of the analyzed organisms to quickly identify the putative functions of their genes of interest. A de novo analysis allows new organisms to be studied.

  16. Unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context

    Directory of Open Access Journals (Sweden)

    Zúñiga Manuel

    2008-05-01

    Full Text Available Abstract Background The phosphoenolpyruvate phosphotransferase system (PTS plays a major role in sugar transport and in the regulation of essential physiological processes in many bacteria. The PTS couples solute transport to its phosphorylation at the expense of phosphoenolpyruvate (PEP and it consists of general cytoplasmic phosphoryl transfer proteins and specific enzyme II complexes which catalyze the uptake and phosphorylation of solutes. Previous studies have suggested that the evolution of the constituents of the enzyme II complexes has been driven largely by horizontal gene transfer whereas vertical inheritance has been prevalent in the general phosphoryl transfer proteins in some bacterial groups. The aim of this work is to test this hypothesis by studying the evolution of the phosphoryl transfer proteins of the PTS. Results We have analyzed the evolutionary history of the PTS phosphoryl transfer chain (PTS-ptc components in 222 complete genomes by combining phylogenetic methods and analysis of genomic context. Phylogenetic analyses alone were not conclusive for the deepest nodes but when complemented with analyses of genomic context and functional information, the main evolutionary trends of this system could be depicted. Conclusion The PTS-ptc evolved in bacteria after the divergence of early lineages such as Aquificales, Thermotogales and Thermus/Deinococcus. The subsequent evolutionary history of the PTS-ptc varied in different bacterial lineages: vertical inheritance and lineage-specific gene losses mainly explain the current situation in Actinobacteria and Firmicutes whereas horizontal gene transfer (HGT also played a major role in Proteobacteria. Most remarkably, we have identified a HGT event from Firmicutes or Fusobacteria to the last common ancestor of the Enterobacteriaceae, Pasteurellaceae, Shewanellaceae and Vibrionaceae. This transfer led to extensive changes in the metabolic and regulatory networks of these bacteria

  17. The priming of priming: Evidence that the N400 reflects context-dependent post-retrieval word integration in working memory.

    Science.gov (United States)

    Steinhauer, Karsten; Royle, Phaedra; Drury, John E; Fromont, Lauren A

    2017-06-09

    Which cognitive processes are reflected by the N400 in ERPs is still controversial. Various recent articles (Lau et al., 2008; Brouwer et al., 2012) have revived the idea that only lexical pre-activation processes (such as automatic spreading activation, ASA) are strongly supported, while post-lexical integrative processes are not. Challenging this view, the present ERP study replicates a behavioral study by McKoon and Ratcliff (1995) who demonstrated that a prime-target pair such as finger - hand shows stronger priming when a majority of other pairs in the list share the analogous semantic relationship (here: part-whole), even at short stimulus onset asynchronies (250ms). We created lists with four different types of semantic relationship (synonyms, part-whole, category-member, and opposites) and compared priming for pairs in a consistent list with those in an inconsistent list as well as unrelated items. Highly significant N400 reductions were found for both relatedness priming (unrelated vs. inconsistent) and relational priming (inconsistent vs. consistent). These data are taken as strong evidence that N400 priming effects are not exclusively carried by ASA-like mechanisms during lexical retrieval but also include post-lexical integration in working memory. We link the present findings to a neurocomputational model for relational reasoning (Knowlton et al., 2012) and to recent discussions of context-dependent conceptual activations (Yee and Thompson-Schill, 2016). Copyright © 2017 Elsevier B.V. All rights reserved.

  18. 基于加权Context建模的DNA序列压缩算法%A Genome Sequence Compression Algorithm Based on the Weighted Context Modeling

    Institute of Scientific and Technical Information of China (English)

    陈旻; 王开云; 贾学明; 薛洁

    2014-01-01

    给出一种基于自适应Context加权的细菌DNA序列压缩算法。不同阶数的Context模型用于描述碱基符号间的关联程度。通过加权的方式将各阶模型进行组合,构建用于驱动算术编码器的条件概率分布。各阶模型对应权值由其相应自适应码长决定。在编码过程中,权值能够根据各阶模型获得的统计计数值自适应更新。实验结果表明,该方法能够获得比其他加权Context建模基因组序列压缩算法更好的压缩效率。%A bacteria genome compression algorithm based on the adaptive weighted context model is present. The context model with different order is used to describe the relation degree of basic group code. The context models are combined by weighting to constitute the conditional probability distribution to drive arithmetic coder and the values of these weights are determined by the corresponding adaptive code length. In the coding process,the values of these weights are adaptively updated according to the statistic count value acquired by the context model. The experimental results indicate that the algorithm presented could produce better compression result than the results by other algorithms.

  19. Expression of the Idefix retrotransposon in early follicle cells in the germarium of Drosophila melanogaster is determined by its LTR sequences and a specific genomic context.

    Science.gov (United States)

    Tcheressiz, S; Calco, V; Arnaud, F; Arthaud, L; Dastugue, B; Vaury, C

    2002-04-01

    Retrotransposons are transcriptionally activated in different tissues and cell types by a variety of genomic and environmental factors. Transcription of LTR retrotransposons is controlled by cis-acting regulatory sequences in the 5' LTR. Mobilization of two LTR retroelements, Idefix and ZAM, occurs in the unstable RevI line of Drosophila melanogaster, in which their copy numbers are high, while they are low in all other stocks tested. Here we show that both a full-length and a subgenomic Idefix transcript that are necessary for its mobilization are present in the Rev1 line, but not in the other lines. Studies on transgenic strains demonstrate that the 5' LTR of Idefix contains sequences that direct the tissue-specific expression of the retroelement in testes and ovaries of adult flies. In ovaries, expression occurs in the early follicle and in other somatic cells of the germarium, and is strictly associated with the unstable genetic context conferred by the RevI line. Control of tissue-specific Idefix expression by interactions between cis-acting sequences of its LTR and trans-acting genomic factors provides an opportunity to use this retroelement as a tool for the study of the early follicle cell lineage in the germarium.

  20. Reflection ciphers

    DEFF Research Database (Denmark)

    Boura, Christina; Canteaut, Anne; Knudsen, Lars Ramkilde

    2017-01-01

    study the necessary properties for this coupling permutation. Special care has to be taken of some related-key distinguishers since, in the context of reflection ciphers, they may provide attacks in the single-key setting.We then derive some criteria for constructing secure reflection ciphers...... and analyze the security properties of different families of coupling permutations. Finally, we concentrate on the case of reflection block ciphers and, as an illustration, we provide concrete examples of key schedules corresponding to several coupling permutations, which lead to new variants of the block...

  1. Inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy

    Directory of Open Access Journals (Sweden)

    Keyhani Nemat O

    2004-06-01

    Full Text Available Abstract Background The growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. Genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. We have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underpins tryptophan biosynthesis. Results In 47 complete-genome Bacteria, the genes encoding the seven catalytic domains that participate in primary tryptophan biosynthesis were distinguished from any paralogs or xenologs engaged in other specialized functions. A reliable list of orthologs with carefully ascertained functional roles has thus been assembled and should be valuable as an annotation resource. The protein domains associated with primary tryptophan biosynthesis were then concatenated, yielding single amino-acid sequence strings that represent the entire tryptophan pathway. Lateral gene transfer of several whole-pathway trp operons was demonstrated by use of phylogenetic analysis. Lateral gene transfer of partial-pathway trp operons was also shown, with newly recruited genes functioning either in primary biosynthesis (rarely or specialized metabolism (more frequently. Conclusions (i Concatenated tryptophan protein trees are congruent with 16S rRNA subtrees provided that the genomes represented are of sufficiently close phylogenetic spacing. There are currently seven tryptophan congruency groups in the Bacteria. Recognition of a succession of others can be expected in the near future, but ultimately these should coalesce to a single grouping that parallels the 16S rRNA tree (except for cases of lateral gene transfer. (ii The vertical trace of evolution for tryptophan biosynthesis can be deduced. The daunting complexities engendered

  2. Inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy.

    Science.gov (United States)

    Xie, Gary; Bonner, Carol A; Song, Jian; Keyhani, Nemat O; Jensen, Roy A

    2004-06-23

    The growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. Genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. We have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underpins tryptophan biosynthesis. In 47 complete-genome Bacteria, the genes encoding the seven catalytic domains that participate in primary tryptophan biosynthesis were distinguished from any paralogs or xenologs engaged in other specialized functions. A reliable list of orthologs with carefully ascertained functional roles has thus been assembled and should be valuable as an annotation resource. The protein domains associated with primary tryptophan biosynthesis were then concatenated, yielding single amino-acid sequence strings that represent the entire tryptophan pathway. Lateral gene transfer of several whole-pathway trp operons was demonstrated by use of phylogenetic analysis. Lateral gene transfer of partial-pathway trp operons was also shown, with newly recruited genes functioning either in primary biosynthesis (rarely) or specialized metabolism (more frequently). (i) Concatenated tryptophan protein trees are congruent with 16S rRNA subtrees provided that the genomes represented are of sufficiently close phylogenetic spacing. There are currently seven tryptophan congruency groups in the Bacteria. Recognition of a succession of others can be expected in the near future, but ultimately these should coalesce to a single grouping that parallels the 16S rRNA tree (except for cases of lateral gene transfer). (ii) The vertical trace of evolution for tryptophan biosynthesis can be deduced. The daunting complexities engendered by paralogy, xenology, and idiosyncrasies of

  3. The issue of food genomics: about uncaring citizens and united experts

    NARCIS (Netherlands)

    Molder, te H.F.M.; Gutteling, J.

    2003-01-01

    In this collection of essays is sought to find applications of genomics technology and the different social contexts in which this is and will be taking place. In this way it will be possible to reflect on the social impacts of food genomics on food production and food consumption. To this end socia

  4. Immediate-Early Gene Transcriptional Activation in Hippocampus Ca1 and Ca3 Does Not Accurately Reflect Rapid, Pattern Completion-Based Retrieval of Context Memory

    Science.gov (United States)

    Pevzner, Aleksandr; Guzowski, John F.

    2015-01-01

    No studies to date have examined whether immediate-early gene (IEG) activation is driven by context memory recall. To address this question, we utilized the context preexposure facilitation effect (CPFE) paradigm. In CPFE, animals acquire contextual fear conditioning through hippocampus-dependent rapid retrieval of a previously formed contextual…

  5. The function genomics study

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  6. A Proposal for a Genome Similarity-Based Taxonomy for Plant-Pathogenic Bacteria that Is Sufficiently Precise to Reflect Phylogeny, Host Range, and Outbreak Affiliation Applied to Pseudomonas syringae sensu lato as a Proof of Concept.

    Science.gov (United States)

    Vinatzer, Boris A; Weisberg, Alexandra J; Monteil, Caroline L; Elmarakeby, Haitham A; Sheppard, Samuel K; Heath, Lenwood S

    2017-01-01

    Taxonomy of plant pathogenic bacteria is challenging because pathogens of different crops often belong to the same named species but current taxonomy does not provide names for bacteria below the subspecies level. The introduction of the host range-based pathovar system in the 1980s provided a temporary solution to this problem but has many limitations. The affordability of genome sequencing now provides the opportunity for developing a new genome-based taxonomic framework. We already proposed to name individual bacterial isolates based on pairwise genome similarity. Here, we expand on this idea and propose to use genome similarity-based codes, which we now call life identification numbers (LINs), to describe and name bacterial taxa. Using 93 genomes of Pseudomonas syringae sensu lato, LINs were compared with a P. syringae genome tree whereby the assigned LINs were found to be informative of a majority of phylogenetic relationships. LINs also reflected host range and outbreak association for strains of P. syringae pathovar actinidiae, a pathovar for which many genome sequences are available. We conclude that LINs could provide the basis for a new taxonomic framework to address the shortcomings of the current pathovar system and to complement the current taxonomic system of bacteria in general.

  7. Weaving Action Learning into the Fabric of Manufacturing: The Impact of Humble Inquiry and Structured Reflection in a Cross-Cultural Context

    Science.gov (United States)

    Luckman, Elizabeth A.

    2017-01-01

    This account of practice examines the implementation of and reactions to action learning through the Lean methodology in a unique, cross-cultural context. I review my time spent as a Lean coach; engaging with, training, and using action learning with employees in a garment manufacturing facility located in Bali, Indonesia. This research addresses…

  8. Reflection and teaching: a taxonomy

    OpenAIRE

    Vos, Henk; Cowan, John

    2009-01-01

    A major problem in teaching reflection is that educational objectives for reflection in terms of student behaviour are lacking. Therefore a taxonomy of reflection has been developed based on Bloom’s taxonomy. Reflective assignments can then be better focused on any chosen educational objectives. The act of reflection has been analysed and abstracted from goal, content, context, means, and moment of reflecting. Reflection was operationalised as answering reflective questions. Bloom’s taxonomy ...

  9. Reflective Learning in Practice.

    Science.gov (United States)

    Brockbank, Anne, Ed.; McGill, Ian, Ed.; Beech, Nic, Ed.

    This book contains 22 papers on reflective learning in practice. The following papers are included: "Our Purpose" (Ann Brockbank, Ian McGill, Nic Beech); "The Nature and Context of Learning" (Ann Brockbank, Ian McGill, Nic Beech); "Reflective Learning and Organizations" (Ann Brockbank, Ian McGill, Nic Beech); "Reflective Learning in Practice" (Ann…

  10. Comparative Genomic Study Reveals a Transition from TA Richness in Invertebrates to GC Richness in Vertebrates at CpG Flanking Sites: An Indication for Context-Dependent Mutagenicity of Methylated CpG Sites

    Institute of Scientific and Technical Information of China (English)

    Yong Wang; Frederick C.C. Leung

    2008-01-01

    Vertebrate genomes are characterized with CpG deficiency, particularly for GC-poor regions. The GC content-related CpG deficiency is probably caused by context-dependent deamination of methylated CpG sites. This hypothesis was examined in this study by comparing nucleotide frequencies at CpG flanking positions among invertebrate and vertebrate genomes. The finding is a transition of nucleotide preference of 5' T to 5' A at the invertebrate-vertebrate boundary, indicating that a large number of CpG sites with 5' Ts were depleted because of global DNA methylation developed in vertebrates. At genome level, we investigated CpG observed/expected (obs/exp) values in 500 bp fragments, and found that higher CpG obs/exp value is shown in GC-poor regions of invertebrate genomes (except sea urchin) but in GC-rich sequences of vertebrate genomes. We next compared GC content at CpG flanking positions with genomic average, showing that the GC content is lower than the average in invertebrate genomes, but higher than that in vertebrate genomes. These results indicate that although 5' T and 5' A are different in inducing deamination of methylated CpG sites, GC content is even more important in affecting the deamination rate. In all the tests, the results of sea urchin are similar to vertebrates perhaps due to its fractional DNA methylation.CpG deficiency is therefore suggested to be mainly a result of high mutation rates of methylated CpG sites in GC-poor regions.

  11. Antarctic Genomics

    Directory of Open Access Journals (Sweden)

    Alex D. Rogers

    2006-03-01

    Full Text Available With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies.

  12. Prosecutor : parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources

    NARCIS (Netherlands)

    Blom, E.J.; Breitling, R.; Hofstede, K.J.; Roerdink, J.B.T.M.; van Hijum, S.A F T; Kuipers, O.P.

    2008-01-01

    Background: Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown. The increasing amount of microarray data for many species allows employing the guilt-by-association principle to predict function on a large scale: genes exhibiting similar

  13. From "Natural Context" to "Reality Context": Reflection on the Folklore Pursuit of Fieldwork%从"自然语境"到"实际语境"——反思民俗学的田野作业追求

    Institute of Scientific and Technical Information of China (English)

    杨利慧

    2006-01-01

    @@ 所谓"自然状态"下进行田野考察曾经是并且至今依然是许多民族志工作者的理想之一.正如美国民俗学家理查德·鲍曼(Richrd Bauman)所指出的:"在追求某一民俗形式的所谓自然语境方面,民俗学家们显示了顽强不懈的动力".1为了追求所谓"自然语境"(natural context),以便了解在不被民俗学家打扰的"自然状态"下民俗存在和表演的状貌,一些人会使用各种方法,努力使研究者"隐蔽"起来,以便使观察和访谈不影响或者尽可能少影响被研究对象的"正常"表演.

  14. The importance of context to the genetic architecture of diabetes-related traits is revealed in a genome-wide scan of a LG/J × SM/J murine model.

    Science.gov (United States)

    Lawson, Heather A; Lee, Arthur; Fawcett, Gloria L; Wang, Bing; Pletscher, L Susan; Maxwell, Taylor J; Ehrich, Thomas H; Kenney-Hunt, Jane P; Wolf, Jason B; Semenkovich, Clay F; Cheverud, James M

    2011-04-01

    Variations in diabetic phenotypes are caused by complex interactions of genetic effects, environmental factors, and the interplay between the two. We tease apart these complex interactions by examining genome-wide genetic and epigenetic effects on diabetes-related traits among different sex, diet, and sex-by-diet cohorts in a Mus musculus model. We conducted a genome-wide scan for quantitative trait loci that affect serum glucose and insulin levels and response to glucose stress in an F(16) Advanced Intercross Line of the LG/J and SM/J intercross (Wustl:LG,SM-G16). Half of each sibship was fed a high-fat diet and half was fed a relatively low-fat diet. Context-dependent genetic (additive and dominance) and epigenetic (parent-of-origin imprinting) effects were characterized by partitioning animals into sex, diet, and sex-by-diet cohorts. We found that different cohorts often have unique genetic effects at the same loci, and that genetic signals can be masked or erroneously assigned to specific cohorts if they are not considered individually. Our data demonstrate that the effects of genes on complex trait variation are highly context-dependent and that the same genomic sequence can affect traits differently depending on an individual's sex and/or dietary environment. Our results have important implications for studies of complex traits in humans.

  15. Aging in cultural context and as narrative process: conceptual foundations of the anthropology of aging as reflected in the works of Margaret Clark and Sharon Kaufman.

    Science.gov (United States)

    Perkinson, Margaret A; Solimeo, Samantha L

    2014-02-01

    Although the discipline of anthropology has much to contribute to the understanding of the nature and experience of aging, it is a relative latecomer to gerontology. After briefly discussing why this is the case, the authors discuss the contributions of two anthropologists who brought a substantive anthropological voice to gerontological discussion of aging. Examining the "ancestral roots" of the anthropology of aging, we spotlight the intellectual heritage of Margaret Clark, arguably the "mother" of this anthropological subfield, and that of Sharon Kaufman, her student, colleague, and a pioneer in her own right. Clark and Anderson's Culture and aging: an anthropological study of older Americans (1967; Springfield, IL: Charles C. Thomas) remains a touchstone for the concept of situated aging. This examination of value orientations and mental health of older San Franciscans is foundational for understanding aging as an interactive, socially embedded process that is adapted to specific sociocultural contexts. Research and therapies grounded in narrativity and meaning benefit from Sharon Kaufman's The ageless self: sources of meaning in late life (1986; Madison, WI: University of Wisconsin Press), which articulated narrative thinking as a conduit for understanding, performing, and constructing identity and meaning. Kaufman's work has ongoing relevance to gerontological research on embodiment, chronic illness, and later life social transitions. Their research has continued relevance to contemporary gerontological scholarship and practice, signaling both prevailing and emergent agendas for anthropologically informed gerontology.

  16. Reflecting reflection in supervision

    DEFF Research Database (Denmark)

    Lystbæk, Christian Tang

    Reflection has moved from the margins to the mainstream in supervision. Notions of reflection have become well established since the late 1980s. These notions have provided useful framing devices to help conceptualize some important processes in guidance and counseling. However, some applications...

  17. Conceptualizations of fairness and legitimacy in the context of Ethiopian health priority setting: Reflections on the applicability of accountability for reasonableness.

    Science.gov (United States)

    Petricca, Kadia; Bekele, Asfaw

    2017-05-22

    A critical element in building stronger health systems involves strengthening good governance to build capacity for transparent and fair health planning and priority setting. Over the past 20 years, the ethical framework Accountability for Reasonableness (A4R) has been a prominent conceptual guide in strengthening fair and legitimate processes of health decision-making. While many of the principles embedded within the framework are congruent with Western conceptualizations of what constitutes procedural fairness, there is a paucity in the literature that captures the degree of resonance between these principles and the views of decision makers from non-Western settings; particularly in Africa, where many countries have only recently, within the last 20-30 years, become more democratic. This paper contributes to the ethics literature by examining how Ethiopian decision makers conceptualize fair and legitimate health decision-making, and reflects on the degree of conceptual resonance between these views and the principles embedded in A4R. A qualitative case study approach from three districts in Ethiopia was undertaken. Fifty-eight decision makers from district, regional, zonal, and national levels were interviewed to describe their conceptualization of fairness and legitimacy in the district health planning process. Findings revealed that Ethiopians have a broad conception of fairness and legitimacy that while congruent with procedural justice, also aligned with principles of distributive and organizational justice. Researchers and practitioners seeking to strengthen procedural fairness in health priority setting must therefore recognize the significance of other philosophical dimensions influencing how fairness and legitimacy of health decision-making are constructed within the Ethiopian setting. © 2017 John Wiley & Sons Ltd.

  18. Reflective Learning in Practice.

    Science.gov (United States)

    Brockbank, Anne, Ed.; McGill, Ian, Ed.; Beech, Nic, Ed.

    This book contains 22 papers on reflective learning in practice. The following papers are included: "Our Purpose" (Ann Brockbank, Ian McGill, Nic Beech); "The Nature and Context of Learning" (Ann Brockbank, Ian McGill, Nic Beech); "Reflective Learning and Organizations" (Ann Brockbank, Ian McGill, Nic Beech);…

  19. Reflection in professional practice

    OpenAIRE

    Hetzner, Stefanie Bianca

    2014-01-01

    The purpose of this thesis is to contribute to the research on professional learning through reflective practice. The main goal is to examine—against the backdrop of workplace changes and errors—individual and contextual factors that are theoretically assumed to influence reflection in the context of professional work. Reflective practice is defined as a retrospective but future- and goal-oriented cognitive-affective process that basically involves (a) the awareness and review of incident...

  20. Genome cartography: charting the apicomplexan genome.

    Science.gov (United States)

    Kissinger, Jessica C; DeBarry, Jeremy

    2011-08-01

    Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. Agency, Context and Meaning

    DEFF Research Database (Denmark)

    Folkmann, Mads Nygaard

    2014-01-01

    history, 2) the question of context in and of design, i.e. which contexts give meaning to design; this question calls for interpretive models of cultural analysis of the circuit of design in acknowledging phases and aspects of production, mediation and consumption, and 3) the question of the meaning...... of meaning formulation and cultural contexts and, by this, contest design. In reflecting the foundational ground of design in terms of its agency, contexts and meaning constituents, design and its questioning of meaning can be critically reframed....

  2. Reflective Teaching

    Science.gov (United States)

    Farrell, Thomas S. C.

    2013-01-01

    Thomas Farrell's "Reflective Teaching" outlines four principles that take teachers from just doing reflection to making it a way of being. Using the four principles, Reflective Practice Is Evidence Based, Reflective Practice Involves Dialogue, Reflective Practice Links Beliefs and Practices, and Reflective Practice Is a Way of Life,…

  3. Arquitectura y diseño, un reflejo del contexto climático y paisajístico = Architecture and design as reflection of climate and landscape context

    Directory of Open Access Journals (Sweden)

    Hector Navarro Martínez

    2016-07-01

    Full Text Available Resumen El contexto climático y paisajístico es esencial para estudiar las raíces de cualquier sociedad y su identidad cultural. En la génesis de las primeras sociedades, su relación con el entorno natural definió las bases de su idiosincrasia y religión, todo ello reflejado en sus manifestaciones artísticas. A través de un análisis de base antropológica, aplicado al caso del mediterráneo, se estudiarán las consecuencias de del clima y el paisaje. La Europa clásica, con sociedades como la romana y la griega, evolucionaron a lo largo del tiempo partiendo de condiciones climatológicas cercanas a las regiones monzónicas, sin embargo terminó importando una religión del desierto. Este tema es básico para poder hacer una lectura de sus manifestaciones artísticas posteriores entendiendo su origen estrechamente ligado a su contexto natural. El Panteón de Roma servirá como estudio de caso para analizarlo desde una nueva perspectiva recogiendo todas las variables previamente estudiadas.    Abstract Climate and landscape context is essential to study the roots of any society and its cultural identity. In the genesis of the first societies, their relationship with the natural environment defined the bases of its idiosyncrasy and religion, all reflected in its art. Through an anthropological analysis based on monsoon and desert climate contexts, the impact of weather conditions and the landscape will be studied in order to apply it to the Mediterranean case. During the Classical Europe period, Romans and Greeks evolved over time based on weather conditions closer to the monsoon regions and ended up importing a religion of the desert. This topic is basic to analyse later artistic examples and the origin closely linked to their natural context. The Pantheon will serve as a study case to analyze it from a new perspective by collecting all the variables previously studied.

  4. Investigation of the biological properties of Cinnulin PF in the context of diabetes: mechanistic insights by genome-wide mRNA-Seq analysis

    Directory of Open Access Journals (Sweden)

    Katherine Ververis

    2012-02-01

    Full Text Available The accumulating evidence of the beneficial effects of cinnamon (Cinnamomum burmanni in type-2 diabetes, a chronic age-associated disease, has prompted the commercialisation of various supplemental forms of the spice. One such supplement, Cinnulin PF®, represents the water soluble fraction containing relatively high levels of the double-linked procyanidin type-A polymers of flavanoids. The overall aim of this study was to utilize genome-wide mRNA-Seq analysis to characterise the changes in gene expression caused by Cinnulin PF in immortalised human keratinocytes and microvascular endothelial cells, which are relevant with respect to diabetic complications. In summary, our findings provide insights into the mechanisms of action of Cinnulin PF in diabetes and diabetic complications. More generally, we identify relevant candidate genes which could provide the basis for further investigation. To access the supplementary material to this article: ‘Supplementary tables 1–3’ please see Supplementary files under Reading Tools online.

  5. Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins

    Directory of Open Access Journals (Sweden)

    Edler Stefanie

    2008-06-01

    Full Text Available Abstract Background The jumonji C (JmjC domain containing gene 6 (Jmjd6, previously known as phosphatidylserine receptor has misleadingly been annotated to encode a transmembrane receptor for the engulfment of apoptotic cells. Given the importance of JmjC domain containing proteins in controlling a wide range of diverse biological functions, we undertook a comparative genomic analysis to gain further insights in Jmjd6 gene organisation, evolution, and protein function. Results We describe here a semiautomated computational pipeline to identify and annotate JmjC domain containing proteins. Using a sequence segment N-terminal of the Jmjd6 JmjC domain as query for a reciprocal BLAST search, we identified homologous sequences in 62 species across all major phyla. Retrieved Jmjd6 sequences were used to phylogenetically analyse corresponding loci and their genomic neighbourhood. This analysis let to the identification and characterisation of a bi-directional transcriptional unit compromising the Jmjd6 and 1110005A03Rik genes and to the recognition of a new, before overseen Jmjd6 exon in mammals. Using expression studies, two novel Jmjd6 splice variants were identified and validated in vivo. Analysis of the Jmjd6 neighbouring gene 1110005A03Rik revealed an incident deletion of this gene in two out of three earlier reported Jmjd6 knockout mice, which might affect previously described conflicting phenotypes. To determine potentially important residues for Jmjd6 function a structural model of the Jmjd6 protein was calculated based on sequence conservation. This approach identified a conserved double-stranded β-helix (DSBH fold and a HxDxnH facial triad as structural motifs. Moreover, our systematic annotation in nine species identified 313 DSBH fold-containing proteins that split into 25 highly conserved subgroups. Conclusion We give further evidence that Jmjd6 most likely has a function as a nonheme-Fe(II-2-oxoglutarate-dependent dioxygenase as

  6. Exploring functional elements and genomic variation in the noncoding genome

    NARCIS (Netherlands)

    van Heesch, S.A.A.C.

    2014-01-01

    Gene expression regulation is a delicate process that depends on multiple aspects including genome structure and transcription factor binding to DNA elements. The majority of our genome consists of noncoding DNA, which was shown to be crucial in providing the correct context for genome function. Alt

  7. Exploring functional elements and genomic variation in the noncoding genome

    NARCIS (Netherlands)

    van Heesch, S.A.A.C.|info:eu-repo/dai/nl/336463286

    2014-01-01

    Gene expression regulation is a delicate process that depends on multiple aspects including genome structure and transcription factor binding to DNA elements. The majority of our genome consists of noncoding DNA, which was shown to be crucial in providing the correct context for genome function. Alt

  8. Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend

    Directory of Open Access Journals (Sweden)

    McCallion Andrew S

    2009-01-01

    Full Text Available Abstract Background Transcriptional regulatory elements are central to development and interspecific phenotypic variation. Current regulatory element prediction tools rely heavily upon conservation for prediction of putative elements. Recent in vitro observations from the ENCODE project combined with in vivo analyses at the zebrafish phox2b locus suggests that a significant fraction of regulatory elements may fall below commonly applied metrics of conservation. We propose to explore these observations in vivo at the human PHOX2B locus, and also evaluate the potential evidence for genome-wide applicability of these observations through a novel analysis of extant data. Results Transposon-based transgenic analysis utilizing a tiling path proximal to human PHOX2B in zebrafish recapitulates the observations at the zebrafish phox2b locus of both conserved and non-conserved regulatory elements. Analysis of human sequences conserved with previously identified zebrafish phox2b regulatory elements demonstrates that the orthologous sequences exhibit overlapping regulatory control. Additionally, analysis of non-conserved sequences scattered over 135 kb 5' to PHOX2B, provides evidence of non-conserved regulatory elements positively biased with close proximity to the gene. Furthermore, we provide a novel analysis of data from the ENCODE project, finding a non-uniform distribution of regulatory elements consistent with our in vivo observations at PHOX2B. These observations remain largely unchanged when one accounts for the sequence repeat content of the assayed intervals, when the intervals are sub-classified by biological role (developmental versus non-developmental, or by gene density (gene desert versus non-gene desert. Conclusion While regulatory elements frequently display evidence of evolutionary conservation, a fraction appears to be undetected by current metrics of conservation. In vivo observations at the PHOX2B locus, supported by our analyses of in

  9. Genomic response to Wnt signalling is highly context-dependent - Evidence from DNA microarray and chromatin immunoprecipitation screens of Wnt/TCF targets

    Energy Technology Data Exchange (ETDEWEB)

    Railo, Antti [Oulu Centre for Cell Matrix Research, Biocenter Oulu, Laboratory of Developmental Biology and Department of Medical Biochemistry and Molecular Biology, FIN-90014, University of Oulu, P. O. Box 5000 (Finland); Pajunen, Antti [Department of Biochemistry, University of Oulu (Finland); Itaeranta, Petri; Naillat, Florence; Vuoristo, Jussi; Kilpelaeinen, Pekka [Oulu Centre for Cell Matrix Research, Biocenter Oulu, Laboratory of Developmental Biology and Department of Medical Biochemistry and Molecular Biology, FIN-90014, University of Oulu, P. O. Box 5000 (Finland); Vainio, Seppo, E-mail: Seppo.Vainio@oulu.fi [Oulu Centre for Cell Matrix Research, Biocenter Oulu, Laboratory of Developmental Biology and Department of Medical Biochemistry and Molecular Biology, FIN-90014, University of Oulu, P. O. Box 5000 (Finland)

    2009-10-01

    Wnt proteins are important regulators of embryonic development, and dysregulated Wnt signalling is involved in the oncogenesis of several human cancers. Our knowledge of the downstream target genes is limited, however. We used a chromatin immunoprecipitation-based assay to isolate and characterize the actual gene segments through which Wnt-activatable transcription factors, TCFs, regulate transcription and an Affymetrix microarray analysis to study the global transcriptional response to the Wnt3a ligand. The anti-{beta}-catenin immunoprecipitation of DNA-protein complexes from mouse NIH3T3 fibroblasts expressing a fusion protein of {beta}-catenin and TCF7 resulted in the identification of 92 genes as putative TCF targets. GeneChip assays of gene expression performed on NIH3T3 cells and the rat pheochromocytoma cell line PC12 revealed 355 genes in NIH3T3 and 129 genes in the PC12 cells with marked changes in expression after Wnt3a stimulus. Only 2 Wnt-regulated genes were shared by both cell lines. Surprisingly, Disabled-2 was the only gene identified by the chromatin immunoprecipitation approach that displayed a marked change in expression in the GeneChip assay. Taken together, our approaches give an insight into the complex context-dependent nature of Wnt pathway transcriptional responses and identify Disabled-2 as a potential new direct target for Wnt signalling.

  10. 从经典著作的原始语境反观法国学派的民族中心主义%Reflecting upon the Ethnocentrism of the French School in the Original Context of the Classic Works

    Institute of Scientific and Technical Information of China (English)

    林满平; 王宁宁

    2012-01-01

    In the pioneering days of comparative literature, the French School, regarding influence research as the essence to rely upon, insists on paying attention to the factual relations in literature among different countries and various ethnic groups. The French School is criticized by later scholars for having fallen into the category of narrow ethnocentrism, due to the unavoidable limitation of history at the beginning, and its own defect that the theory has been divorced from the practice. The author holds that one should carefully read and reflect upon classic works of disciplines to comprehensively learn about the influence research of the French School, and grasp it as a whole in the original context of those classic works.%比较文学初创时期的法国学派,坚持以实证主义的态度,关照不同国家不同民族之间文学上的事实联系,以影响研究为自己安身立命之根本。法国学派在初创时期因为历史无可避免的局限性,以其自身理论与实践相脱节的缺陷,被后来学者指责陷入了狭隘的民族中心主义。笔者认为,对法国学派的影响研究的全面认识。应该细读和反思元典著作,立足于学科经典著作的原始语境来整体把握。

  11. Genome-wide effects of MELK-inhibitor in triple-negative breast cancer cells indicate context-dependent response with p53 as a key determinant.

    Science.gov (United States)

    Simon, Marisa; Mesmar, Fahmi; Helguero, Luisa; Williams, Cecilia

    2017-01-01

    Triple-negative breast cancer (TNBC) is an aggressive, highly recurrent breast cancer subtype, affecting approximately one-fifth of all breast cancer patients. Subpopulations of treatment-resistant cancer stem cells within the tumors are considered to contribute to disease recurrence. A potential druggable target for such cells is the maternal embryonic leucine-zipper kinase (MELK). MELK expression is upregulated in mammary stem cells and in undifferentiated cancers, where it correlates with poor prognosis and potentially mediates treatment resistance. Several MELK inhibitors have been developed, of which one, OTSSP167, is currently in clinical trials. In order to better understand how MELK and its inhibition influence TNBC, we verified its anti-proliferative and apoptotic effects in claudin-low TNBC cell lines MDA-MB-231 and SUM-159 using MTS assays and/or trypan blue viability assays together with analysis of PARP cleavage. Then, using microarrays, we explored which genes were affected by OTSSP167. We demonstrate that different sets of genes are regulated in MDA-MB-231 and SUM-159, but in both cell lines genes involved in cell cycle, mitosis and protein metabolism and folding were regulated. We identified p53 (TP53) as a potential upstream regulator of the regulated genes. Using western blot we found that OTSSP167 downregulates mutant p53 in all tested TNBC cell lines (MDA-MB-231, SUM-159, and BT-549), but upregulates wild-type p53 in the luminal A subtype MCF-7 cell line. We propose that OTSSP167 might have context-dependent or off-target effects, but that one consistent mechanism of action could involve the destabilization of mutant p53.

  12. Genome-wide effects of MELK-inhibitor in triple-negative breast cancer cells indicate context-dependent response with p53 as a key determinant

    Science.gov (United States)

    Simon, Marisa; Mesmar, Fahmi; Helguero, Luisa

    2017-01-01

    Triple-negative breast cancer (TNBC) is an aggressive, highly recurrent breast cancer subtype, affecting approximately one-fifth of all breast cancer patients. Subpopulations of treatment-resistant cancer stem cells within the tumors are considered to contribute to disease recurrence. A potential druggable target for such cells is the maternal embryonic leucine-zipper kinase (MELK). MELK expression is upregulated in mammary stem cells and in undifferentiated cancers, where it correlates with poor prognosis and potentially mediates treatment resistance. Several MELK inhibitors have been developed, of which one, OTSSP167, is currently in clinical trials. In order to better understand how MELK and its inhibition influence TNBC, we verified its anti-proliferative and apoptotic effects in claudin-low TNBC cell lines MDA-MB-231 and SUM-159 using MTS assays and/or trypan blue viability assays together with analysis of PARP cleavage. Then, using microarrays, we explored which genes were affected by OTSSP167. We demonstrate that different sets of genes are regulated in MDA-MB-231 and SUM-159, but in both cell lines genes involved in cell cycle, mitosis and protein metabolism and folding were regulated. We identified p53 (TP53) as a potential upstream regulator of the regulated genes. Using western blot we found that OTSSP167 downregulates mutant p53 in all tested TNBC cell lines (MDA-MB-231, SUM-159, and BT-549), but upregulates wild-type p53 in the luminal A subtype MCF-7 cell line. We propose that OTSSP167 might have context-dependent or off-target effects, but that one consistent mechanism of action could involve the destabilization of mutant p53. PMID:28235006

  13. Reflective Writing

    DEFF Research Database (Denmark)

    Ahrenkiel Jørgensen, Andriette

    2016-01-01

    Høeg etetera. The dialogues work as a tool of reflection in terms of providing opportunity to examine his own beliefs, to explore the possible reasons for engaging in a particular activity. On the basis of Sven-Ingvar Andersson’s book a teaching program at the Aarhus School of Architecture provides...... a contribution to the discussions about the role of reflection in design work and in learning situations at large. By engaging with the dialogic reflection, which is one of the four essential types of reflection, (the three others being descriptive writing, descriptive reflection and critical reflection...

  14. Methodological Reflections: Inter- ethnic Research

    DEFF Research Database (Denmark)

    Singla, Rashmi

    2010-01-01

    This article reflects on the methodological and epistemological aspects of the ethical issues involved in encounters between researcher and research participants with ethnic minority background in contexts with diversity. Specific challenges involved in longitudinal research (10 - 15 years) are a...

  15. Novel strategies to identify relevant molecular signatures for complex human diseases based on data of identical-by-decent profiles and genomic context%基于IBD谱和基因组结构的复杂疾病相关分子标记识别的新策略

    Institute of Scientific and Technical Information of China (English)

    李传星; 杜磊; 李霞; 宫滨生; 张杰; 饶绍奇

    2006-01-01

    Objective: To develop novel strategies to identify relevant molecular signatures for complex human diseases based on data of identical-by-decent profiles and genomic context.Methods: In the proposed strategies, we define four relevancy criteria for mapping SNP-phenotype relationships-point-wise IBD mean difference, averaged IBD difference for window, Z curve and averaged slope for window.Results: Application of these criteria and permutation test to 100 simulated replicates for two hypothetical American populations to extract the relevant SNPs for alcoholism based on sib-pair IBD profiles of pedigrees demonstrates that the proposed strategies have successfully identified most of the simulated true loci.Conclusion: The data mining practice implies that IBD statistic and genomic context could be used as the informatics for locating the underlying genes for complex human diseases. Compared with the classical Haseman-Elston sib-pair regression method, the proposed strategies are more efficient for large-scale genomic mining.

  16. Operation Context

    DEFF Research Database (Denmark)

    Stüben, Henning; Tietjen, Anne

    2006-01-01

    Abstract: This paper seeks to challenge the notion of context from an operational perspective. Can we grasp the forces that shape the complex conditions for an architectural or urban design within the notion of context? By shifting the gaze towards the agency of architecture, contextual analysis...

  17. The Aesthetic Reflection on Literary Experience Crisis in the Context of Media Culture%传媒文化语境下文学经验危机的美学反思∗

    Institute of Scientific and Technical Information of China (English)

    王岩

    2016-01-01

    The media culture effectively changes the way of people′s life style, the way of feeling and the understanding, and also brings the unprecedented experience crisis to the literature and art. Literature experience is the essence of human experience, it was born in the collision between fiction and perceptual, fusion, as well as the perceptual existence and verbal behavior of the"fracture". But in the context of media culture, the phenomena of life is over explained"through", the"story" with rich connotation transform into"accident", experience is abstracted. In addition, the tool of language and the holographic nature, narrative and disorder of the media discourse, which is eliminating the border breeding experience. Even more serious is that, in the media era, "reality" is being too much of the symbols, information siege and suspension, literary experience has been drawn away. From the perspective of experience aesthetics to reflect the crisis of literature is an ideal way to promote literature out of the plight.%由电子媒介推动的传媒文化,有力地改变着人们的生存方式、感受方式和理解方式,也给文学艺术带来空前的经验危机。文学经验的本质是人的经验,它诞生于虚构和感性之间的碰撞、融合,以及人的感性生存和言语行为之间的“裂隙”。但在传媒文化语境下,生活现象被过度解释“透穿”,内蕴丰富的“故事”蜕变为“事故”,经验被抽象化;语言的工具化以及媒介话语的全息性、叙事性和无序性,消弭着滋生经验的边界。更严重的是,在“伪经验”盛产的传媒时代,“现实”正被过量的符号、信息围困和悬置,可供提取的文学经验已然被抽离。从经验美学视角反思文学的危机,是推动文学艺术走出困境的一条理想路径。

  18. Context in a wider context

    Directory of Open Access Journals (Sweden)

    John Traxler

    2011-07-01

    Full Text Available This paper attempts to review and reconsider the role of context in mobile learning and starts by outlining definitions of context-aware mobile learning as the technologies have become more mature, more robust and more widely available and as the notion of context has become progressively richer. The future role of context-aware mobile learning is considered within the context of the future of mobile learning as it moves from the challenges and opportunities of pedagogy and technology to the challenges and opportunities of policy, scale, sustainability, equity and engagement with augmented reality, «blended learning», «learner devices», «user-generated contexts» and the «internet of things». This is essentially a perspective on mobile learning, and other forms of technology-enhanced learning (TEL, where educators and their institutions set the agenda and manage change. There are, however, other perspectives on context. The increasing availability and use of smart-phones and other personal mobile devices with similar powerful functionality means that the experience of context for many people, in the form of personalized or location-based services, is an increasingly social and informal experience, rather than a specialist or educational experience. This is part of the transformative impact of mobility and connectedness on our societies brought about by these universal, ubiquitous and pervasive technologies. This paper contributes a revised understanding of context in the wider context (sic of the transformations taking place in our societies. These are subtle but pervasive transformations of jobs, work and the economy, of our sense of time, space and place, of knowing and learning, and of community and identity. This leads to a radical reconsideration of context as the notions of ‹self› and ‹other› are transformed.

  19. Local Contexts

    Directory of Open Access Journals (Sweden)

    Philippe Schlenker

    2009-07-01

    Full Text Available The dynamic approach posits that a presupposition must be satisfied in its local context. But how is a local context derived from the global one? Extant dynamic analyses must specify in the lexical entry of any operator what its 'Context Change Potential' is, and for this very reason they fail to be sufficiently explanatory. To circumvent the problem, we revise two assumptions of the dynamic approach: we take the update process to be derivative from a classical, non-dynamic semantics -- which obviates the need for dynamic lexical entries; and we deny that a local context encodes what the speech act participants 'take for granted.' Instead, we take the local context of an expression E in a sentence S to be the smallest domain that one may restrict attention to when assessing E without jeopardizing the truth conditions of S. To match the results of dynamic semantics, local contexts must be computed incrementally, using only information about the expressions that precede E. This version of the theory can be shown to be nearly equivalent to the dynamic theory of Heim 1983 -- but unlike the latter, it is entirely predictive. We also suggest that local contexts can, at some cost, be computed symmetrically, taking into account information about all of S (except E; this leads to gradient predictions, whose assessment is left for future research. doi:10.3765/sp.2.3 BibTeX info

  20. Context Awareness

    DEFF Research Database (Denmark)

    Brønsted, Jeppe

    forståelse. Traditionelt har denne form for information ikke været tilstede i informationssystemer, men med bølgen af Pervasive Computing og Communication begynder ting så småt at ændre sig. Et af målene for context aware computing er, at udnytte denne ekstra ressource af informationer der ellers er...... forbeholdt mennesker, til at forbedre interaktionen med og udnyttelsen af IT-systemer. Information om kontekst fra forskellige kilder kombineres og systemet foreslår relevante handlinger eller udfører dem automatisk. I dette dokument beskrives begreberne context og context awareness og hvorfor de er vigtige...

  1. Context Awareness

    DEFF Research Database (Denmark)

    Brønsted, Jeppe

    forståelse. Traditionelt har denne form for information ikke været tilstede i informationssystemer, men med bølgen af Pervasive Computing og Communication begynder ting så småt at ændre sig. Et af målene for context aware computing er, at udnytte denne ekstra ressource af informationer der ellers er...... forbeholdt mennesker, til at forbedre interaktionen med og udnyttelsen af IT-systemer. Information om kontekst fra forskellige kilder kombineres og systemet foreslår relevante handlinger eller udfører dem automatisk. I dette dokument beskrives begreberne context og context awareness og hvorfor de er vigtige...

  2. Context matters!

    DEFF Research Database (Denmark)

    Bojesen, Anders

    2004-01-01

    This paper explores how the context of competencies affects the way we see and value competence and how it thereby forms communication and strategies of action. The paper puts forward the view that the context of competence is often spoken of in incomprehensible terms and generally taken...... for granted and unproblematic, although it is agreed to be of great importance. By crystallising three different modes of contextualised competence thinking (prescriptive, descriptive and analytical) the paper shows that the underlying assumptions about context - the interaction between the individual...... and the social - has major consequences for the specific enactment of competence. The paper argues in favour of a second order observation strategy for the context of competence. But in doing so it also shows that prevailing second-order competence theories so far, in criticising (counter) positions (and...

  3. Breeding-assisted genomics.

    Science.gov (United States)

    Poland, Jesse

    2015-04-01

    The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition.

  4. Quantifying Reflection

    DEFF Research Database (Denmark)

    Alcock, Gordon Lindsay

    2013-01-01

    This paper documents 1st semester student reflections on “learning to learn” in a team-based PBL environment with quantitative and qualitative student reflective feedback on the learning gains of 60 Architectural Technology and Construction Management students at VIA University College, Denmark....... It contrasts the students’ self-assessment in a range of ‘product’ skills such as Revit, Structural Design, Mathematics of construction, Technical Installations; as well as ‘process’ competencies such as ‘Working in a team’, Sharing knowledge, Maintaining a portfolio and Reflecting ON learning and FOR learning......´ These are all based on Blooms taxonomy and levels of competence and form a major part of individual student and group learning portfolios. Key Words :Project-Based learning, Reflective Portfolios, Self assessment, Defining learning gains, Developing learning strategies , Reflections on and for learning...

  5. Context trees

    OpenAIRE

    Ganzinger, Harald; Nieuwenhuis, Robert; Nivela, Pilar

    2001-01-01

    Indexing data structures are well-known to be crucial for the efficiency of the current state-of-the-art theorem provers. Examples are \\emph{discrimination trees}, which are like tries where terms are seen as strings and common prefixes are shared, and \\emph{substitution trees}, where terms keep their tree structure and all common \\emph{contexts} can be shared. Here we describe a new indexing data structure, \\emph{context trees}, where, by means of a limited kind of conte...

  6. Sub-method Structural and Behavioral Reflection

    OpenAIRE

    Denker, Marcus

    2008-01-01

    Computational reflection is a fundamental mechanism in object oriented languages. Reflection has proved useful in many contexts, such as in the design of development environments, language extension, and the dynamic, unanticipated adaptation of running systems We identify three problems with the current approach to reflection in object oriented languages: partial behavioral reflection needs to be anticipated, structural reflection is limited to the granularity of a method, and behavioral refl...

  7. Escherichia coli frameshift mutation rate depends on the chromosomal context but not on the GATC content near the mutation site.

    Directory of Open Access Journals (Sweden)

    Mariana A Martina

    Full Text Available Different studies have suggested that mutation rate varies at different positions in the genome. In this work we analyzed if the chromosomal context and/or the presence of GATC sites can affect the frameshift mutation rate in the Escherichia coli genome. We show that in a mismatch repair deficient background, a condition where the mutation rate reflects the fidelity of the DNA polymerization process, the frameshift mutation rate could vary up to four times among different chromosomal contexts. Furthermore, the mismatch repair efficiency could vary up to eight times when compared at different chromosomal locations, indicating that detection and/or repair of frameshift events also depends on the chromosomal context. Also, GATC sequences have been proved to be essential for the correct functioning of the E. coli mismatch repair system. Using bacteriophage heteroduplexes molecules it has been shown that GATC influence the mismatch repair efficiency in a distance- and number-dependent manner, being almost nonfunctional when GATC sequences are located at 1 kb or more from the mutation site. Interestingly, we found that in E. coli genomic DNA the mismatch repair system can efficiently function even if the nearest GATC sequence is located more than 2 kb away from the mutation site. The results presented in this work show that even though frameshift mutations can be efficiently generated and/or repaired anywhere in the genome, these processes can be modulated by the chromosomal context that surrounds the mutation site.

  8. Escherichia coli frameshift mutation rate depends on the chromosomal context but not on the GATC content near the mutation site.

    Science.gov (United States)

    Martina, Mariana A; Correa, Elisa M E; Argaraña, Carlos E; Barra, José L

    2012-01-01

    Different studies have suggested that mutation rate varies at different positions in the genome. In this work we analyzed if the chromosomal context and/or the presence of GATC sites can affect the frameshift mutation rate in the Escherichia coli genome. We show that in a mismatch repair deficient background, a condition where the mutation rate reflects the fidelity of the DNA polymerization process, the frameshift mutation rate could vary up to four times among different chromosomal contexts. Furthermore, the mismatch repair efficiency could vary up to eight times when compared at different chromosomal locations, indicating that detection and/or repair of frameshift events also depends on the chromosomal context. Also, GATC sequences have been proved to be essential for the correct functioning of the E. coli mismatch repair system. Using bacteriophage heteroduplexes molecules it has been shown that GATC influence the mismatch repair efficiency in a distance- and number-dependent manner, being almost nonfunctional when GATC sequences are located at 1 kb or more from the mutation site. Interestingly, we found that in E. coli genomic DNA the mismatch repair system can efficiently function even if the nearest GATC sequence is located more than 2 kb away from the mutation site. The results presented in this work show that even though frameshift mutations can be efficiently generated and/or repaired anywhere in the genome, these processes can be modulated by the chromosomal context that surrounds the mutation site.

  9. Generative Contexts

    Science.gov (United States)

    Lyles, Dan Allen

    Educational research has identified how science, technology, engineering, and mathematics (STEM) practice and education have underperforming metrics in racial and gender diversity, despite decades of intervention. These disparities are part of the construction of a culture of science that is alienating to these populations. Recent studies in a social science framework described as "Generative Justice" have suggested that the context of social and scientific practice might be modified to bring about more just and equitable relations among the disenfranchised by circulating the value they and their non-human allies create back to them in unalienated forms. What is not known are the underlying principles of social and material space that makes a system more or less generative. I employ an autoethnographic method at four sites: a high school science class; a farm committed to "Black and Brown liberation"; a summer program geared towards youth environmental mapping; and a summer workshop for Harlem middle school students. My findings suggest that by identifying instances where material affinity, participatory voice, and creative solidarity are mutually reinforcing, it is possible to create educational contexts that generate unalienated value, and circulate it back to the producers themselves. This cycle of generation may help explain how to create systems of justice that strengthen and grow themselves through successive iterations. The problem of lack of diversity in STEM may be addressed not merely by recruiting the best and the brightest from underrepresented populations, but by changing the context of STEM education to provide tools for its own systematic restructuring.

  10. Reflective optics

    CERN Document Server

    Korsch, Dietrich

    1991-01-01

    This is the first book dedicated exclusively to all-reflective imaging systems. It is a teaching tool as well as a practical design tool for anyone who specializes in optics, particularly for those interested in telescopes, infrared, and grazing-incidence systems. The first part of the book describes a unified geometric optical theory of all-reflective imaging systems (from near-normal to grazing incidence) developed from basic principles. The second part discusses correction methods and a multitude of closed-form solutions of well-corrected systems, supplemented with many conventional and unc

  11. Genomic medicine implementation: learning by example.

    Science.gov (United States)

    Williams, Marc S

    2014-03-01

    Genomic Medicine is beginning to emerge into clinical practice. The National Human Genome Research Institute's Genomic Medicine Working Group consists of organizations that have begun to implement some aspect of genomic medicine (e.g., family history, systematic implementation of Mendelian disease program, pharmacogenomics, whole exome/genome sequencing). This article concisely reviews the working group and provides a broader context for the articles in the special issue including an assessment of anticipated provider needs and ethical, legal, and social issues relevant to the implementation of genomic medicine. The challenges of implementation of innovation in clinical practice and the potential value of genomic medicine are discussed.

  12. National context

    DEFF Research Database (Denmark)

    Ravn, Tine

    2011-01-01

    This document forms part of the tasks of Work Package 3 for the European project PLACES (Platform of Local Authorities and Communicators Engaged in Science) whose main goal is to offer to a wide and diverse community of actors a common platform to structure their science communication activities,......, at a city/regional level (www.openplaces.eu). The main objective of this document is to have an overview of different contexts of scientific culture that are present around Europe with a particular focus on the local dimension of the initiatives and policies in science communication....

  13. Reflective equilibrium

    NARCIS (Netherlands)

    van der Burg, W.; van Willigenburg, T.

    1998-01-01

    The basic idea of reflective equilibrium, as a method for theory construction and decision making in ethics, is that we should bring together a broad variety of moral and non-moral beliefs and, through a process of critical scrutiny and mutual adjustment, combine these into one coherent belief syste

  14. Reflective equilibrium

    NARCIS (Netherlands)

    van der Burg, W.; van Willigenburg, T.

    1998-01-01

    The basic idea of reflective equilibrium, as a method for theory construction and decision making in ethics, is that we should bring together a broad variety of moral and non-moral beliefs and, through a process of critical scrutiny and mutual adjustment, combine these into one coherent belief syste

  15. The promise of insect genomics

    DEFF Research Database (Denmark)

    Grimmelikhuijzen, Cornelis J P; Cazzamali, Giuseppe; Williamson, Michael

    2007-01-01

    Insects are the largest animal group in the world and are ecologically and economically extremely important. This importance of insects is reflected by the existence of currently 24 insect genome projects. Our perspective discusses the state-of-the-art of these genome projects and the impacts tha...

  16. Human social genomics.

    Directory of Open Access Journals (Sweden)

    Steven W Cole

    2014-08-01

    Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

  17. Putting tumours in context

    Energy Technology Data Exchange (ETDEWEB)

    Bissell, Mina J.; Radisky, Derek

    2001-10-01

    progresses, the normal organization of the organ is replaced by a functional disorder. If there are pre-existing epithelial cells within this changing context that possess tumorigenic potential, they can start to proliferate. Alternatively, the abnormal interactions might lead to genomic instability within the epithelial cells and the acquisition of tumorigenic potential. The proliferating cancer cells can then interact with their microenvironment and enhance the abnormal interactions. At this point, the tumor has become its own organ, with a distinct context that now defines all its cellular responses. Here, we will examine how the mechanisms that contribute to the normal context also act to suppress developing tumors, how disruption of this context initiates and supports the process of tumorigenicity, and how some cells with a tumorigenic genotype can become phenotypically normal if the context is appropriately manipulated.

  18. Dissociation between Complete Hippocampal Context Memory Formation and Context Fear Acquisition

    Science.gov (United States)

    Leake, Jessica; Zinn, Raphael; Corbit, Laura; Vissel, Bryce

    2017-01-01

    Rodents require a minimal time period to explore a context prior to footshock to display plateau-level context fear at test. To investigate whether this rapid fear plateau reflects complete memory formation within that short time-frame, we used the immediate-early gene product Arc as an indicator of hippocampal context memory formation-related…

  19. Constraint Programming for Context Comprehension

    DEFF Research Database (Denmark)

    Christiansen, Henning

    2014-01-01

    of knowledge. The language of Constraint Handling Rules, CHR, is suggested for defining constraint solvers that reflect “world knowledge” for the given domain, and driver algorithms may be ex- pressed in Prolog or additional rules of CHR. It is argued that this way of doing context comprehension is an instance...

  20. The genomics of adaptation.

    Science.gov (United States)

    Radwan, Jacek; Babik, Wiesław

    2012-12-22

    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

  1. Toward genome-enabled mycology.

    Science.gov (United States)

    Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

    2013-01-01

    Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

  2. The constitutional issues of the Empire: the legal and political context reflected in the stories “Fulano” and “Um homem célebre,” Machado de Assis

    Directory of Open Access Journals (Sweden)

    Tito Lívio Cabral Renovato Silva

    2015-10-01

    Full Text Available This article will examine the constitutional issues that occurred in the second half of the nineteenth century, such as the “religious issue”, “military issue” and “abolition of slavery”, which led to the end of the monarchy in Brazil. We will treat the historical panorama of the time, the current legal and constitutional crises of the Empire, where we analyze the 1824 Constitution and its articles that discuss the division of powers and functions concerning the moderating power. Analyze all these issues by Machado de Assis vision reflected in the characters of the stories “Fulano” and “Um homem célebre”, under an interdisciplinary method, targeting the relations between Law and Literature.

  3. Comparative Genome Analysis in the Integrated Microbial Genomes(IMG) System

    Energy Technology Data Exchange (ETDEWEB)

    Kyrpides, Nikos C.; Markowitz, Victor M.

    2006-03-01

    Comparative genome analysis is critical for the effectiveexploration of a rapidly growing number of complete and draft sequencesfor microbial genomes. The Integrated Microbial Genomes (IMG) system(img.jgi.doe.gov) has been developed as a community resource thatprovides support for comparative analysis of microbial genomes in anintegrated context. IMG allows users to navigate the multidimensionalmicrobial genome data space and focus their analysis on a subset ofgenes, genomes, and functions of interest. IMG provides graphicalviewers, summaries and occurrence profile tools for comparing genes,pathways and functions (terms) across specific genomes. Genes can befurther examined using gene neighborhoods and compared with sequencealignment tools.

  4. On Reflection

    DEFF Research Database (Denmark)

    Blasco, Maribel

    2012-01-01

    This article explores how the concept of reflexivity is used in intercultural education. Reflexivity is often presented as a key learning goal in acquiring intercultural competence (ICC). Yet, reflexivity can be defined in different ways, and take different forms across time and space, depending...... on the concepts of selfhood that prevail and how notions of difference are constructed. First, I discuss how the dominant usages of reflexivity in intercultural education reflect and reproduce a Cartesian view of the self that shapes how ICC is conceptualized and taught. I discuss three assumptions that this view...... in designing learning objectives in intercultural education and in devising ways to attain them. Greater attention is also needed in intercultural education to the ways in which selfhood, and hence also reflexivity and constructions of difference, differ across space and time....

  5. Inspiring Reflections

    DEFF Research Database (Denmark)

    Muchie, Mammo

    2011-01-01

    contributions have been put together. There are a number of ways to continue Chris Freeman's legacy on innovation research. The first is to build in a critical tradition in the economics of innovation research by introducing fearlessly emancipatory epistemology. Second the economic system that dominates social......A numberof Chris Freeman's colleagues were asked to reflect on what they thought describes his life and work in a few words. Some of the colleagues replied including former SPRU students that were taught or supervised by Chris Freeman. Their views on what they thought were Chris Freeman's defining...... life is not free from fluctuations, cycles, disruptions, crises and destructions both human and ecological. Innovation research ought to position itself to address environmental, financial and economic crises. The third is innovation research for development by addressing not only poverty erdaication...

  6. The genome BLASTatlas - a GeneWiz extension for visualization of whole-genome homology

    DEFF Research Database (Denmark)

    Hallin, Peter Fischer; Binnewies, Tim Terence; Ussery, David

    2008-01-01

    the Clostridium tetani plasmid p88, where homologues for toxin genes can be easily visualized in other sequenced Clostridium genomes, and for a Clostridium botulinum genome, compared to 14 other Clostridium genomes. DNA structural information is also included in the atlas to visualize the DNA chromosomal context...

  7. Ensembl Genomes 2013: scaling up access to genome-wide data

    Science.gov (United States)

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provi...

  8. 全球化背景下美国文化霸权的多维思考%A multi-dimensional reflection on American cultural hegemony in the context of globalization

    Institute of Scientific and Technical Information of China (English)

    方宗祥

    2011-01-01

    In the 21st century,globalization becomes an irreversible historical trend.In such a context,America,with its strong political,financial and military forces,has not only controlled the world political,economic and military order,but has intended to promote its American culture world-widely by performing American hegemony.The essence of American cultural hegemony is to occupy cultural commodity market shares economically,for the plunder of cultural resources and wealth;and to conquer the souls of other nations politically,for the legitimacy to dominate the world.American cultural hegemony is against the historical trend,and is doomed to fail.%21世纪的今天,世界政治、经济和文化的全球化已成为不可阻挡的发展趋势和现实。在此背景下,美国凭借其雄厚的政治、经济和军事实力,不仅干涉着全球的政治、经济和军事秩序,而且试图从文化上推行其美国标准于全球,实施文化霸权主义。美国文化霸权的实质,即经济上攫取文化商品市场,掠夺文化资源和财富;政治上征服他国民众之心灵,为其称霸世界寻找合法外衣。美国文化霸权是逆历史潮流而动的,必将以失败而告终。

  9. Reflected Glory

    Science.gov (United States)

    2011-02-01

    The nebula Messier 78 takes centre stage in this image taken with the Wide Field Imager on the MPG/ESO 2.2-metre telescope at the La Silla Observatory in Chile, while the stars powering the bright display take a backseat. The brilliant starlight ricochets off dust particles in the nebula, illuminating it with scattered blue light. Igor Chekalin was the overall winner of ESO's Hidden Treasures 2010 astrophotography competition with his image of this stunning object. Messier 78 is a fine example of a reflection nebula. The ultraviolet radiation from the stars that illuminate it is not intense enough to ionise the gas to make it glow - its dust particles simply reflect the starlight that falls on them. Despite this, Messier 78 can easily be observed with a small telescope, being one of the brightest reflection nebulae in the sky. It lies about 1350 light-years away in the constellation of Orion (The Hunter) and can be found northeast of the easternmost star of Orion's belt. This new image of Messier 78 from the MPG/ESO 2.2-metre telescope at the La Silla Observatory is based on data selected by Igor Chekalin in his winning entry to the Hidden Treasures competition [1]. The pale blue tint seen in the nebula in this picture is an accurate representation of its dominant colour. Blue hues are commonly seen in reflection nebulae because of the way the starlight is scattered by the tiny dust particles that they contain: the shorter wavelength of blue light is scattered more efficiently than the longer wavelength red light. This image contains many other striking features apart from the glowing nebula. A thick band of obscuring dust stretches across the image from the upper left to the lower right, blocking the light from background stars. In the bottom right corner, many curious pink structures are also visible, which are created by jets of material being ejected from stars that have recently formed and are still buried deep in dust clouds. Two bright stars, HD 38563A and

  10. Commentary on: Are we overpathologizing everyday life? A tenable blueprint for behavioral addiction research. Can the emerging domain of behavioral addictions bring a new reflection for the field of addictions, by stressing the issue of the context of addiction development?

    Science.gov (United States)

    de Timary, Philippe; Philippot, Pierre

    2015-09-01

    This paper is a commentary to the article entitled: "Are we overpathologizing everyday life? A tenable blueprint for behavioral addiction research", by Billieux, Schimmenti, Khazaal, Maurage and Heeren (2015). In this manuscript, we commented on two aspects developed by the authors. Billieux et al. (2015) propose that the recent development of propositions of behavioral addiction is driven by an unwise application of an addiction model to excessive behaviors and rests on a confirmatory research strategy that does not question the psychological processes underlying the development of the conduct. They also show that applying a process driven strategy leads to a more appropriate description of the reality of the behavior and conduct, in particular by describing a variety of motivations for the excessive behavior, which is central to understanding the nature of the conduct. We believe that this new approach, which is fruitful to the emerging domain of behavioral addictions, could also apply to the domain of addictions in general. The latter is characterized by the application of a generic biological model, largely influenced by animal models, focusing on neurophysiological determinants of addiction. This approach may have decreased the attention paid to dimensions of addictions that are more specifically human. We will firstly briefly argue on the limitation of this neurophysiological addiction model for the field of excessive behavioral conducts. Secondly, we will argue for an approach centered on the differentiation of motivations and on the adaptive dimension of the behavior when it first developed and on the evocation of a transition where the conduct became independent of its original function. The emerging domain of behavioral addictions, where no animal model has been developed so far, may bring a new reflection that may apply to the domain of addictions in general, with a specific attention to human questions.

  11. Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable rates of evolution within a core genome

    Science.gov (United States)

    Background: Biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context. We sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricu...

  12. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  13. Grupos de investigación en contextos organizacionales académicos: una reflexión sobre los procesos de cambio y los retos futuros Research groups in academic organizational contexts: a reflection on change and future challenges

    Directory of Open Access Journals (Sweden)

    Mónica Izquierdo Alonso

    2008-04-01

    Full Text Available Reflexión sobre los cambios habidos en el modelo de ciencia académica, en el contexto de una nueva política científica y de desarrollo tecnológico e innovador. Desde este marco emergente, se muestra cómo afectan dichas transformaciones a las instituciones universitarias y a los grupos de investigación académicos (GIA, desde su doble función formativa e investigadora. Todo ello, a partir de un análisis fundamentado en tres dimensiones: una contextual, considerando el sistema y los modelos científicos; otra basada en el análisis de la propia institución universitaria y, finalmente, una que hace consideraciones globales sobre las estructuras, dinámicas y procesos de los grupos académicos de investigación. Se concluye con la defensa de un papel activo y determinante para la Universidad, como agente decisivo en el proceso de gestión y transferencia del conocimiento. Para ello, ésta ha de asumir su función vital de dirección estratégica de los recursos de investigación y arbitrar, desde una dimensión científica y sistemática, una didáctica de la investigación y de la gestión académica. Se defiende, asimismo, la necesidad de un nuevo marco de gestión inteligente de los GIA, ya que éstos constituyen un espacio de interacción y diálogo, y, en suma, un paso para la transformación de las Universidades.A reflection is presented on the need of a new framework for scientific knowledge, and its implications for universities. The analysis looks at the changes that have occurred in academic research models from different standpoints: the contextual, the institutional, and the structure; dynamics and processes of research groups.

  14. Reflexões sobre práticas de letramento em contexto escolar de língua minoritária Reflections on literacy practices developed in minority language school context

    Directory of Open Access Journals (Sweden)

    Maristela Pereira Fritzen

    2011-01-01

    Full Text Available Objetiva-se neste artigo refletir sobre as práticas de letramento em alemão, introduzidas em uma escola rural a partir da implementação de mudanças nas políticas linguísticas municipais, e sua interface com as práticas de letramento locais em uma comunidade bilíngue de imigração alemã. Os dados da pesquisa, gerados a partir de um estudo de cunho etnográfico e analisados à luz dos Novos Estudos do Letramento e do bi/ multilinguismo de grupos de minorias linguísticas, sugerem que as professoras pertencentes ao grupo étnico-linguístico local esforçam-se por reconhecer a língua de herança das crianças e da comunidade, embora sofram pressão do currículo escolar, assentado, prioritariamente, no monolinguismo em português. Dentro de um cenário sociolinguístico complexo, as professoras necessitam tomar decisões pedagógicas sobre que práticas de letramento e em que língua valorizar na escola.We aim, in this article, to reflect on literacy practices in German language introduced in a rural school from the implementation of changes in the municipal language policies, and their interface with local literacy practices within a bilingual community of German immigration. The research data, which came from an ethnographic study and was analyzed under the light of the New Literacy Studies and of the bi/multilingualism of minority language groups, suggest that the teachers belonging to the local ethnic-linguistic group try to recognize the inherited language of both the children and the community, although they suffer the pressure of the school curriculum, based, mainly, in the Portuguese monolingualism. Within a complex sociolinguistic scenario, teachers should take pedagogic decisions over the literacy practices and language they should value at school.

  15. An archaeal genomic signature

    Science.gov (United States)

    Graham, D. E.; Overbeek, R.; Olsen, G. J.; Woese, C. R.

    2000-01-01

    Comparisons of complete genome sequences allow the most objective and comprehensive descriptions possible of a lineage's evolution. This communication uses the completed genomes from four major euryarchaeal taxa to define a genomic signature for the Euryarchaeota and, by extension, the Archaea as a whole. The signature is defined in terms of the set of protein-encoding genes found in at least two diverse members of the euryarchaeal taxa that function uniquely within the Archaea; most signature proteins have no recognizable bacterial or eukaryal homologs. By this definition, 351 clusters of signature proteins have been identified. Functions of most proteins in this signature set are currently unknown. At least 70% of the clusters that contain proteins from all the euryarchaeal genomes also have crenarchaeal homologs. This conservative set, which appears refractory to horizontal gene transfer to the Bacteria or the Eukarya, would seem to reflect the significant innovations that were unique and fundamental to the archaeal "design fabric." Genomic protein signature analysis methods may be extended to characterize the evolution of any phylogenetically defined lineage. The complete set of protein clusters for the archaeal genomic signature is presented as supplementary material (see the PNAS web site, www.pnas.org).

  16. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

    DEFF Research Database (Denmark)

    Carlton, Jane M.; Hirt, Robert P.; Silva, Joana C.

    2007-01-01

    We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion...

  17. Reflective Communication: Cultivating Mindsight through Nurturing Relationships

    Science.gov (United States)

    Siegel, Daniel J.; Shahmoon-Shanok, Rebecca

    2010-01-01

    This article integrates ideas about mindsight, developed by Daniel Siegel, with those of reflective supervision in the zero-to-three field. The authors explore how the flow of energy and information in the context of nurturing relationships through reflective supervision supports the capacity to develop mindsight. Mindsight is the ability to have…

  18. Biocommunication and natural genome editing

    Institute of Scientific and Technical Information of China (English)

    Guenther; Witzany

    2010-01-01

    The biocommunicative approach investigates communication processes within and among cells,tissues,organs and organisms as sign-mediated interactions,and nucleotide sequences as code,i.e.language-like text,which follows in parallel three kinds of rules:combinatorial (syntactic),context-sensitive(pragmatic),and contentspecific(semantic).Natural genome editing from a bio-communicative perspective is competent agent-driven generation and integration of meaningful nucleotide sequences into pre-existing genomic content arrangements and the ability to(re-)combine and(re-)regulate them according to context-dependent(i.e.adaptational) purposes of the host organism.

  19. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  20. The coffee genome hub: a resource for coffee genomes.

    Science.gov (United States)

    Dereeper, Alexis; Bocs, Stéphanie; Rouard, Mathieu; Guignon, Valentin; Ravel, Sébastien; Tranchant-Dubreuil, Christine; Poncet, Valérie; Garsmeur, Olivier; Lashermes, Philippe; Droc, Gaëtan

    2015-01-01

    The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Context-dependent metabolic networks

    CERN Document Server

    Beguerisse-Díaz, Mariano; Oyarzún, Diego; Picó, Jesús; Barahona, Mauricio

    2016-01-01

    Cells adapt their metabolism to survive changes in their environment. We present a framework for the construction and analysis of metabolic reaction networks that can be tailored to reflect different environmental conditions. Using context-dependent flux distributions from Flux Balance Analysis (FBA), we produce directed networks with weighted links representing the amount of metabolite flowing from a source reaction to a target reaction per unit time. Such networks are analyzed with tools from network theory to reveal salient features of metabolite flows in each biological context. We illustrate our approach with the directed network of the central carbon metabolism of Escherichia coli, and study its properties in four relevant biological scenarios. Our results show that both flow and network structure depend drastically on the environment: networks produced from the same metabolic model in different contexts have different edges, components, and flow communities, capturing the biological re-routing of metab...

  2. Using context to treat traumatized children.

    Science.gov (United States)

    Terr, Lenore C

    2009-01-01

    When treating childhood psychic trauma, context means "putting a perspective to the terrifying experience"--"seeing it in a new light", one might say, or understanding its magnitude and meaning. Of three essential mechanisms behind a young person's psychological recovery from a stress disorder--abreaction, context, and correction-context is the most reflective, cognitive, and conscious of these processes; while abreaction is primarily emotive, and correction is primarily behavioral (involving real or fantasied action). Because context, newly introduced by this author to the psychiatric literature (Terr, 2003), is the most recent and the least well understood of the three mechanisms, it will be the sole focus here.

  3. Heterogeneous genome divergence, differential introgression, and the origin and structure of hybrid zones.

    Science.gov (United States)

    Harrison, Richard G; Larson, Erica L

    2016-06-01

    Hybrid zones have been promoted as windows on the evolutionary process and as laboratories for studying divergence and speciation. Patterns of divergence between hybridizing species can now be characterized on a genomewide scale, and recent genome scans have focused on the presence of 'islands' of divergence. Patterns of heterogeneous genomic divergence may reflect differential introgression following secondary contact and provide insights into which genome regions contribute to local adaptation, hybrid unfitness and positive assortative mating. However, heterogeneous genome divergence can also arise in the absence of any gene flow, as a result of variation in selection and recombination across the genome. We suggest that to understand hybrid zone origins and dynamics, it is essential to distinguish between genome regions that are divergent between pure parental populations and regions that show restricted introgression where these populations interact in hybrid zones. The latter, more so than the former, reveal the likely genetic architecture of reproductive isolation. Mosaic hybrid zones, because of their complex structure and multiple contacts, are particularly good subjects for distinguishing primary intergradation from secondary contact. Comparisons among independent hybrid zones or transects that involve the 'same' species pair can also help to distinguish between divergence with gene flow and secondary contact. However, data from replicate hybrid zones or replicate transects do not reveal consistent patterns; in a few cases, patterns of introgression are similar across independent transects, but for many taxa, there is distinct lack of concordance, presumably due to variation in environmental context and/or variation in the genetics of the interacting populations.

  4. Expertise for Teaching Biology Situated in the Context of Genetic Testing

    Science.gov (United States)

    Van der Zande, Paul; Akkerman, Sanne F.; Brekelmans, Mieke; Waarlo, Arend Jan; Vermunt, Jan D.

    2012-07-01

    Contemporary genomics research will impact the daily practice of biology teachers who want to teach up-to-date genetics in secondary education. This article reports on a research project aimed at enhancing biology teachers' expertise for teaching genetics situated in the context of genetic testing. The increasing body of scientific knowledge concerning genetic testing and the related consequences for decision-making indicate the societal relevance of an educational approach based on situated learning. What expertise do biology teachers need for teaching genetics in the personal health context of genetic testing? This article describes the required expertise by exploring the educational practice. Nine experienced teachers were interviewed about the pedagogical content, moral and interpersonal expertise areas concerning how to teach genetics in the personal health context of genetic testing, and the lessons of five of them were observed. The findings showed that the required teacher expertise encompasses specific pedagogical content expertise, interpersonal expertise and a preference for teacher roles and teaching approaches for the moral aspects of teaching in this context. A need for further development of teaching and learning activities for (reflection on) moral reasoning came to the fore. Suggestions regarding how to apply this expertise into context-based genetics education are discussed.

  5. Organizations & development: epistemological reflections

    Directory of Open Access Journals (Sweden)

    Fernando Batista Bandeira Fontoura

    2016-01-01

    Full Text Available This theoretical test consists of an epistemic study on the nature and limits of relations between subject and society, from a historical context considering the pre-industrial and industrial macroperíodos and expanding post-industrial contexts. It emphasizes the conceptual and theoretical aspects of these macroperíodos highlighting the year 1970 as a symbol of the Taylor system crisis / Fordist contextualized by the automotive industry, which migrated from one-dimensional industrialization processes for multidimensional processes and customized beyond the advent of globalization and dispossession within a multimarket vision. Conclusively, the development models are still characterized by periods whose social concepts are linked to forms of perception of reality by man and their accumulation processes are entitled to this epistemic reflection on organizations and development and its social impacts, as well as the thesis crisis in still homogenizing mentality in economic and organizational terms in terms of environmental uncertainties macro and micro economic historically impacted the society and organizations.

  6. Playing with heart and soul…and genomes: sports implications and applications of personal genomics

    Directory of Open Access Journals (Sweden)

    Jennifer K. Wagner

    2013-08-01

    Full Text Available Whether the integration of genetic/omic technologies in sports contexts will facilitate player success, promote player safety, or spur genetic discrimination depends largely upon the game rules established by those currently designing genomic sports medicine programs. The integration has already begun, but there is not yet a playbook for best practices. Thus far discussions have focused largely on whether the integration would occur and how to prevent the integration from occurring, rather than how it could occur in such a way that maximizes benefits, minimizes risks, and avoids the exacerbation of racial disparities. Previous empirical research has identified members of the personal genomics industry offering sports-related DNA tests, and previous legal research has explored the impact of collective bargaining in professional sports as it relates to the employment protections of the Genetic Information Nondiscrimination Act (GINA. Building upon that research and upon participant observations with specific sports-related DNA tests purchased from four direct-to-consumer companies in 2011 and broader personal genomics (PGx services, this anthropological, legal, and ethical (ALE discussion highlights fundamental issues that must be addressed by those developing personal genomic sports medicine programs, either independently or through collaborations with commercial providers. For example, the vulnerability of student-athletes creates a number of issues that require careful, deliberate consideration. More broadly, however, this ALE discussion highlights potential sports-related implications (that ultimately might mitigate or, conversely, exacerbate racial disparities among athletes of whole exome/genome sequencing conducted by biomedical researchers and clinicians for non-sports purposes. For example, the possibility that exome/genome sequencing of individuals who are considered to be non-patients, asymptomatic, normal, etc. will reveal the presence

  7. Playing with heart and soul…and genomes: sports implications and applications of personal genomics.

    Science.gov (United States)

    Wagner, Jennifer K

    2013-01-01

    Whether the integration of genetic/omic technologies in sports contexts will facilitate player success, promote player safety, or spur genetic discrimination depends largely upon the game rules established by those currently designing genomic sports medicine programs. The integration has already begun, but there is not yet a playbook for best practices. Thus far discussions have focused largely on whether the integration would occur and how to prevent the integration from occurring, rather than how it could occur in such a way that maximizes benefits, minimizes risks, and avoids the exacerbation of racial disparities. Previous empirical research has identified members of the personal genomics industry offering sports-related DNA tests, and previous legal research has explored the impact of collective bargaining in professional sports as it relates to the employment protections of the Genetic Information Nondiscrimination Act (GINA). Building upon that research and upon participant observations with specific sports-related DNA tests purchased from four direct-to-consumer companies in 2011 and broader personal genomics (PGx) services, this anthropological, legal, and ethical (ALE) discussion highlights fundamental issues that must be addressed by those developing personal genomic sports medicine programs, either independently or through collaborations with commercial providers. For example, the vulnerability of student-athletes creates a number of issues that require careful, deliberate consideration. More broadly, however, this ALE discussion highlights potential sports-related implications (that ultimately might mitigate or, conversely, exacerbate racial disparities among athletes) of whole exome/genome sequencing conducted by biomedical researchers and clinicians for non-sports purposes. For example, the possibility that exome/genome sequencing of individuals who are considered to be non-patients, asymptomatic, normal, etc. will reveal the presence of variants of

  8. Cultural Context and Translation

    Institute of Scientific and Technical Information of China (English)

    张敏

    2009-01-01

    cultural context plays an important role in translation. Because translation is a cross-culture activity, the culture context that influ-ences translating is consisted of both the culture contexts of source language and target language. This article firstly analyzes the concept of context and cultural context, then according to the procedure of translating classifies cultural context into two stages and talks about how they respectively influence translating.

  9. Intergenerational transmission of reflective functioning

    Directory of Open Access Journals (Sweden)

    Anna Maria Rosso

    2016-12-01

    Full Text Available The present study investigated whether, and to what extent, reflective functioning (RF during preadolescence is associated with maternal attachment security and reflective functioning, and with the child’s attachment security. Thirty-nine mother-preadolescent child dyads from a non clinical population participated in the study. Maternal and child RF were assessed by applying the Reflective Functioning Scale (RFS to the Adult Attachment Interview (AAI and to the Child Attachment Interview (CAI transcripts. Children of mothers who showed a secure attachment model regarding the relationship with their parents during childhood reported higher levels of RF than the children of mothers who were classified as insecure on the AAI. Child RF was positively associated with maternal Coherence of the Mind on the AAI and negatively associated with maternal derogation of attachment.A strong, significant association was also found between child attachment security and child reflective functioning. Children who were rated as being more emotionally open, more able to balance positive and negative descriptions of their parents, more prone to support their assertions through examples, and more able to positively resolve conflicts with their parents showed higher reflective functioning. On the contrary, children who resorted to a higher extent to idealization and dismissal towards their parents showed a lesser degree of reflective functioning. Notably, a very strong association was found between the score on the Overall coherence subscale and the child’s ability to mentalise mixed-ambivalent mental states in the context of their family relationships.As expected, child and maternal reflective functioning resulted significantly positively correlated with each other. In particular, only maternal reflective functioning (and not maternal attachment security predicted child reflective functioning, and only maternal ability to mentalise mixed-ambivalent mental states

  10. The Arab genome: Health and wealth.

    Science.gov (United States)

    Zayed, Hatem

    2016-11-01

    The 22 Arab nations have a unique genetic structure, which reflects both conserved and diverse gene pools due to the prevalent endogamous and consanguineous marriage culture and the long history of admixture among different ethnic subcultures descended from the Asian, European, and African continents. Human genome sequencing has enabled large-scale genomic studies of different populations and has become a powerful tool for studying disease predictions and diagnosis. Despite the importance of the Arab genome for better understanding the dynamics of the human genome, discovering rare genetic variations, and studying early human migration out of Africa, it is poorly represented in human genome databases, such as HapMap and the 1000 Genomes Project. In this review, I demonstrate the significance of sequencing the Arab genome and setting an Arab genome reference(s) for better understanding the molecular pathogenesis of genetic diseases, discovering novel/rare variants, and identifying a meaningful genotype-phenotype correlation for complex diseases.

  11. Context-Based Questions: Optics in Animal Eyes

    Science.gov (United States)

    Kaltakci, Derya; Eryilmaz, Ali

    2011-01-01

    Context is important as a motivational factor for student involvement with physics. The diversity in the types and the functions of animal eyes is an excellent context in which to achieve this goal. There exists a range of subtopics in optics including pinhole, reflection, refraction, and superposition that can be discussed in the context of the…

  12. Reflections on intuition and expertise.

    Science.gov (United States)

    Perry, M A

    2000-01-01

    Reflective practice now appears firmly established in the English speaking world of professional nursing practice and development. Outside this linguistic context, however, the concept seems less well-known. This paper describes an experience drawn from clinical practice and education in French-speaking Switzerland followed by explicit reflection grounded in questions generated by Johns' model for structured reflection. Thus, a concept well-described in the English-language literature underpins an innovative approach to a French-language clinical teaching situation. The professional implications of this situation are explored through meaningful reflection providing new insight into familiar circumstances as they relate to the nurse tutor's role. This exploration is followed by a critical approach to the experience and the subsequent structured reflection in order to address relationships between intuition and expertise and self-awareness through reflection. A hermeneutic perspective provides additional insight into the nurse-patient relationship where both come to the situation with their own 'pre-understandings'. Individual horizons thus endorse a new understanding going beyond taken-for-granted meanings.

  13. Insights into structural variations and genome rearrangements in prokaryotic genomes.

    Science.gov (United States)

    Periwal, Vinita; Scaria, Vinod

    2015-01-01

    Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing.

  14. Reflecting on Early Literacy Development in the Context of Vanuatu

    Science.gov (United States)

    Hughes, Desma

    2004-01-01

    A low level of literacy development plagues many parts of the Pacific region despite the fact that parents are very keen for their children to become literate in order to embrace the modern world. Issues concerning early education and the attainment of literacy are still a challenge in the Pacific. In order to understand the reasons for the low…

  15. Genome Size Dynamics and Evolution in Monocots

    Directory of Open Access Journals (Sweden)

    Ilia J. Leitch

    2010-01-01

    Full Text Available Monocot genomic diversity includes striking variation at many levels. This paper compares various genomic characters (e.g., range of chromosome numbers and ploidy levels, occurrence of endopolyploidy, GC content, chromosome packaging and organization, genome size between monocots and the remaining angiosperms to discern just how distinctive monocot genomes are. One of the most notable features of monocots is their wide range and diversity of genome sizes, including the species with the largest genome so far reported in plants. This genomic character is analysed in greater detail, within a phylogenetic context. By surveying available genome size and chromosome data it is apparent that different monocot orders follow distinctive modes of genome size and chromosome evolution. Further insights into genome size-evolution and dynamics were obtained using statistical modelling approaches to reconstruct the ancestral genome size at key nodes across the monocot phylogenetic tree. Such approaches reveal that while the ancestral genome size of all monocots was small (1C=1.9 pg, there have been several major increases and decreases during monocot evolution. In addition, notable increases in the rates of genome size-evolution were found in Asparagales and Poales compared with other monocot lineages.

  16. Algumas reflexões sobre produção da categoria de gênero em contextos como o movimento feminista e o poder judiciário Some reflections on the production of the gender category in contexts such as the feminist movement and the judiciary

    Directory of Open Access Journals (Sweden)

    Karla Galvão Adrião

    2006-01-01

    Full Text Available Pensando na discussão instaurada com a modernidade (em distintos contextos sociais, sobre a constituição dos sujeitos de direitos humanos universais, o presente trabalho buscará refletir sobre o indivíduo em sua interface com a busca de "cidadania" e do "acesso à justiça". Para tanto, analisaremos três casos concretos: duas conferências de Políticas para Mulheres, tidas aqui como rituais do movimento feminista no Brasil. Ambas dizem respeito à relação entre políticas para mulheres em duas perspectivas não-excludentes; uma delas entre as próprias mulheres - lésbicas, heterossexuais, brancas, negras, deficientes - e suas tensões direcionadas ora aos direitos individuais, ora aos direitos coletivos, num momento de discussão por cotas. A outra conferência aborda a tensão entre sexo e gênero, entre diferença como sinônimo de desigualdade. O terceiro caso retrata um julgamento de guarda e responsabilidade voltado à não-concessão da maternidade a uma mulher homossexual, mas seu deferimento ao pai tido como biológico. Por fim, sugerimos pensar como, nos dois contextos rituais distintos (Judiciário e Movimento Feminista, a categoria de gênero é produzida e se produz atrelada ao binômio biológico "macho e fêmea".Concerning the discussion arisen by modern times (in different social contexts, about the constitution of universal human rights subjects, this paper aims to reflect upon the individual and his search for "citizenship" and "access to justice". Three cases will be analyzed: two conferences on Women"s Politics, important in the Brazilian feminist movement. Both concern the relation among women"s politics within two non exclusive perspectives: one among women themselves - lesbians, heterosexual, white, black. handicapped - and their tensions related either to individual rights or to collective rights, in a time when quotas are being discussed. The other conference approaches the tension between sex and gender

  17. Perceptual processing of a complex musical context

    DEFF Research Database (Denmark)

    Quiroga Martinez, David Ricardo; Hansen, Niels Christian; Højlund, Andreas

    The mismatch negativity (MMN) is a brain response elicited by deviants in a series of repetitive sounds. It reflects the perception of change in low-level sound features and reliably measures auditory memory and predictive processes. MMN is a valuable tool for the study of music perception. However......, most designs use simple tone patterns as stimuli, failing to represent the complexity of everyday music. We aim to develop a new MMN paradigm using more real-sounding stimuli. We want to determine how the complexity of the context affects auditory predictions as reflected by the MMN. For this purpose...... about music perception and learning in more realistic sound contexts....

  18. Intercultural Learning Across Contexts

    Directory of Open Access Journals (Sweden)

    Kristin Beate VASBØ

    2013-10-01

    Full Text Available International youth work in Europe (i.e. non-formal learning demands a renewal of the prominent intercultural theory and framework in the youth field in order to cope with contemporary questions concerning pluralism and global challenges. This article provides a new theoretical framework for intercultural learning that departs from a complex, multicultural, social reality. Furthermore, the article explores how young people today experience international youth exchanges as arenas for learning in relation to other learning arenas in and out of school. The data consists of interviews and participant observation of a Norwegian youth group preparing for, participating in and reflecting on their experiences in an international youth exchange programme. The findings show that participation in international youth exchanges, in addition to cultural knowledge, may contribute to increased motivation for learning, enhanced self-understanding and personal growth that seems transferable to other contexts. Furthermore,global youth culture plays a crucial role in young people`s experiences of being like one another across national borders, cultures and social realities.

  19. The Nostoc punctiforme Genome

    Energy Technology Data Exchange (ETDEWEB)

    John C. Meeks

    2001-12-31

    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  20. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  1. The contexts of penitentiary pedagogy

    Directory of Open Access Journals (Sweden)

    Paweł Szczepaniak

    2011-12-01

    Full Text Available This article contains a sketch of the interpretation of penitentiary pedagogy. There arediscussed, among others, etymology and the definition of penitentiary pedagogy, its subject- matter, goals, axiological, teleological, theoretical and methodological foundations and its place and role among other scientific disciplines. Along with the development of multiple methodological options and changes in social life, the reflection concerning the identity and place of penitentiary pedagogy demands a new articulation. The author submits and gives grounds for a proposition for the penitentiary pedagogy to reap gain in a wider scope from the achievements of social pedagogy, which in the context of citizens’ life deals with designing, carrying out and evaluating educational efforts and the regulation of social relations in the context of social policy, according to an open citizen society (inclusive idea.

  2. Life insurance: genomic stratification and risk classification.

    Science.gov (United States)

    Joly, Yann; Burton, Hilary; Knoppers, Bartha Maria; Feze, Ida Ngueng; Dent, Tom; Pashayan, Nora; Chowdhury, Susmita; Foulkes, William; Hall, Alison; Hamet, Pavel; Kirwan, Nick; Macdonald, Angus; Simard, Jacques; Van Hoyweghen, Ine

    2014-05-01

    With the development and increasing accessibility of new genomic tools such as next-generation sequencing, genome-wide association studies, and genomic stratification models, the debate on genetic discrimination in the context of life insurance became even more complex, requiring a review of current practices and the exploration of new scenarios. In this perspective, a multidisciplinary group of international experts representing different interests revisited the genetics and life insurance debate during a 2-day symposium 'Life insurance: breast cancer research and genetic risk prediction seminar' held in Quebec City, Canada on 24 and 25 September 2012. Having reviewed the current legal, social, and ethical issues on the use of genomic information in the context of life insurance, the Expert Group identified four main questions: (1) Have recent developments in genomics and related sciences changed the contours of the genetics and life insurance debate? (2) Are genomic results obtained in a research context relevant for life insurance underwriting? (3) Should predictive risk assessment and risk stratification models based on genomic data also be used for life insurance underwriting? (4) What positive actions could stakeholders in the debate take to alleviate concerns over the use of genomic information by life insurance underwriters? This paper presents a summary of the discussions and the specific action items recommended by the Expert Group.

  3. Generalization as creative and reflective act

    DEFF Research Database (Denmark)

    Tateo, Luca

    2013-01-01

    It is argued that generalization in psychology is a creative, interpretative, and reflective act of thought, by accessing a higher level of abstraction from meaningful events. In the context of clarification of this claim, a fresh look at Lewin’s argumentation about the “Aristotelian” and “Galile......It is argued that generalization in psychology is a creative, interpretative, and reflective act of thought, by accessing a higher level of abstraction from meaningful events. In the context of clarification of this claim, a fresh look at Lewin’s argumentation about the “Aristotelian...

  4. Total centromere size and genome size are strongly correlated in ten grass species.

    Science.gov (United States)

    Zhang, Han; Dawe, R Kelly

    2012-05-01

    It has been known for decades that centromere size varies across species, but the factors involved in setting centromere boundaries are unknown. As a means to address this question, we estimated centromere sizes in ten species of the grass family including rice, maize, and wheat, which diverged 60~80 million years ago and vary by 40-fold in genome size. Measurements were made using a broadly reactive antibody to rice centromeric histone H3 (CENH3). In species-wide comparisons, we found a clear linear relationship between total centromere size and genome size. Species with large genomes and few chromosomes tend to have the largest centromeres (e.g., rye) while species with small genomes and many chromosomes have the smallest centromeres (e.g., rice). However, within a species, centromere size is surprisingly uniform. We present evidence from three oat-maize addition lines that support this claim, indicating that each of three maize centromeres propagated in oat are not measurably different from each other. In the context of previously published data, our results suggest that the apparent correlation between chromosome and centromere size is incidental to a larger trend that reflects genome size. Centromere size may be determined by a limiting component mechanism similar to that described for Caenorhabditis elegans centrosomes.

  5. Reflectable bases for affine reflection systems

    CERN Document Server

    Azam, Saeid; Yousofzadeh, Malihe

    2011-01-01

    The notion of a "root base" together with its geometry plays a crucial role in the theory of finite and affine Lie theory. However, it is known that such a notion does not exist for the recent generalizations of finite and affine root systems such as extended affine root systems and affine reflection systems. As an alternative, we introduce the notion of a "reflectable base", a minimal subset $\\Pi$ of roots such that the non-isotropic part of the root system can be recovered by reflecting roots of $\\Pi$ relative to the hyperplanes determined by $\\Pi$. We give a full characterization of reflectable bases for tame irreducible affine reflection systems of reduced types, excluding types $E_{6,7,8}$. As a byproduct of our results, we show that if the root system under consideration is locally finite then any reflectable base is an integral base.

  6. Bacterial genes in the aphid genome: absence of functional gene transfer from Buchnera to its host.

    Directory of Open Access Journals (Sweden)

    Naruo Nikoh

    2010-02-01

    Full Text Available Genome reduction is typical of obligate symbionts. In cellular organelles, this reduction partly reflects transfer of ancestral bacterial genes to the host genome, but little is known about gene transfer in other obligate symbioses. Aphids harbor anciently acquired obligate mutualists, Buchnera aphidicola (Gammaproteobacteria, which have highly reduced genomes (420-650 kb, raising the possibility of gene transfer from ancestral Buchnera to the aphid genome. In addition, aphids often harbor other bacteria that also are potential sources of transferred genes. Previous limited sampling of genes expressed in bacteriocytes, the specialized cells that harbor Buchnera, revealed that aphids acquired at least two genes from bacteria. The newly sequenced genome of the pea aphid, Acyrthosiphon pisum, presents the first opportunity for a complete inventory of genes transferred from bacteria to the host genome in the context of an ancient obligate symbiosis. Computational screening of the entire A. pisum genome, followed by phylogenetic and experimental analyses, provided strong support for the transfer of 12 genes or gene fragments from bacteria to the aphid genome: three LD-carboxypeptidases (LdcA1, LdcA2,psiLdcA, five rare lipoprotein As (RlpA1-5, N-acetylmuramoyl-L-alanine amidase (AmiD, 1,4-beta-N-acetylmuramidase (bLys, DNA polymerase III alpha chain (psiDnaE, and ATP synthase delta chain (psiAtpH. Buchnera was the apparent source of two highly truncated pseudogenes (psiDnaE and psiAtpH. Most other transferred genes were closely related to genes from relatives of Wolbachia (Alphaproteobacteria. At least eight of the transferred genes (LdcA1, AmiD, RlpA1-5, bLys appear to be functional, and expression of seven (LdcA1, AmiD, RlpA1-5 are highly upregulated in bacteriocytes. The LdcAs and RlpAs appear to have been duplicated after transfer. Our results excluded the hypothesis that genome reduction in Buchnera has been accompanied by gene transfer to the

  7. Conflicting values in reflection on professional practice

    OpenAIRE

    Siebert, Sabina; Costley, Carol

    2013-01-01

    Purpose – The purpose of this paper is to examine the use of reflection as a tool of enquiry within the context of higher education work based learning. The aim of the study is to investigate how reflection on professional practice brings about a review of the values underpinning that practice. Design/methodology/approach – The data were collected from a group of undergraduate students undertaking their studies by work based learning in the area of management in a Scottish University. ...

  8. CONTEXT 2015 Doctorial Symposium

    DEFF Research Database (Denmark)

    2015-01-01

    What is the CONTEXT 2015 Doctoral Symposium? The CONTEXT 2015 Doctoral Symposium is an opportunity for doctoral researchers to showcase their work and discuss problems, challenges, and ideas in an open and collegial environment with expert feedback. The Doctoral Symposium is a workshop for doctoral...... day, Monday November 2, 2015, the day prior to the start of the main CONTEXT 2015 conference....

  9. Meaning in Context

    DEFF Research Database (Denmark)

    Christiansen, Henning; Dahl, Veronica

    2005-01-01

    A model for context-dependent natural language semantics is proposed and formalized in terms of possible worlds. The meaning of a sentence depends on context and at the same time affects that context representing the knowledge about the world collected from a discourse. The model fits well...

  10. Description logics of context

    CSIR Research Space (South Africa)

    Klarman, S

    2013-05-01

    Full Text Available We introduce Description Logics of Context (DLCs) - an extension of Description Logics (DLs) for context-based reasoning. Our approach descends from J. McCarthy's tradition of treating contexts as formal objects over which one can quantify...

  11. Pseudomonas aeruginosa genomic structure and diversity

    Directory of Open Access Journals (Sweden)

    Jens eKlockgether

    2011-07-01

    Full Text Available The Pseudomonas aeruginosa genome (G + C content 65-67%, size 5.5 – 7 Mbp is made up of a single circular chromosome and a variable number of plasmids. Sequencing of complete genomes or blocks of the accessory genome has revealed that the genome encodes a large repertoire of transporters, transcriptional regulators and two-component regulatory systems which reflects its metabolic diversity to utilize a broad range of nutrients. The conserved core component of the genome is largely collinear among P. aeruginosa strains and exhibits an interclonal sequence diversity of 0.5 – 0.7%. Only a few loci of the core genome are subject to diversifying selection. Genome diversity is mainly caused by accessory DNA elements located in 79 regions of genome plasticity that are scattered around the genome and show an anomalous usage of mono- to tetradecanucleotides. Genomic islands of the pKLC102/PAGI-2 family that integrate into tRNALys or tRNAGly genes represent hotspots of inter- and intraclonal genomic diversity. The individual islands differ in their repertoire of metabolic genes that make a large contribution to the pangenome. In order to unravel intraclonal diversity of P. aeruginosa, the genomes of two members of the PA14 clonal complex from diverse habitats and geographic origin were compared. The genome sequences differed by less than 0.01% from each other. 198 of the 231 SNPs were non-randomly distributed in the genome. Non-synonymous SNPs were mainly found in an integrated Pf1-like phage and in genes involved in transcriptional regulation, membrane and extracellular constituents, transport and secretion. In summary, P. aeruginosa is endowed with a highly conserved core genome of low sequence diversity and a highly variable accessory genome that communicates with other pseudomonads and genera via horizontal gene transfer.

  12. A Scalable Genome-Editing-Based Approach for Mapping Multiprotein Complexes in Human Cells

    Directory of Open Access Journals (Sweden)

    Mathieu Dalvai

    2015-10-01

    Full Text Available Conventional affinity purification followed by mass spectrometry (AP-MS analysis is a broadly applicable method used to decipher molecular interaction networks and infer protein function. However, it is sensitive to perturbations induced by ectopically overexpressed target proteins and does not reflect multilevel physiological regulation in response to diverse stimuli. Here, we developed an interface between genome editing and proteomics to isolate native protein complexes produced from their natural genomic contexts. We used CRISPR/Cas9 and TAL effector nucleases (TALENs to tag endogenous genes and purified several DNA repair and chromatin-modifying holoenzymes to near homogeneity. We uncovered subunits and interactions among well-characterized complexes and report the isolation of MCM8/9, highlighting the efficiency and robustness of the approach. These methods improve and simplify both small- and large-scale explorations of protein interactions as well as the study of biochemical activities and structure-function relationships.

  13. Reflective Reconstruction of Visual Products

    DEFF Research Database (Denmark)

    Otrel-Cass, Kathrin

    2018-01-01

    of visuals. A case of a New Zealand year 7/8 primary science class studying the water cycle is presented. It is argued that teaching science concepts like the water cycle through visualizations cannot be an abstract endeavor because even when abstract ideas are presented, they are visualized as concrete......This paper presents an argument about the cultural construction of visual products. Based on data from video observations, interviews and the collection of student-produced (visual) artifacts, a material ethnography approach is presented. Applying reflexivity with the use of visuals, the following...... argument is made. Instead of revealing insights through just one approach, a reflective methodology should consider: (a) the context in which the visual was produced; (b) the content of the visual; (c) the contexts in, and subjectivities through, which visuals are viewed; and (d) the materiality and agency...

  14. Middle Leaders' Learning in a University Context

    Science.gov (United States)

    Franken, Margaret; Penney, Dawn; Branson, Christopher

    2015-01-01

    This article focuses on the phenomenon of middle leadership in a university context and directs attention to the significance of learning as a central facet of leadership development. Drawing on the reflections of two of the authors as new middle leaders (chairpersons of departments), this article critically examines how middle leaders learn…

  15. ANTHROPOLOGY AND HERITAGE IN THE MULTICULTURAL CONTEXT

    Directory of Open Access Journals (Sweden)

    Angélica Núñez

    2014-11-01

    Full Text Available This reflection is focused on the role of anthropology in the issue of cultural heritage and cultural policies and their relation with the local identities in the Colombian multicultural context, highlighting the archaeological heritage and the museums as important fields to explore the topic with an anthropological perspective

  16. Temporal Context, Preference, and Resistance to Change

    Science.gov (United States)

    Podlesnik, Christopher A.; Jimenez-Gomez, Corina; Thrailkill, Eric A.; Shahan, Timothy A.

    2011-01-01

    According to behavioral momentum theory, preference and relative resistance to change in concurrent chains schedules are correlated and reflect the relative conditioned value of discriminative stimuli. In the present study, we explore the generality of this relation by manipulating the temporal context within a concurrent-chains procedure through…

  17. Genome databases

    Energy Technology Data Exchange (ETDEWEB)

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  18. Context and Pavlovian conditioning.

    Science.gov (United States)

    Landeira-Fernandez, J

    1996-02-01

    Procedurally, learning has to occur in a context. Several lines of evidence suggest that contextual stimuli actively affect learning and expression of the conditional response. The experimental context can become associated with the unconditional stimulus (US), especially when the US is presented in a context in the absence of a discrete conditional stimulus (CS). Moreover, context can modulate CS-US associations. Finally, it appears that context can become associated with the CS when it is presented before the CS-US training. The purpose of the present paper is to review some of the relevant literature that considers the context as an important feature of Pavlovian conditioning and to discuss some of the main learning theories that incorporate the context into their theoretical framework. The paper starts by mentioning historical positions that considered context an important variable in conditioning and then describes how the approach to contextual conditioning changed with the modern study of Pavlovian conditioning. Various forms of measurement of context conditioning are presented and the associative strength attached to context in several experimental paradigms is examined. The possible functions that context may acquire during conditioning are pointed out and related to major learning theories. Moreover, the effect of certain neurological manipulations on context conditioning is presented and these results are discussed in terms of possible functions that the context might acquire during Pavlovian conditioning. It is concluded that contextual stimuli acquire different functions during normal conditioning. A procedure in which animals are exposed to an aversive US immediately after they are placed in the experimental context is suggested as a useful control for the study of context conditioning.

  19. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae : Implications for the microbial "pan-genome"

    NARCIS (Netherlands)

    Tettelin, H; Masignani, [No Value; Cieslewicz, MJ; Donati, C; Medini, D; Ward, NL; Angiuoli, SV; Crabtree, J; Jones, AL; Durkin, AS; DeBoy, RT; Davidsen, TM; Mora, M; Scarselli, M; Ros, IMY; Peterson, JD; Hauser, CR; Sundaram, JP; Nelson, WC; Madupu, R; Brinkac, LM; Dodson, RJ; Rosovitz, MJ; Sullivan, SA; Daugherty, SC; Haft, DH; Selengut, J; Gwinn, ML; Zhou, LW; Zafar, N; Khouri, H; Radune, D; Dimitrov, G; Watkins, K; O'Connor, KJB; Smith, S; Utterback, TR; White, O; Rubens, CE; Grandi, G; Madoff, LC; Kasper, DL; Telford, JL; Wessels, MR; Rappuoli, R; Fraser, CM

    2005-01-01

    The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and als

  20. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae : Implications for the microbial "pan-genome"

    NARCIS (Netherlands)

    Tettelin, H; Masignani, [No Value; Cieslewicz, MJ; Donati, C; Medini, D; Ward, NL; Angiuoli, SV; Crabtree, J; Jones, AL; Durkin, AS; DeBoy, RT; Davidsen, TM; Mora, M; Scarselli, M; Ros, IMY; Peterson, JD; Hauser, CR; Sundaram, JP; Nelson, WC; Madupu, R; Brinkac, LM; Dodson, RJ; Rosovitz, MJ; Sullivan, SA; Daugherty, SC; Haft, DH; Selengut, J; Gwinn, ML; Zhou, LW; Zafar, N; Khouri, H; Radune, D; Dimitrov, G; Watkins, K; O'Connor, KJB; Smith, S; Utterback, TR; White, O; Rubens, CE; Grandi, G; Madoff, LC; Kasper, DL; Telford, JL; Wessels, MR; Rappuoli, R; Fraser, CM

    2005-01-01

    The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and als

  1. Context and Listening Comprehension

    Institute of Scientific and Technical Information of China (English)

    Qin Yingying

    2016-01-01

    Context is very important factor that can't be ignored in speech communication. Context contributes much to understanding the meaning of words. The exact and thorough interpretation of words and utterance results from contexts. The relation is discussed between context and listening comprehension, and the functions of context are analyzed in listening. It is pointed out that the analysis of contextual clues is useful in understanding listening materials and also introduces some ways on contextual clues in listening so as to improve listening comprehension.

  2. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....

  3. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  4. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  5. Language teaching and its contexts

    Directory of Open Access Journals (Sweden)

    Michael Byram

    2013-01-01

    Full Text Available The title of this new journal provides opportunity to review the many contexts which need to be taken into account in reflecting upon foreign language teaching. These contexts include the educational, the fact that much language teaching takes place within general educational and often compulsory educational settings and institutions. Learners thus encounter foreign languages alongside other languages – their language of the home, the official language of the country, languages of minorities and others – and this needs to be part of the thinking about learning and teaching. Furthermore, since language is the tool for learning throughout life and especially in educational institutions, where the languages of other subjects are languages in themselves which learners have to learn if they are to be successful in education, teachers of all subjects need to be aware of language as the tool of learning. Yet another issue is the relationship of language teaching with citizenship education and the development of ‘intercultural citizenship’. The title of the journal also refers to ‘research’ and here too there is potential for reflection on the modes and paradigms of research which are relevant to investigating language teaching and learning. Distinctions of quantitative and qualitative research are misleading and need to be reviewed. The higher order distinctions are between research which seeks explanation, that which seeks understanding and that which involves advocacy.

  6. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  7. Theory and context / Theory in context

    DEFF Research Database (Denmark)

    Glaveanu, Vlad Petre

    2014-01-01

    It is debatable whether the psychology of creativity is a field in crisis or not. There are clear signs of increased fragmenta-tion and a scarcity of integrative efforts, but is this necessari-ly bad? Do we need more comprehensive theories of creativ-ity and a return to old epistemological......’, theoreti-cal work in the psychology of creativity can be integrative without having the ambition to explain or, even more, predict, creative expression across all people, at all times, and in all domains. To avoid such ambition, the psychology of creativi-ty requires a theory of context that doesn...... trans-disciplinary manner. Consideration needs to be given as well to connected scholarship focusing on imagination, innova-tion, and improvisation. Last but not least, an expanded the-ory of context cannot ignore the institutional context of doing research on creativity. Creativity scholars are facing...

  8. Reflections on a participatory documentary process

    DEFF Research Database (Denmark)

    Velez Torres, Irene

    2013-01-01

    and within the communities themselves. The project involved 14 local young participants and four professionals who collectively produced a documentary on the rural context of violence in La Toma District, Colombia. By enabling the reflections and intentions of young participants in the research process, PDP...

  9. Theory and context / Theory in context

    DEFF Research Database (Denmark)

    Glaveanu, Vlad Petre

    2014-01-01

    It is debatable whether the psychology of creativity is a field in crisis or not. There are clear signs of increased fragmenta-tion and a scarcity of integrative efforts, but is this necessari-ly bad? Do we need more comprehensive theories of creativ-ity and a return to old epistemological...... trans-disciplinary manner. Consideration needs to be given as well to connected scholarship focusing on imagination, innova-tion, and improvisation. Last but not least, an expanded the-ory of context cannot ignore the institutional context of doing research on creativity. Creativity scholars are facing...

  10. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen;

    2015-01-01

    , archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  11. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...

  12. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  13. What makes a good reflective paper?

    Science.gov (United States)

    Walling, Anne; Shapiro, Johanna; Ast, Terry

    2013-01-01

    Reflective papers are increasingly recognized as potentially important contributors to clinical education and practice; however, few quality guidelines are available for potential authors or reviewers. We sought to identify key characteristics of effective reflective papers and to clarify factors that increased or reduced the probability of acceptance for publication. A 10-item survey addressing the definition, purpose, and quality characteristics of reflective papers was developed based on a literature review and analysis of the author instructions of 14 journals that regularly publish reflective papers and are likely to be read by primary care physicians. The survey was sent electronically to the editor or associate editor responsible for reflective papers at each journal. Seven completed surveys were returned. The essential element defining a reflective paper was identified as narration of a specific professional experience that resonated with readers and conveyed deeper meaning. All respondents rated emotional engagement as very important, followed by stimulating reflection in the reader, providing a lesson applicable to patient care, and stimulating discussion with colleagues and/or learners. Reasons for acceptance or rejection of reflective submissions to journals were identified in issues related to writing style, topic selection, and reader reaction. Writing and reviewing reflective papers is strongly dependent on context, personal values, experience, and emotional reaction; nevertheless, core quality features can be identified to guide both writers and editors/reviewers without destroying the unique nature of these papers.

  14. Shock wave reflection phenomena

    CERN Document Server

    Ben-dor, Gabi

    2007-01-01

    This book provides a comprehensive state-of-the-knowledge description of the shock wave reflection phenomena from a phenomenological point of view. The first part is a thorough introduction to oblique shock wave reflections, presenting the two major well-known reflection wave configurations, namely, regular (RR) and Mach (MR) reflections, the corresponding two- and three-shock theories, their analytical and graphical solution and the proposed transition boundaries between these two reflection-wave configurations. The second, third and fourth parts describe the reflection phenomena in steady, pseudo-steady and unsteady flows, respectively. Here, the possible specific types of reflection wave configurations are described, criteria for their formation and termination are presented and their governing equations are solved analytically and graphically and compared with experimental results. The resolution of the well-known von Neumann paradox and a detailed description of two new reflection-wave configurations - t...

  15. Integrated Genome-Based Studies of Shewanella Ecophysiology

    Energy Technology Data Exchange (ETDEWEB)

    Andrei L. Osterman, Ph.D.

    2012-12-17

    Integration of bioinformatics and experimental techniques was applied to mapping and characterization of the key components (pathways, enzymes, transporters, regulators) of the core metabolic machinery in Shewanella oneidensis and related species with main focus was on metabolic and regulatory pathways involved in utilization of various carbon and energy sources. Among the main accomplishments reflected in ten joint publications with other participants of Shewanella Federation are: (i) A systems-level reconstruction of carbohydrate utilization pathways in the genus of Shewanella (19 species). This analysis yielded reconstruction of 18 sugar utilization pathways including 10 novel pathway variants and prediction of > 60 novel protein families of enzymes, transporters and regulators involved in these pathways. Selected functional predictions were verified by focused biochemical and genetic experiments. Observed growth phenotypes were consistent with bioinformatic predictions providing strong validation of the technology and (ii) Global genomic reconstruction of transcriptional regulons in 16 Shewanella genomes. The inferred regulatory network includes 82 transcription factors, 8 riboswitches and 6 translational attenuators. Of those, 45 regulons were inferred directly from the genome context analysis, whereas others were propagated from previously characterized regulons in other species. Selected regulatory predictions were experimentally tested. Integration of this analysis with microarray data revealed overall consistency and provided additional layer of interactions between regulons. All the results were captured in the new database RegPrecise, which is a joint development with the LBNL team. A more detailed analysis of the individual subsystems, pathways and regulons in Shewanella spp included bioinfiormatics-based prediction and experimental characterization of: (i) N-Acetylglucosamine catabolic pathway; (ii)Lactate utilization machinery; (iii) Novel Nrt

  16. Identifying elemental genomic track types and representing them uniformly

    Directory of Open Access Journals (Sweden)

    Gundersen Sveinung

    2011-12-01

    Full Text Available Abstract Background With the recent advances and availability of various high-throughput sequencing technologies, data on many molecular aspects, such as gene regulation, chromatin dynamics, and the three-dimensional organization of DNA, are rapidly being generated in an increasing number of laboratories. The variation in biological context, and the increasingly dispersed mode of data generation, imply a need for precise, interoperable and flexible representations of genomic features through formats that are easy to parse. A host of alternative formats are currently available and in use, complicating analysis and tool development. The issue of whether and how the multitude of formats reflects varying underlying characteristics of data has to our knowledge not previously been systematically treated. Results We here identify intrinsic distinctions between genomic features, and argue that the distinctions imply that a certain variation in the representation of features as genomic tracks is warranted. Four core informational properties of tracks are discussed: gaps, lengths, values and interconnections. From this we delineate fifteen generic track types. Based on the track type distinctions, we characterize major existing representational formats and find that the track types are not adequately supported by any single format. We also find, in contrast to the XML formats, that none of the existing tabular formats are conveniently extendable to support all track types. We thus propose two unified formats for track data, an improved XML format, BioXSD 1.1, and a new tabular format, GTrack 1.0. Conclusions The defined track types are shown to capture relevant distinctions between genomic annotation tracks, resulting in varying representational needs and analysis possibilities. The proposed formats, GTrack 1.0 and BioXSD 1.1, cater to the identified track distinctions and emphasize preciseness, flexibility and parsing convenience.

  17. Context in place

    DEFF Research Database (Denmark)

    Nordentoft, Helle Merete; Thomsen, Rie

    The purpose of this paper is to provide a theoretical framework - i.e. a vocabulary - for understanding the importance of integrating context in analyses of guidance practices. The paper delineates a conceptual landscape of context based on social practice and interactional theories on context. We...... specifically argue for a more grounded approach to the conception of context - a topographic approach - in which the physical setting - i.e. 'the place' becomes an inevitable part of analyses of guidance practices in order to understand participants' sense-making processes. In the paper we draw on two case...

  18. Genome cartography through domain annotation.

    Science.gov (United States)

    Ponting, C P; Dickens, N J

    2001-01-01

    The evolutionary history of eukaryotic proteins involves rapid sequence divergence, addition and deletion of domains, and fusion and fission of genes. Although the protein repertoires of distantly related species differ greatly, their domain repertoires do not. To account for the great diversity of domain contexts and an unexpected paucity of ortholog conservation, we must categorize the coding regions of completely sequenced genomes into domain families, as well as protein families.

  19. Liberating Moral Reflection

    Science.gov (United States)

    Horell, Harold D.

    2013-01-01

    The author argues that if we are to foster life-giving and liberating moral reflection, we must first liberate moral reflection from distortions; specifically, from the distorting effects of moral insensitivity, destructive moral relativism, and confusions resulting from a failure to understand the dynamics of moral reflection. The author proposes…

  20. Knowledge-Level Reflection

    NARCIS (Netherlands)

    Harmelen, van F.A.H.; Wielinga, B.J.; Bredeweg, Bert; Schreiber, G.; Karbach, Werner; Reinders, Martin; Voss, A.; Akkermans, H.; Bartsch-Spoerl, Brigitte; Vinkhuyzen, Erik

    This paper presents an overview of the REFLECT project. It defines the notion of knowledge level reflection that has been central to the project, it compares this notion with existing approaches to reflection in related fields, and investigates some of the consequences of the concept of knowledge le

  1. Liberating Moral Reflection

    Science.gov (United States)

    Horell, Harold D.

    2013-01-01

    The author argues that if we are to foster life-giving and liberating moral reflection, we must first liberate moral reflection from distortions; specifically, from the distorting effects of moral insensitivity, destructive moral relativism, and confusions resulting from a failure to understand the dynamics of moral reflection. The author proposes…

  2. Imaging seismic reflections

    NARCIS (Netherlands)

    Op 't Root, Timotheus Johannes Petrus Maria

    2011-01-01

    The goal of reflection seismic imaging is making images of the Earth subsurface using surface measurements of reflected seismic waves. Besides the position and orientation of subsurface reflecting interfaces it is a challenge to recover the size or amplitude of the discontinuities. We investigate tw

  3. Bioprospecting in the genomic age.

    Science.gov (United States)

    Hicks, Michael A; Prather, Kristala L J

    2014-01-01

    The genomic revolution promises great advances in the search for useful biocatalysts. Function-based metagenomic approaches have identified several enzymes with properties that make them useful candidates for a variety of bioprocesses. As DNA sequencing costs continue to decline, the volume of genomic data, along with their corresponding predicted protein sequences, will continue to increase dramatically, necessitating new approaches to leverage this information for gene-based bioprospecting efforts. Additionally, as new functions are discovered and correlated with this sequence information, the knowledge of the often complex relationship between a protein's sequence and function will improve. This in turn will lead to better gene-based bioprospecting approaches and facilitate the tailoring of desired properties through protein engineering projects. In this chapter, we discuss a number of recent advances in bioprospecting within the context of the genomic age.

  4. Reflection a neglected art in health promotion.

    Science.gov (United States)

    Fleming, Paul

    2007-10-01

    Evaluation and quality assurance have, over time, become the bedrock of health promotion practice in ensuring effectiveness and efficiency of programme planning and delivery. There has been less emphasis, however, on formal recognition of the contribution of the personal characteristics and perspectives of those who plan and deliver programmes and to the more subtle underlying effects of prevailing societal and professional norms. This paper seeks to highlight the neglect of formal reflection as a key professional skill in professional health promotion practice. It outlines key theories underpinning the development of the concepts of reflection and reflective practice. The role of reflection in critical health education as it contributes to critical consciousness raising is highlighted through its contribution to the empowerment of change agents in a societal change context. A conceptual typology of reflective practice is described which provides a flexible structure with which professionals can reflect on the role of self, the context and the process of health promotion programme planning. Its use is illustrated from the author's published work in health promotion which is related to prevention of workplace violence.

  5. Investigating novice doctors' reflections in debriefings after simulation scenarios

    DEFF Research Database (Denmark)

    Kihlgren, Per; Spanager, Lene; Dieckmann, Peter

    2015-01-01

    BACKGROUND: Debriefing is pivotal to the simulation learning process, and the reflection that it aims to foster is fundamental in experiential learning. Despite its importance, essential aspects of debriefing remain unclear. STUDY OBJECTIVE: To investigate reflection in debriefings by assessing p...... be appropriated to the given context. The rating of reflection levels is a promising approach to analyze reflection in conversation in experience-based learning situations.......BACKGROUND: Debriefing is pivotal to the simulation learning process, and the reflection that it aims to foster is fundamental in experiential learning. Despite its importance, essential aspects of debriefing remain unclear. STUDY OBJECTIVE: To investigate reflection in debriefings by assessing...... was the highest reached. No salient differences were found in debriefers' utterances across occurrences of higher and lower reflection. CONCLUSION: Participants' reflection levels were low in this cohort of novice doctors training leadership skills in acute situations. However, the desired reflection should...

  6. Reflection Positive Doubles

    CERN Document Server

    Jaffe, Arthur

    2016-01-01

    Here we introduce reflection positive doubles, a general framework for reflection positivity, covering a wide variety of systems in statistical physics and quantum field theory. These systems may be bosonic, fermionic, or parafermionic in nature. Within the framework of reflection positive doubles, we give necessary and sufficient conditions for reflection positivity. We use a reflection-invariant cone to implement our construction. Our characterization allows for a direct interpretation in terms of coupling constants, making it easy to check in concrete situations. We illustrate our methods with numerous examples.

  7. Nanotechnology and Social Context

    Science.gov (United States)

    Sandler, Ronald

    2007-01-01

    The central claims defended in this article are the following: (a) The social and ethical challenges of nanotechnology can be fully identified only if both the characteristic features of nanotechnologies and the social contexts into which they are emerging are considered. (b) When this is done, a host of significant social context issues, or…

  8. Incest in Context.

    Science.gov (United States)

    Taubman, Stan

    1984-01-01

    Presents a comprehensive view of the societal, cultural, familial, and personality factors that form the context of people at risk for incest and associated problems. Summarizes the consequences and the causal context of incest and describes an ecosystems approach to intervention. (Author/LLL)

  9. CONTEXT 2015 Doctorial Symposium

    DEFF Research Database (Denmark)

    2015-01-01

    What is the CONTEXT 2015 Doctoral Symposium? The CONTEXT 2015 Doctoral Symposium is an opportunity for doctoral researchers to showcase their work and discuss problems, challenges, and ideas in an open and collegial environment with expert feedback. The Doctoral Symposium is a workshop for doctor...

  10. Ancient genomics.

    Science.gov (United States)

    Der Sarkissian, Clio; Allentoft, Morten E; Ávila-Arcos, María C; Barnett, Ross; Campos, Paula F; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D; Moreno-Mayar, J Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M Thomas P; Willerslev, Eske; Orlando, Ludovic

    2015-01-19

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

  11. How Critical Reflection Benefits Faculty as They Implement Learner-Centered Teaching

    Science.gov (United States)

    Blumberg, Phyllis

    2015-01-01

    Critical reflection assists faculty as they transition to using learner-centered approaches. When this reflection occurs within the context of social media, they can obtain reinforcing feedback and support.

  12. Wave Reflection Coefficient Spectrum

    Institute of Scientific and Technical Information of China (English)

    俞聿修; 邵利民; 柳淑学

    2003-01-01

    The wave reflection coefficient frequency spectrum and directional spectrum for concrete face slope breakwaters and rubble mound breakwaters are investigated through physical model tests in the present study. The reflection coefficients of oblique irregular waves are analyzed by the Modified Two-Point Method (MTPM) proposed by the authors. The results show that the wave reflection coefficient decreases with increasing wave frequency and incident angle or decreasing structure slope. The reflection coefficient frequency spectrum and its variation with Iribarren number are given in this paper. The paper also suggests an empirical 3-dimensional reflection coefficient spectrum, i.e. reflection coefficient directional spectrum, which can be used to illustrate quantitatively the variation of reflection coefficient with the incident angle and the Iribarren number for oblique irregular waves.

  13. Evaluation in Context

    DEFF Research Database (Denmark)

    Jaap, Kamps; Lalmas, Mounia; Larsen, Birger

    All search happens in a particular context - such as the particular collection of a digital library, its associated search tasks, and its associated users. Information retrieval researchers usually agree on the importance of context, but they rarely address the issue. In particular, evaluation...... in the Cranfield tradition requires abstracting away from individual differences between users. This paper investigates if we can bring some of this context into the Cranfield paradigm. Our approach is the following: we will attempt to record the "context" of the humans already in the loop - the topic authors....../assessors - by designing targeted questionnaires. The questionnaire data becomes part of the evaluation test-suite as valuable data on the context of the search requests.We have experimented with this questionnaire approach during the evaluation campaign of the INitiative for the Evaluation of XML Retrieval (INEX...

  14. Context Sensitive Health Informatics

    DEFF Research Database (Denmark)

    Healthcare information technologies are now routinely deployed in a variety of healthcare contexts. These contexts differ widely, but the smooth integration of IT systems is crucial, so the design, implementation, and evaluation of safe, effective, efficient and easy to adopt health informatics...... involves careful consideration of both human and organizational factors. This book presents the proceedings of the Context Sensitive Health Informatics (CSHI) conference, held in Copenhagen, Denmark, in August 2013. The theme of this year’s conference is human and sociotechnical approaches. The Human......: patients and IT; usability test and evaluation; work tasks and related contexts; human factors and simulation; and context and systems design, and outline theories and models for studying contextual issues and insights related to how health information technologies can be better designed to accommodate...

  15. A historiografia francesa da educação em um contexto memorialístico: reflexões sobre algumas problemáticas evoluções - He french education historiography in a memorialistic context: reflections about some problematic evolutions

    Directory of Open Access Journals (Sweden)

    Pierre Caspard, Traduação Maria Helena Camara Bastos

    2011-03-01

    Full Text Available Resumo Há um fosso crescente entre as análises as mais sutis que os historiadores propõem para compreender o passado da educação francesa, e os parâmetros de referência que oferece a produção memorial para situar a escola atual em relação ao passado. O artigo propõe algumas explicações para essa discrepância, que dizem respeito às mudanças recentes no sistema educativo, nas condições em que operam os historiadores da educação, e da evanescência de dois quadros de análise há muito tempo paradigmáticos: as classes sociais e a nação. Palavras-chave: Historiografia da educação; Educação na França; Cultura profissional dos professores.   HE FRENCH EDUCATION HISTORIOGRAPHY IN A MEMORIALISTIC CONTEXT: REFLECTIONS ABOUT SOME PROBLEMATIC EVOLUTIONS Abstract We can observe a growing discrepancy between the increasingly subtle analyses of education historians offer in order to explain the past and the over-simplicity of reference points used by memorial vulgate to situate contemporary education in relationship to this very same past. This article offers some explanations of this discrepancy. They relate to the recent upheavals within the educational system, the conditions under which education historians operate, and the evanescence of two longstanding paradigmatic analytical frameworks – social classes and the nation. Keywords: Historiography of education; French Education; Teacher’s professional Culture   LA HISTORIOGRAFÍA FRANCESA DE LA EDUCACIÓN EN UN CONTEXTO MEMORIALÍSTICO: REFLEXIONES SOBRE ALGUNAS PROBLEMÁTICAS EVOLUCIONES Resumen Hay un surco creciente entre las análisis las más sutiles que los historiadores proponen para comprender el pasado de la educación francesa, y los parámetros de referencia que ofrece la producción memorial para situar la escuela actual en relación al pasado. El artículo propone algunas explicaciones para esa discrepancia, que dicen respecto a las mudanzas recientes en el

  16. Predicting biological networks from genomic data

    DEFF Research Database (Denmark)

    Harrington, Eoghan D; Jensen, Lars J; Bork, Peer

    2008-01-01

    Continuing improvements in DNA sequencing technologies are providing us with vast amounts of genomic data from an ever-widening range of organisms. The resulting challenge for bioinformatics is to interpret this deluge of data and place it back into its biological context. Biological networks...... provide a conceptual framework with which we can describe part of this context, namely the different interactions that occur between the molecular components of a cell. Here, we review the computational methods available to predict biological networks from genomic sequence data and discuss how they relate...

  17. Política educacional e a re-estruturação do trabalho docente: reflexões sobre o contexto Latino-americano Educational policies and the re-structuring of teachers' work: reflections on the Latin-American context

    Directory of Open Access Journals (Sweden)

    Dalila Andrade Oliveira

    2007-08-01

    Full Text Available Este artigo discute como as políticas educacionais latino-americanas têm alterado a realidade escolar e, particularmente, a relação entre trabalhadores docentes e escola. Parte de referenciais teóricos desenvolvidos em outros contextos - Europa e América do Norte - para analisar resultados de pesquisa documental realizada sobre a política educacional em curso em alguns países latino-americanos e pesquisa empírica desenvolvida com trabalhadores docentes de escola básica pública no Brasil. Constata-se que tais políticas têm engendrado nova organização do trabalho escolar que reflete um modelo de regulação educativa, produto de novas articulações entre as demandas globais e as respostas locais. Por meio da descentralização administrativa, financeira e pedagógica as escolas têm adquirido maior flexibilidade e autonomia, mas também têm respondido a uma demanda crescente de atividades e responsabilidades, o que tem contribuído para a intensificação e auto-intensificação do trabalho docente.This paper discusses how the Latin-American educational policies have altered school reality and, more particularly, the relationship between teachers and school. Based on references developed in other contexts - Europe and North America -, it analyses the results of documental research on the educational policies cur rently applied in some Latin-American countries and of empirical research developed with basic school teachers in Brazil. It notices that such policies have generated a new organization of school work that reflects a model of educational regulation produced by the articulation between global demands and local responses. Through their administrative, financial and pedagogic decentralization, schools have acquired more flexibility and autonomy, but have also responded to a growing demand for activities and responsibilities. This has contributed to intensify and self-intensify teachers' work.

  18. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D.; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a My

  19. Genomic disorders: A window into human gene and genome evolution

    Science.gov (United States)

    Carvalho, Claudia M. B.; Zhang, Feng; Lupski, James R.

    2010-01-01

    Gene duplications alter the genetic constitution of organisms and can be a driving force of molecular evolution in humans and the great apes. In this context, the study of genomic disorders has uncovered the essential role played by the genomic architecture, especially low copy repeats (LCRs) or segmental duplications (SDs). In fact, regardless of the mechanism, LCRs can mediate or stimulate rearrangements, inciting genomic instability and generating dynamic and unstable regions prone to rapid molecular evolution. In humans, copy-number variation (CNV) has been implicated in common traits such as neuropathy, hypertension, color blindness, infertility, and behavioral traits including autism and schizophrenia, as well as disease susceptibility to HIV, lupus nephritis, and psoriasis among many other clinical phenotypes. The same mechanisms implicated in the origin of genomic disorders may also play a role in the emergence of segmental duplications and the evolution of new genes by means of genomic and gene duplication and triplication, exon shuffling, exon accretion, and fusion/fission events. PMID:20080665

  20. Inclusive education in risk’s contexts

    Directory of Open Access Journals (Sweden)

    Fausta Sabatano

    2015-12-01

    Full Text Available This paper intends to propose a reflection on the meaning of inclusion in emergency situations, the aim of realizing educational actions that really allow the emancipation of the subjects. For this purpose reference is made to an action-research, made in a project that for about ten years is realized in the Campania Region. The research proposal, which fits inside the hermeneutic phenomenological approach, identifies its focus in the relationship seen as privileged context of the educational process. You intend identifying possible elements of transferability in similar contexts, documenting the educational activity, assessing the efficacy and validity, and systematizing the methodological choices made.

  1. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    Energy Technology Data Exchange (ETDEWEB)

    Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

    2011-08-01

    Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics

  2. Dance in the Educational Context

    Directory of Open Access Journals (Sweden)

    Gregorio Vicente Nicolás

    2010-01-01

    Full Text Available This paper provides an overview of the phenomenon of dance in the field of education. At first, it is made a presentation of the different components or aspects of human beings on that dance impacts in a more obvious way. Subsequently, we present a review of the definitions proposed by different authors that we consider most relevant and it is included a personal definition of the concept. It also highlights the contributions of dance to education in terms of social, physical, intellectual and emotional development and identifies the major problems that this discipline has had to be included as a subject: lack of teacher training, lack of adequate space and resources and gender discrimination. Finally, it concludes with a reflection on the most appropriate forms of dance in the educational context.

  3. Climate oscillations reflected within the microbiome of Arabian Sea sediments

    KAUST Repository

    Orsi, William D.

    2017-07-14

    Selection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5–15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.

  4. Asymptotic theory for spiral wave reflections

    CERN Document Server

    Langham, Jacob; Barkley, Dwight

    2014-01-01

    Resonantly forced spiral waves in excitable media drift in straight-line paths, their rotation centers behaving as point-like objects moving along trajectories with a constant velocity. Interaction with medium boundaries alters this velocity and may often result in a reflection of the drift trajectory. Such reflections have diverse characteristics and are known to be highly non-specular in general. In this context we apply the theory of response functions, which via numerically computable integrals, reduces the reaction-diffusion equations governing the whole excitable medium to the dynamics of just the rotation center and rotation phase of a spiral wave. Spiral reflection trajectories are computed by this method for both small and large-core spiral waves. Such calculations provide insight into the process of reflection as well as explanations for differences in trajectories across parameters, including the effects of incidence angle and forcing amplitude. Qualitative aspects of these results are preserved fa...

  5. Developing Critical Reflection in Professional Focused Doctorates: A Facilitator's Perspective

    Science.gov (United States)

    Sambrook, Sally; Stewart, Jim

    2008-01-01

    Purpose: This paper aims to explore the challenges and opportunities for expediting critical reflection in management education and development to highlight particularly how critical reflection has been facilitated within the context of a professionally focused doctoral programme. Design/methodology/approach: The paper draws on empirical research…

  6. Reflective Subjects in Kant and Architectural Design Education

    Science.gov (United States)

    Rawes, Peg

    2007-01-01

    In architectural design education, students develop drawing, conceptual, and critical skills which are informed by their ability to reflect upon the production of ideas in design processes and in the urban, environmental, social, historical, and cultural context that define architecture and the built environment. Reflective actions and thinking…

  7. "The Fly on the Wall" Reflecting Team Supervision.

    Science.gov (United States)

    Prest, Layne E.; And Others

    1990-01-01

    Adapts reflecting team concept, a practical application of constructivist ideas, for use in group supervision. Evolving model includes a focus on the unique "fly on the wall" perspective of the reflecting team. Trainees are introduced to a multiverse of new ideas and perspectives in a context which integrates some of the most challenging…

  8. Facilitating ethical reflection among scientists using the ethical matrix

    DEFF Research Database (Denmark)

    Jensen, Karsten Klint; Forsberg, Ellen-Marie; Gamborg, Christian

    2011-01-01

    assessment of the process, this independent reflective exercise was deemed to be successful. The discussions demonstrated a high level of complexity and depth, with participants demonstrating a clear perception of uncertainties and the context in which their research operates. Reflection on stakeholder views...

  9. Scaffolding Collaborative Reflective Writing in a VET Curriculum

    Science.gov (United States)

    Boldrini, Elena; Cattaneo, Alberto

    2014-01-01

    Learning journal writing is an effective tool to foster the development of reflective capacity in the context of Vocational Education and Training (VET) if conceived as a collection of descriptions and reflections on real professional experiences. Reporting professional situations in a learning journal outside the workplace in turn fosters the…

  10. Reflective Subjects in Kant and Architectural Design Education

    Science.gov (United States)

    Rawes, Peg

    2007-01-01

    In architectural design education, students develop drawing, conceptual, and critical skills which are informed by their ability to reflect upon the production of ideas in design processes and in the urban, environmental, social, historical, and cultural context that define architecture and the built environment. Reflective actions and thinking…

  11. Dynamic context bindings : infrastructural support for context-aware applications

    OpenAIRE

    Broens, Tom Henri Ferdinand

    2008-01-01

    The world is increasingly equipped with high-capacity, interconnected, mobile and embedded computing devices. Context-awareness provides an attractive approach to personalize applications such that they better suit the user’s needs in this rich computing environment. Context-aware applications use context information, offered by context sources, to adapt their behavior to the situation at hand. The exchange of context information requires an association between a context consuming context-awa...

  12. Incorporating genomics into the toolkit of nematology.

    Science.gov (United States)

    Dillman, Adler R; Mortazavi, Ali; Sternberg, Paul W

    2012-06-01

    The study of nematode genomes over the last three decades has relied heavily on the model organism Caenorhabditis elegans, which remains the best-assembled and annotated metazoan genome. This is now changing as a rapidly expanding number of nematodes of medical and economic importance have been sequenced in recent years. The advent of sequencing technologies to achieve the equivalent of the $1000 human genome promises that every nematode genome of interest will eventually be sequenced at a reasonable cost. As the sequencing of species spanning the nematode phylum becomes a routine part of characterizing nematodes, the comparative approach and the increasing use of ecological context will help us to further understand the evolution and functional specializations of any given species by comparing its genome to that of other closely and more distantly related nematodes. We review the current state of nematode genomics and discuss some of the highlights that these genomes have revealed and the trend and benefits of ecological genomics, emphasizing the potential for new genomes and the exciting opportunities this provides for nematological studies.

  13. Context updates are hierarchical

    Directory of Open Access Journals (Sweden)

    Anton Karl Ingason

    2016-10-01

    Full Text Available This squib studies the order in which elements are added to the shared context of interlocutors in a conversation. It focuses on context updates within one hierarchical structure and argues that structurally higher elements are entered into the context before lower elements, even if the structurally higher elements are pronounced after the lower elements. The crucial data are drawn from a comparison of relative clauses in two head-initial languages, English and Icelandic, and two head-final languages, Korean and Japanese. The findings have consequences for any theory of a dynamic semantics.

  14. Context Sensitive Health Informatics

    DEFF Research Database (Denmark)

    Healthcare information technologies are now routinely deployed in a variety of healthcare contexts. These contexts differ widely, but the smooth integration of IT systems is crucial, so the design, implementation, and evaluation of safe, effective, efficient and easy to adopt health informatics...... involves careful consideration of both human and organizational factors. This book presents the proceedings of the Context Sensitive Health Informatics (CSHI) conference, held in Copenhagen, Denmark, in August 2013. The theme of this year’s conference is human and sociotechnical approaches. The Human...

  15. Context Sensitive Health Informatics

    DEFF Research Database (Denmark)

    2013-01-01

    Context is a key consideration when designing and evaluating health information technology (HIT) and cannot be overstated. Unintended consequences are common post HIT implementation and even well designed technology may not achieve desired outcomes because of contextual issues. While context should...... be considered in the design and evaluation of health information systems (HISs) there is a shortcoming of empirical research on contextual aspects of HIT. This conference integrates the sociotechnical and Human-Centered-Design (HCD) approaches and showcases current research on context sensitive health...

  16. Media for Reflection

    DEFF Research Database (Denmark)

    Knudsen, Morten

    2016-01-01

    This article develops the concept media for reflection in the interest of conceptualizing the interpretative frames that enable and limit reflection in management and leadership education. The concept ‘media for reflection’ allows us to conceptualize the social and cultural mediation of reflection...... without reducing reflection to an effect of the social structures and cultural norms in which it is embedded. Based on the developed theoretical framework, this article analyses how a renaissance ‘mirror for princes’ and contemporary research-based management education mediate reflection. The content...... of the mediations is analysed as well as the societal and organizational background. Furthermore, the means by which the two media enable and limit reflection in different ways is compared. Finally, the article discusses possible implications of the analysis in terms of management and leadership education....

  17. MycoCosm, an Integrated Fungal Genomics Resource

    Energy Technology Data Exchange (ETDEWEB)

    Shabalov, Igor; Grigoriev, Igor

    2012-03-16

    MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/month or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.

  18. Unanticipated Partial Behavioral Reflection

    OpenAIRE

    Roethlisberger, David; Denker, Marcus; Tanter, Éric

    2006-01-01

    International audience; Dynamic, unanticipated adaptation of running systems is of interest in a variety of situations, ranging from functional upgrades to on-the-fly debugging or monitoring of critical applications. In this paper we study a particular form of computational reflection, called unanticipated partial behavioral reflection, which is particularly well-suited for unanticipated adaptation of real-world systems. Our proposal combines the dynamicity of unanticipated reflection, i.e., ...

  19. X-ray Reflection

    Science.gov (United States)

    Fabian, A. C.; Ross, R. R.

    2010-12-01

    Material irradiated by X-rays produces backscattered radiation which is commonly known as the Reflection Spectrum. It consists of a structured continuum, due at high energies to the competition between photoelectric absorption and electron scattering enhanced at low energies by emission from the material itself, together with a complex line spectrum. We briefly review the history of X-ray reflection in astronomy and discuss various methods for computing the reflection spectrum from cold and ionized gas, illustrated with results from our own work reflionx. We discuss how the reflection spectrum can be used to obtain the geometry of the accretion flow, particularly the inner regions around black holes and neutron stars.

  20. Pseudomonas genomes: diverse and adaptable.

    Science.gov (United States)

    Silby, Mark W; Winstanley, Craig; Godfrey, Scott A C; Levy, Stuart B; Jackson, Robert W

    2011-07-01

    Members of the genus Pseudomonas inhabit a wide variety of environments, which is reflected in their versatile metabolic capacity and broad potential for adaptation to fluctuating environmental conditions. Here, we examine and compare the genomes of a range of Pseudomonas spp. encompassing plant, insect and human pathogens, and environmental saprophytes. In addition to a large number of allelic differences of common genes that confer regulatory and metabolic flexibility, genome analysis suggests that many other factors contribute to the diversity and adaptability of Pseudomonas spp. Horizontal gene transfer has impacted the capability of pathogenic Pseudomonas spp. in terms of disease severity (Pseudomonas aeruginosa) and specificity (Pseudomonas syringae). Genome rearrangements likely contribute to adaptation, and a considerable complement of unique genes undoubtedly contributes to strain- and species-specific activities by as yet unknown mechanisms. Because of the lack of conserved phenotypic differences, the classification of the genus has long been contentious. DNA hybridization and genome-based analyses show close relationships among members of P. aeruginosa, but that isolates within the Pseudomonas fluorescens and P. syringae species are less closely related and may constitute different species. Collectively, genome sequences of Pseudomonas spp. have provided insights into pathogenesis and the genetic basis for diversity and adaptation.

  1. From context to condition

    DEFF Research Database (Denmark)

    Larsen, Niels Martin; Peder Pedersen, Claus

    2012-01-01

    Based on studies at Morphogenetic Studio, the article discusses how the term context in relation to generative design techniques can be understood as conditions integrated in both the form development and the production process.......Based on studies at Morphogenetic Studio, the article discusses how the term context in relation to generative design techniques can be understood as conditions integrated in both the form development and the production process....

  2. Definitions of Critical Thinking in Context

    OpenAIRE

    Gyenes, Adam

    2015-01-01

    With the impact of increasing global competition, calls for greater emphasis on critical thinking in secondary and higher education are frequently heard in Japan, yet there is a lack of agreement on what is meant by the term “critical thinking.” This paper provides a review of selected literature, charting the chronological development of definitions of critical thinking in education during the twentieth century, and reflections on the application of critical thinking to different contexts. W...

  3. Reflecting on life, not on the mind – The concept of self-reflection without stability

    DEFF Research Database (Denmark)

    Jensen, Lasse Meinert

    with “stability”. When self-reflection is conceptualized as a second-order process charged with creating diachronic continuity in the person’s life, as it often is in both philosophy (Frankfurt, 1971), cognitive theory (Carver, Scheier & Fulton, 2008), and narrative theories of personality (McAdams, 2008......), “Stability” and how it is brought about, becomes the main concern. But presupposing “stability” as the main aim of self-reflection isolates reflection to a mental realm. Human beings are certainly self-conscious, but – following Dreier (1999), when he points out that reflection is not a distancing from......, but part of the person’s engagement with the world – I’ll focus on a theoretical conceptualization of reflection as an activity that persons carry out in the context of their life course. I’ll take up Schatzki’s notion of social order as an arrangement in which entities relate, occupy positions...

  4. Knowledge in Context

    Directory of Open Access Journals (Sweden)

    Nikola Kompa

    2014-04-01

    Full Text Available My aim in this paper is to motivate and defend a version of epistemic contextualism; a version, that is, of what came to be called attributor or ascriber contextualism. I will begin by outlining, in the first part, what I take to be the basic idea of and motivation behind the version of epistemic contextualism that I favor. In the second part, a couple of examples will be presented in order to illustrate the contextualist point. Since epistemic (ascriber contextualists commonly claim that knowledge ascriptions are context-sensitive, the third part of the paper will be concerned with the phenomenon of context-sensitivity at a more general level. A more detailed inquiry into the context-sensitivity natural language expressions exhibit will prove helpful in order to counter the objection that postulating context-sensitivity in the case of knowledge ascriptions is an ad-hoc-maneuver. Given that epistemic contextualism is partly an epistemological thesis, party a linguistic thesis, the remainder of the paper will be devoted to the question of how to semantically model the kind of context-sensitivity exhibited by knowledge ascriptions. The upshot will be that there are two differ-ent ways of semantically accommodating the context-sensitivity at issue. Both call for a more or less drastic departure from epistemological and semantic orthodoxy.

  5. Genomic Signatures in Microbes—Properties and Applications

    Directory of Open Access Journals (Sweden)

    Jon Bohlin

    2011-01-01

    Full Text Available The ratio of genomic oligonucleotide frequencies relative to the mean genomic AT/GC content has been shown to be similar for closely related species and, therefore, said to reflect a “genomic signature”. The genomic signature has been found to be more similar within genomes than between closely related genomes. Furthermore, genomic signatures of closely related organisms are, in turn, more similar than more distantly related organisms. Since the genomic signature is remarkably stable within a genome, it can be extracted from only a fraction of the genomic DNA sequence. Genomic signatures, therefore, have many applications. The most notable examples include recognition of pathogenicity islands in microbial genomes and identification of hosts from arbitrary DNA sequences, the latter being of great importance in metagenomics. What shapes the genomic signature in microbial DNA has been readily discussed, but difficult to pinpoint exactly. Most attempts so far have mainly focused on correlations from in silico data. This mini-review seeks to summarize possible influences shaping the genomic signature and to survey a set of applications.

  6. GLAMM: Genome-Linked Application for Metabolic Maps

    Energy Technology Data Exchange (ETDEWEB)

    Bates, John; Chivian, Dylan; Arkin, Adam

    2011-05-29

    The Genome-Linked Application for Metabolic Maps (GLAMM) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks, and investigating the construction of novel, transgenic pathways. This simple, user-friendly interface is tightly integrated with the comparative genomics tools of MicrobesOnline. GLAMM is available for free to the scientific community at glamm.lbl.gov.

  7. GLAMM: Genome-Linked Application for Metabolic Maps

    Energy Technology Data Exchange (ETDEWEB)

    Bates, John; Chivian, Dylan; Arkin, Adam

    2011-05-29

    The Genome-Linked Application for Metabolic Maps (GLAMM) is a unified web interface for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic networks, and investigating the construction of novel, transgenic pathways. This simple, user-friendly interface is tightly integrated with the comparative genomics tools of MicrobesOnline. GLAMM is available for free to the scientific community at glamm.lbl.gov.

  8. Transparencies and Reflections.

    Science.gov (United States)

    Hubbard, Guy

    1999-01-01

    Discusses the use of perspective, or showing things as the human eye sees them, when creating reflections and transparencies in works of art. Provides examples of artwork using transparency, reflection, and refraction by M. C. Escher, Richard Estes, and Janet Fish to give students an opportunity to learn about these three art techniques. (CMK)

  9. Reflective Practitioner Account

    Institute of Scientific and Technical Information of China (English)

    干青

    2009-01-01

    This article focus on the reflective account of an English teacher learning and teaching in higher education with the British post-graduate certificate program of the Yunnan Agdculture University.As n practitioner for smny years in English learning and teaching for many years,it reflects in four fields.

  10. Dissenting in Reflective Conversations

    DEFF Research Database (Denmark)

    Bjørn, Pernille; Boulus, Nina

    2011-01-01

    a methodological reflective approach that provides space for taking seriously uncertainties experienced in the field as these can be a catalyst for learning and sharpening our theoretical and empirical skills as action researchers. Through first-person inquiry, we investigate how our reflective conversations...

  11. Improving reflectance reconstruction from tristimulus values by adaptively combining colorimetric and reflectance similarities

    Science.gov (United States)

    Cao, Bin; Liao, Ningfang; Li, Yasheng; Cheng, Haobo

    2017-05-01

    The use of spectral reflectance as fundamental color information finds application in diverse fields related to imaging. Many approaches use training sets to train the algorithm used for color classification. In this context, we note that the modification of training sets obviously impacts the accuracy of reflectance reconstruction based on classical reflectance reconstruction methods. Different modifying criteria are not always consistent with each other, since they have different emphases; spectral reflectance similarity focuses on the deviation of reconstructed reflectance, whereas colorimetric similarity emphasizes human perception. We present a method to improve the accuracy of the reconstructed spectral reflectance by adaptively combining colorimetric and spectral reflectance similarities. The different exponential factors of the weighting coefficients were investigated. The spectral reflectance reconstructed by the proposed method exhibits considerable improvements in terms of the root-mean-square error and goodness-of-fit coefficient of the spectral reflectance errors as well as color differences under different illuminants. Our method is applicable to diverse areas such as textiles, printing, art, and other industries.

  12. Theory and context / Theory in context

    DEFF Research Database (Denmark)

    Glaveanu, Vlad Petre

    2014-01-01

    It is debatable whether the psychology of creativity is a field in crisis or not. There are clear signs of increased fragmenta-tion and a scarcity of integrative efforts, but is this necessari-ly bad? Do we need more comprehensive theories of creativ-ity and a return to old epistemological...... questions? This de-pends on how one understands theory. Against a view of theoretical work as aiming towards generality, universality, uniformity, completeness, and singularity, I advocate for a dynamic perspective in which theory is plural, multifaceted, and contextual. Far from ‘waiting for the Messiah......’, theoreti-cal work in the psychology of creativity can be integrative without having the ambition to explain or, even more, predict, creative expression across all people, at all times, and in all domains. To avoid such ambition, the psychology of creativi-ty requires a theory of context that doesn...

  13. Using context to improve protein domain identification

    Directory of Open Access Journals (Sweden)

    Llinás Manuel

    2011-03-01

    Full Text Available Abstract Background Identifying domains in protein sequences is an important step in protein structural and functional annotation. Existing domain recognition methods typically evaluate each domain prediction independently of the rest. However, the majority of proteins are multidomain, and pairwise domain co-occurrences are highly specific and non-transitive. Results Here, we demonstrate how to exploit domain co-occurrence to boost weak domain predictions that appear in previously observed combinations, while penalizing higher confidence domains if such combinations have never been observed. Our framework, Domain Prediction Using Context (dPUC, incorporates pairwise "context" scores between domains, along with traditional domain scores and thresholds, and improves domain prediction across a variety of organisms from bacteria to protozoa and metazoa. Among the genomes we tested, dPUC is most successful at improving predictions for the poorly-annotated malaria parasite Plasmodium falciparum, for which over 38% of the genome is currently unannotated. Our approach enables high-confidence annotations in this organism and the identification of orthologs to many core machinery proteins conserved in all eukaryotes, including those involved in ribosomal assembly and other RNA processing events, which surprisingly had not been previously known. Conclusions Overall, our results demonstrate that this new context-based approach will provide significant improvements in domain and function prediction, especially for poorly understood genomes for which the need for additional annotations is greatest. Source code for the algorithm is available under a GPL open source license at http://compbio.cs.princeton.edu/dpuc/. Pre-computed results for our test organisms and a web server are also available at that location.

  14. Participação e autonomia nos espaços interculturais de Saúde Indígena: reflexões a partir do sul do Brasil Participation and autonomy in the intercultural contexts of Indian Health: reflections from southern Brazil

    Directory of Open Access Journals (Sweden)

    Esther Jean Langdon

    2007-08-01

    established in 1999. Since the implementation of the Subsystem seven years ago, there have been few reflections regarding the praxis of its key concepts in intercultural contexts: differentiated attention, Indian Health Agents and participation and social control. Considering these aspects, this article evaluates the model of attention to Indian health. Based on research from Southern Brazil, specifically from the State of Santa Catarina, and on the experience of participation in situations of social control, the authors hope to contribute to an evaluation of the Subsystem, which is imperative at this moment.

  15. The analysis of children’s books in the context of how they reflect environmental issuesÇocuk edebiyatı yapıtlarının çevre sorunlarını yansıtışı bağlamında incelenmesi

    Directory of Open Access Journals (Sweden)

    Canan Aslan

    2015-12-01

    Full Text Available Children’s books are among important variables that contribute to raising children as individuals sensitive to environment through providing aesthetic experiences. The purpose of this study is to analyze literary children’s books in the context of how they reflect environmental issues. The data sources of the study included the books covering environmental issues and first published in 2014 or 2015. The data were collected through document analysis that is a qualitative research method and were analyzed descriptively. As a result of the study it was seen that the analyzed books cover many topics related to environmental pollution and that environmental pollution is caused by lack of education, unawareness or insensitivity mostly for economic or arbitrary reasons. According to the books, everyone from administrators to large companies and local administrations is responsible for environmental pollution. The study showed that children and women are more sensitive to environment. The books of which the content is supported with quality visuals make children feel future problems and their solutions through the use of a literary language and in a way appropriate for the age and development of children.   Özet Çocukların çevreye duyarlı bireyler olarak yetişmelerinde katkı sağlayacak önemli bir değişken de etkisini estetik yaşantı sağlayarak gösteren çocuk edebiyatı yapıtlarıdır. Bu çalışmanın amacı, yazınsal çocuk kitaplarını çevre sorunlarını yansıtışı bağlamında incelemektir. Çalışmanın veri kaynağını, 2014-2015 yıllarında ilk baskıları yapılan çevre sorunları konulu kitaplar oluşturmaktadır. Veriler, nitel araştırma yöntemlerinden doküman incelemesi yoluyla toplanmış, betimsel olarak çözümlenmiştir. Araştırma sonucunda incelenen kitaplarda çevre kirliliğine ilişkin birçok konunun ele alındığı ve çevrenin; eğitimsizliğin, bilinçsizliğin ve duyarsızlığın bir

  16. Trabalho e cuidado no contexto da atenção psicossocial: algumas reflexões Trabajo y cuidado en el contexto de la atención psicosocial: algunas reflexiones Work and care in the psychosocial attention context: some reflections

    Directory of Open Access Journals (Sweden)

    Alice Guimarães Bottaro de Oliveira

    2006-12-01

    incluye a trabajadores y pacientes en una dialéctica. La ampliación de capacitación técnico-político de los trabajadores y los enfrentamientos de las contradicciones de ese trabajo puede permitir la construcción, siempre provisional, de la atención psicosocialBased on the data of a local study, we present a reflection about the care work and practices carried out by the two teams of the Psychosocial Attention Centers (CAPS, in light of the theoretical, administrative and technical-assistance presuppositions of the Psychiatric Reform and the historicity, materiality and contradictions of the teamwork within the matogrossense context. In the reality studied, the kind of management in mental health conditions the model of attention and, in great measure, reduces the collective and individual creative potential of the workers and the users. We emphasize the innovative and creative potential of this new technology, which, however, when being nationally standardized, simultaneously warrants resources and institutionalizes the care and mobilizes the therapeutic practices. Work and care is a dynamical process including workers and patients into a dialectic. The enlargement of the technical-political habilitation of the workers and the act of facing the contradictions inherent to this work allows to construct the always provisional psychosocial attention.

  17. Context: The strategic management Rosetta Stone

    Directory of Open Access Journals (Sweden)

    R. V. Weeks

    2007-12-01

    Full Text Available Purpose: The purpose of this paper is to analyse context as a means for interpreting and making sense of evolving strategic management theory and practice. Problem investigated: Traditional strategic management theory based on rational deductive methodologies assumes contextual predictability, yet contemporary conditions tend to contradict this assumption. In response, alternative theories and practices for dealing with complex contexts have emerged (Brews & Purohit, 2006; Grant, 2003; Kurt & Snowden, 2003and Stacey, 1995. Methodology: A literature study was undertaken to determine the nature of emergent strategic management theory and practice, in response to contextual complexity and how it differs from traditional practice (Mintzberg, 1994 and Weeks &Lessing, 1993. Findings: An important conclusion drawn from the study is that context acts as a determinant for making sense of the evolution of strategic management theory and practice. While traditional strategic management practice still assumes relevance in contexts of linear causality, it breaks down in complex contexts. Emergent strategic management theory, based on complex adaptive systems, is increasingly assuming relevance. Notably, many institutions are still attempting to make use of scenario planning in an attempt to deal with contextual complexity, a practice not supported by leading researchers(Stacey, 1995 and Kurt & Snowden, 2003. Value of the research: The insights gained from the study assume relevance, in view of the contextual complexity confronting modern-day institutions. The findings suggest that emergent strategy based on complex adaptive system theory needs to be considered as a means for dealing with increasing environmental turbulence. Conclusion: It is concluded that context serves as the Rosetta stone for making sense of strategic management theory and practice. In view of the research findings, as reflected in the literature, it would seem that the use of complex

  18. Reflectivity in Research Practice

    Directory of Open Access Journals (Sweden)

    Luigina Mortari

    2015-11-01

    Full Text Available The article grounds on the assumption that researchers, in order to be not mere technicians but competent practitioners of research, should be able to reflect in a deep way. That means they should reflect not only on the practical acts of research but also on the mental experience which constructs the meaning about practice. Reflection is a very important mental activity, both in private and professional life. Learning the practice of reflection is fundamental because it allows people to engage into a thoughtful relationship with the world-life and thus gain an awake stance about one’s lived experience. Reflection is a crucial cognitive practice in the research field. Reflexivity is largely practiced in qualitative research, where it is used to legitimate and validate research procedures. This study introduces different perspectives of analysis by focusing the discourse on the main philosophical approaches to reflection: pragmatistic, critical, hermeneutic, and finally phenomenological. The thesis of this study is that the phenomenological theory makes possible to analyze in depth the reflective activity and just by that to support an adequate process of training of the researcher.

  19. Review of Teacher's Teaching Reflection

    Institute of Scientific and Technical Information of China (English)

    王爽爽

    2015-01-01

    Teacher's teaching reflection has become the core focus in school.However,there are different understandings of the concept of teacher's teaching reflection.The paper introduces and compares different understandings of the concept of teachers' teaching reflection.Based on the summarizing of the concept on reflection and teaching reflection,this paper tries to provide reference for the teacher's teaching reflection.

  20. Theorising context in psychology

    DEFF Research Database (Denmark)

    Glaveanu, Vlad Petre

    2014-01-01

    This article aims to address the issue of what context is and how it can be incorporated in psychological theory by using the case study of creativity research. It starts from a basic definition of context as the spatiotemporal continuum that, together with psychological phenomena, constitutes...... a totality and should be considered a single, integrated whole. As such, contexts are neither subjective, existing only in perception, nor are they a set of variables external to the person, but participate directly in the processes under study in psychology. We can therefore distinguish between “flat......” theorising, one-dimensional and overconcerned with intra-psychological factors, and “3-D” models trying to articulate the psychological, the spatial (sociomaterial), and the temporal. These categories are illustrated by different theoretical approaches to creativity. It is argued here that a cultural...

  1. Context, you need

    DEFF Research Database (Denmark)

    Kristensen, Line Burholt

    that object-initial clauses like “Her, he invited” are more difficult to read and comprehend than subject-initial clauses like “He invited her”. Neuroimaging studies have shown that the difference particularly affects a brain area known by the name of Broca’s area. Whether one says “He invited her” or “Her......, he invited” depends on the context – it is therefore relevant to take contextual factors into account when examining how language users process information structure. The dissertation is based on a psycholinguistic reading experiment and three neuroimaging experiments that all examine the interplay...... between context and information structure. The experimental results indicate that context plays a significant role when it comes to sentence comprehension and that the activity in Broca’s area is also affected by contextual factors. Based on the results of the four language experiments, it is also argued...

  2. Habit and context

    DEFF Research Database (Denmark)

    Mueller Loose, Simone; Jaeger, S. R.

    Although research into contextual influences on food/beverage choices is increasing, limited knowledge exists about the relative impact context variables and to which degree these factors interact with each other. Habit is also acknowledged as being important in shaping food/beverage choices......, but like the influence of context, quantification of its importance is lacking. To contribute to a closing of this gap, we analyse food dairy data from 100+ New Zealand consumers quantitatively with a variance component analysis. Food diaries, recording the eating occasion, beverages and meal food...... among the context factors studied. For instance hot beverages were more likely to be consumed at breakfast, while alcoholic beverages were strongly related to dinner meals. Beer/wine was considerably more likely to be consumed outside home or in on-premise locations in the presence of friends or family...

  3. Genomic stuff: Governing the (immatter of life

    Directory of Open Access Journals (Sweden)

    Gísli Pálsson

    2011-09-01

    Full Text Available Emphasizing the context of what has often been referred to as “scarce natural resources”, in particular forests, meadows, and fishing stocks, Elinor Ostrom’s important work Governing the commons (1990 presents an institutional framework for discussing the development and use of collective action with respect to environmental problems. In this article we discuss extensions of Ostrom’s approach to genes and genomes and explore its limits and usefulness. With the new genetics, we suggest, the biological gaze has not only been turned inward to the management and mining of the human body, also the very notion of the “biological” has been destabilized. This shift and destabilization, we argue, which is the result of human refashioning and appropriation of “life itself”, raises important questions about the relevance and applicability of Ostrom’s institutional framework in the context of what we call “genomic stuff”, genomic material, data, and information.

  4. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis

    NARCIS (Netherlands)

    Carlton, Jane M.; Hirt, Robert P.; Silva, Joana C.; Delcher, Arthur L.; Schatz, Michael; Zhao, Qi; Wortman, Jennifer R.; Bidwell, Shelby L.; Alsmark, U. Cecilia M.; Besteiro, Sebastien; Sicheritz-Ponten, Thomas; Noel, Christophe J.; Dacks, Joel B.; Foster, Peter G.; Simillion, Cedric; Van de Peer, Yves; Miranda-Saavedra, Diego; Barton, Geoffrey J.; Westrop, Gareth D.; Mueller, Sylke; Dessi, Daniele; Fiori, Pier Luigi; Ren, Qinghu; Paulsen, Ian; Zhang, Hanbang; Bastida-Corcuera, Felix D.; Simoes-Barbosa, Augusto; Brown, Mark T.; Hayes, Richard D.; Mukherjee, Mandira; Okumura, Cheryl Y.; Schneider, Rachel; Smith, Alias J.; Vanacova, Stepanka; Villalvazo, Maria; Haas, Brian J.; Pertea, Mihaela; Feldblyum, Tamara V.; Utterback, Terry R.; Shu, Chung-Li; Osoegawa, Kazutoyo; de Jong, Pieter J.; Hrdy, Ivan; Horvathova, Lenka; Zubacova, Zuzana; Dolezal, Pavel; Malik, Shehre-Banoo; Logsdon, John M.; Henze, Katrin; Gupta, Arti; Wang, Ching C.; Dunne, Rebecca L.; Upcroft, Jacqueline A.; Upcroft, Peter; White, Owen; Salzberg, Steven L.; Tang, Petrus; Chiu, Cheng-Hsun; Lee, Ying-Shiung; Embley, T. Martin; Coombs, Graham H.; Mottram, Jeremy C.; Tachezy, Jan; Fraser-Liggett, Claire M.; Johnson, Patricia J.

    2007-01-01

    We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the similar to 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction wi

  5. Plant Genome Duplication Database.

    Science.gov (United States)

    Lee, Tae-Ho; Kim, Junah; Robertson, Jon S; Paterson, Andrew H

    2017-01-01

    Genome duplication, widespread in flowering plants, is a driving force in evolution. Genome alignments between/within genomes facilitate identification of homologous regions and individual genes to investigate evolutionary consequences of genome duplication. PGDD (the Plant Genome Duplication Database), a public web service database, provides intra- or interplant genome alignment information. At present, PGDD contains information for 47 plants whose genome sequences have been released. Here, we describe methods for identification and estimation of dates of genome duplication and speciation by functions of PGDD.The database is freely available at http://chibba.agtec.uga.edu/duplication/.

  6. A Brief History of Context

    CERN Document Server

    Wan, Kaiyu

    2009-01-01

    Context is a rich concept and is an elusive concept to define. The concept of context has been studied by philosophers, linguists, psychologists, and recently by computer scientists. Within each research community the term context was interpreted in a certain way that is well-suited for their goals, however no attempt was made to define context. In many areas of research in computer science, notably on web-based services, human-computer interaction (HCI), ubiquitous computing applications, and context-aware systems there is a need to provide a formal operational definition of context. In this brief survey an account of the early work on context, as well as the recent work on many working definitions of context, context modeling, and a formalization of context are given. An attempt is made to unify the different context models within the formalization. A brief commentary on the usefulness of the formalization in the development of context-aware and dependable systems is included.

  7. Context-dependent generalization.

    Science.gov (United States)

    Taylor, Jordan A; Ivry, Richard B

    2013-01-01

    The pattern of generalization following motor learning can provide a probe on the neural mechanisms underlying learning. For example, the breadth of generalization to untrained regions of space after visuomotor adaptation to targets in a restricted region of space has been attributed to the directional tuning properties of neurons in the motor system. Building on this idea, the effect of different types of perturbations on generalization (e.g., rotation vs. visual translation) have been attributed to the selection of differentially tuned populations. Overlooked in this discussion is consideration of how the context of the training environment may constrain generalization. Here, we explore the role of context by having participants learn a visuomotor rotation or a translational shift in two different contexts, one in which the array of targets were presented in a circular arrangement and the other in which they were presented in a rectilinear arrangement. The perturbation and environments were either consistent (e.g., rotation with circular arrangement) or inconsistent (e.g., rotation with rectilinear arrangement). The pattern of generalization across the workspace was much more dependent on the context of the environment than on the perturbation, with broad generalization for the rectilinear arrangement for both types of perturbations. Moreover, the generalization pattern for this context was evident, even when the perturbation was introduced in a gradual manner, precluding the use of an explicit strategy. We describe how current models of generalization might be modified to incorporate these results, building on the idea that context provides a strong bias for how the motor system infers the nature of the visuomotor perturbation and, in turn, how this information influences the pattern of generalization.

  8. Context-dependent Generalization

    Directory of Open Access Journals (Sweden)

    Jordan A Taylor

    2013-05-01

    Full Text Available The pattern of generalization following motor learning can provide a probe on the neural mechanisms underlying learning. For example, the breadth of generalization to untrained regions of space after visuomotor adaptation to targets in a restricted region of space has been attributed to the directional tuning properties of neurons in the motor system. Building on this idea, the effect of different types of perturbations on generalization (e.g., rotation versus visual translation have been attributed to the selection of differentially tuned populations. Overlooked in this discussion is consideration of how the context of the training environment may constrain generalization. Here, we explore the role of context by having participants learn a visuomotor rotation or a translational shift in two different contexts, one in which the array of targets were presented in a circular arrangement and the other in which they were presented in a rectilinear arrangement. The perturbation and environments were either consistent (e.g., rotation with circular arrangement or inconsistent (e.g., rotation with rectilinear arrangement. The pattern of generalization across the workspace was much more dependent on the context of the environment than on the perturbation, with broad generalization for the rectilinear arrangement for both types of perturbations. Moreover, the generalization pattern for this context was evident, even when the perturbation was introduced in a gradual manner, precluding the use of an explicit strategy. We describe how current models of generalization might be modified to incorporate these results, building on the idea that context provides a strong bias for how the motor system infers the nature of the visuomotor perturbation and, in turn, how this information influences the pattern of generalization.

  9. Generalized framework for context-specific metabolic model extraction methods

    Directory of Open Access Journals (Sweden)

    Semidán eRobaina Estévez

    2014-09-01

    Full Text Available Genome-scale metabolic models are increasingly applied to investigate the physiology not only of simple prokaryotes, but also eukaryotes, such as plants, characterized with compartmentalized cells of multiple types. While genome-scale models aim at including the entirety of known metabolic reactions, mounting evidence has indicated that only a subset of these reactions is active in a given context, including: developmental stage, cell type, or environment. As a result, several methods have been proposed to reconstruct context-specific models from existing genome-scale models by integrating various types of high-throughput data. Here we present a mathematical framework that puts all existing methods under one umbrella and provides the means to better understand their functioning, highlight similarities and differences, and to help users in selecting a most suitable method for an application.

  10. Self-Reflection

    DEFF Research Database (Denmark)

    Fausing, Bent

    2016-01-01

    will take a look at the establishing of the modern self and possibilities of self-reflection, too. My examples will be from the so-called dark-selfies and from a new selfie form, which merge the present with the previous progressing into the future. I will discuss the media reflections as loos and/or gain....... As another but short viewpoint telepresence, Skype, will be discussed, where new screen types, presence and reflections are established. In a perspective, I debate my term sore-society in relation to my topic and especially the dark selfies....

  11. Mobile Context Toolbox

    DEFF Research Database (Denmark)

    Stopczynski, Arkadiusz; Larsen, Jakob Eg; Skomail, Lukasz

    2010-01-01

    In this paper we describe an open framework utilizing sensors and application data on the Maemo mobile platform enabling rapid prototyping of context-aware mobile applications. The framework has an extensible layered architecture allowing new hardware and software sensors and features to be added...... to the context framework. We present initial results from in-the-wild experiments where contextual data was acquired using the tool. In the experiments 6 participants were using a Nokia N900 mobile phone continuously with a logger application for an average of 33 days. The study has provided valuable insights...

  12. Context and Implicature

    DEFF Research Database (Denmark)

    Benotti, Luciana; Blackburn, Patrick Rowan

    2014-01-01

    that has a lot in common with non-linguistic behavior. But what exactly is its role? We invite the reader to view conversational implicature as a way of negotiating meaning in conversational contexts. Along the way, the reader will learn something of the theoretical properties of implicatures, why...... they are tricky to work with empirically, what can be done with them computationally, and (perhaps) where future research on the topic may lead. But the basic message of the paper is actually quite simple: context and conversational implicature are highly intertwined, and unravelling their interactions...

  13. GUESSING WORDS FROM CONTEXT

    Institute of Scientific and Technical Information of China (English)

    LiLing; YangWeidong

    2004-01-01

    For the large number of low-frequency words in .foreign language vocabulary acquisition, the strategy many experts in language teaching methods have been advocating is to teach the students the ways to guess .from context. However, two American scholars, Schatz and Baldwin (1986), on the basis of their experiments made on American students, argued that contextual clues are unreliable predictors of word meanigs.Context does not usually provide clues, but inhibit the correct prediction of word meanings just as o[ten as they facilitate them.

  14. Adaptive Context Tree Weighting

    CERN Document Server

    O'Neill, Alexander; Shao, Wen; Sunehag, Peter

    2012-01-01

    We describe an adaptive context tree weighting (ACTW) algorithm, as an extension to the standard context tree weighting (CTW) algorithm. Unlike the standard CTW algorithm, which weights all observations equally regardless of the depth, ACTW gives increasing weight to more recent observations, aiming to improve performance in cases where the input sequence is from a non-stationary distribution. Data compression results show ACTW variants improving over CTW on merged files from standard compression benchmark tests while never being significantly worse on any individual file.

  15. Context and English Teaching

    Institute of Scientific and Technical Information of China (English)

    黄念峰

    2004-01-01

    The exponents of Functional Teaching Approach hold that only when the linguistic expressions are presented(by the teacher)and practised(by the students)in the specifte context,can language teaching cultivate students' competence of understanding and using language forms.Based on two years' practice,The author argues that excellent effects on setting up context can livene up the atmosphere of the classroom,foster the students' competitive consciousness and collective spirit,stimulate the students' rich imagination and creativity,satisfy their thirst for knowledge,promote the harmonious relationship between teacher and students and improve the quality of teaching.

  16. Learning in context

    DEFF Research Database (Denmark)

    Keiding, Tina Bering

    2007-01-01

    This article offers a re-description of the concept of learning context. Drawing on Niklas Luhmann and Gregory Bateson it suggests an alternative to situated, social learning and activity theory. The conclusion is that learning context designates an individual's reconstruction of the environment...... through contingent handling of differences and that the individual emerge as learning through the actual construction. Selection of differences is influenced by the learner's actual knowledge, the nature of the environment and the current horizon of meaning in which the current adaptive perspective...... becomes a significant factor. The re-description contributes to didaktik  through renewed understandings of participants' background in teaching and learning....

  17. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P. falciparu

  18. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  19. Troubling Muddy Waters: Problematizing Reflective Practice in Global Medical Education.

    Science.gov (United States)

    Naidu, Thirusha; Kumagai, Arno K

    2016-03-01

    The idea of exporting the concept of reflective practice for a global medical education audience is growing. However, the uncritical export and adoption of Western concepts of reflection may be inappropriate in non-Western societies. The emphasis in Western medical education on the use of reflection for a specific end--that is, the improvement of individual clinical practice--tends to ignore the range of reflective practice, concentrating on reflection alone while overlooking critical reflection and reflexivity. This Perspective places the concept of reflective practice under a critical lens to explore a broader view for its application in medical education outside the West. The authors suggest that ideas about reflection in medicine and medical education may not be as easily transferable from Western to non-Western contexts as concepts from biomedical science are. The authors pose the question, When "exporting" Western medical education strategies and principles, how often do Western-trained educators authentically open up to the possibility that there are alternative ways of seeing and knowing that may be valuable in educating Western physicians? One answer lies in the assertion that educators should aspire to turn exportation of educational theory into a truly bidirectional, collaborative exchange in which culturally conscious views of reflective practice contribute to humanistic, equitable patient care. This discussion engages in troubling the already-muddy waters of reflective practice by exploring the global applicability of reflective practice as it is currently applied in medical education. The globalization of medical education demands critical reflection on reflection itself.

  20. Parameters affecting genome simulation for evaluating genomic selection method.

    Science.gov (United States)

    Nishio, Motohide; Satoh, Masahiro

    2014-10-01

    The present study investigated the parameter settings for obtaining a simulated genome at steady state of allele frequency (mutation-drift equilibrium) and linkage disequilibrium (LD), and evaluated the impact of whether or not the simulated genome reached steady state of allele frequency and LD on the accuracy of genomic estimated breeding values (GEBVs). After 500 to 50,000 historical generations, the base population and subsequent seven generations were generated as recent populations. The allele frequency distribution of the last generations of the historical population and LD in the base population were calculated when varying the values of five parameters: initial minor allele frequency, mutation rate, effective population size, number of markers and chromosome length. The accuracies of GEBVs in the last generation of the recent population were calculated by genomic best linear unbiased prediction. The number of historical generations required to reach mutation-drift equilibrium depended on the initial allele frequency and mutation rate. Regardless of the parameters, LD reached a steady state before allele frequency distribution reached mutation-drift equilibrium. The accuracies of GEBVs largely reflect the extent of linkage disequilibrium with the exception of varying chromosome length, although there were no associations between the accuracies of GEBVs and allele frequency distribution. © 2014 Japanese Society of Animal Science.

  1. Genome-wide screening and identification of antigens for rickettsial vaccine development

    Science.gov (United States)

    The capacity to identify immunogens for vaccine development by genome-wide screening has been markedly enhanced by the availability of complete microbial genome sequences coupled to rapid proteomic and bioinformatic analysis. Critical to this genome-wide screening is in vivo testing in the context o...

  2. Encouraging Counsellor Reflection.

    Science.gov (United States)

    Upton, David; Asch, Rachel

    1999-01-01

    Describes the evolution and testing of an "attributes checklist" tool for assisting counselor development. These attributes relate to characteristics of case notes that indicate evidence of counselor reflection and consideration of the counseling process. (Author/GCP)

  3. The hippocampus is sensitive to the mismatch in novelty between items and their contexts.

    Science.gov (United States)

    Thakral, Preston P; Yu, Sarah S; Rugg, Michael D

    2015-03-30

    In previous functional magnetic resonance imaging (fMRI) studies of continuous recognition memory it was reported that new items elicit greater hippocampal activity than old (repeated) items (hippocampal 'novelty' effects). Rather than reflecting recency differences between new and old items, hippocampal novelty effects may instead reflect the novelty of the association between test items and the experimental context, or a mismatch in the novelty of the test item and the context. The present continuous recognition study assessed these possibilities by manipulating item-context associations on a trial-by-trial basis. Each trial comprised the presentation of an object-word (context-item) pair. Repeated items were paired either with the same context as on their first presentation, a different but previously presented context, or a new context. The task was to judge whether each item was old or new, regardless of the study status of the associated context. We found no evidence that hippocampal novelty effects reflected either item and context recency, or the novelty of the item-context association. Rather, enhanced hippocampal activity was elicited when the novelty of the item and its context mismatched. These findings support the possibility that hippocampal novelty effects reflect, at least in part, the disjunction in novelty between test items and their contexts.

  4. Formative Assessment in Context

    Science.gov (United States)

    Oxenford-O'Brian, Julie

    2013-01-01

    This dissertation responds to critical gaps in current research on formative assessment practice which could limit successful implementation of this practice within the K-12 classroom context. The study applies a socio cultural perspective of learning to interpret a cross-case analysis of formative assessment practice occurring during one…

  5. Context 2010/2011

    DEFF Research Database (Denmark)

    2012-01-01

    CONTEXT 2010/2011 består af 16 artikler og essays, forfattet af forskere og undervisere på Arkitektskolen Aarhus. Forfatterne præsenterer hér deres individuelle, faglige tilgange til kontekst-begrebet, som det helt aktuelt anvendes i forskning og undervisning på Arkitektskolen. Teksterne ledsages...

  6. The Policy Context

    DEFF Research Database (Denmark)

    Panagakos, George

    2015-01-01

    Green project. The term ‘green’ is used in the sustainability context, meaning that it features economic and social dimensions in addition to the usual environmental one. The most important EU transport policy documents are reviewed and briefly presented by transportation mode. Horizontal documents covering all...

  7. DANS LE CONTEXTE IVOIRIEN

    African Journals Online (AJOL)

    LA RELATION "GENRE" ET SES IMPLICATIONS SOCIOLOGIQUES. DANS LE CONTEXTE IVOIRIEN ... de base et de la gestion des affaires publiques en milieu rural .... Les raisons économiques; du fait du faible pouvoir d'achat des parents face au ..... cause de rupture du contrat, toute femme a le droit de suspendre son.

  8. Context, Learning, and Extinction

    Science.gov (United States)

    Gershman, Samuel J.; Blei, David M.; Niv, Yael

    2010-01-01

    A. Redish et al. (2007) proposed a reinforcement learning model of context-dependent learning and extinction in conditioning experiments, using the idea of "state classification" to categorize new observations into states. In the current article, the authors propose an interpretation of this idea in terms of normative statistical inference. They…

  9. Context Construction Through Competition

    DEFF Research Database (Denmark)

    Kjær, Poul F.

    2015-01-01

    This article examines the relationship between the evolution of statehood and competition in the European context. To begin with, a particular take on the evolution of modern political power in the state form in Europe is developed. Against this background, the article reconstructs how the instit...

  10. Adaptive context exploitation

    Science.gov (United States)

    Steinberg, Alan N.; Bowman, Christopher L.

    2013-05-01

    This paper presents concepts and an implementation scheme to improve information exploitation processes and products by adaptive discovery and processing of contextual information. Context is used in data fusion - and in inferencing in general - to provide expectations and to constrain processing. It also is used to infer or refine desired information ("problem variables") on the basis of other available information ("context variables"). Contextual exploitation becomes critical in several classes of inferencing problems in which traditional information sources do not provide sufficient resolution between entity states or when such states are poorly or incompletely modeled. An adaptive evidence-accrual inference method - adapted from developments in target recognition and scene understanding - is presented; whereby context variables are selected on the basis of (a) their utility in refining explicit problem variables, (b) the probability of evaluating these variables to within a given accuracy, given candidate system actions (data collection, mining or processing), and (c) the cost of such actions. The Joint Directors of Laboratories (JDL) Data Fusion Model, with its extension to dual Resource Management functions, has been adapted to accommodate adaptive information exploitation, to include adaptive context exploitation. The interplay of Data Fusion and Resource Management (DF&RM) functionality in exploiting contextual information is illustrated in terms of the dual-node DF&RM architecture. An important advance is in the integration of data mining methods for data search/discovery and for abductive model refinement.

  11. Context modification in action

    NARCIS (Netherlands)

    Visser, A.

    2008-01-01

    In this paper we develop the positive fragment of Context Modification Logic. This logical system is a variant of Dynamic Predicate Logic that employs multiple-access variables and that treats argument places in the same way as Latin. The positive fragment is purely incremental.

  12. Thoughts on Reflection (Editorial

    Directory of Open Access Journals (Sweden)

    Denise Koufogiannakis

    2010-06-01

    Full Text Available There has been some acknowledgement in the published literature that reflection is a crucial element of the evidence based library and information practice (EBLIP model we have adopted (Booth 2004, 2006; Grant 2007; Helliwell 2007. As we work through a problem and try to incorporate the best available evidence into our decision making, reflection is required at several stages, including the very identification of the problem through to our assessment of the process itself and what we have learned in order to inform future practice. However, reflection and reflective writing have not fully been integrated into the process we espouse, and very little has been done to look more closely at this element of the model and how it can be integrated into professional learning.In a recently published research article, Sen (2010 confirms the relationship between reflection and several aspects of professional practice. These include critical review and decision making, two aspects that are tied closely to the evidence based process. Sen notes: Students were more likely to show evidence of learning, self‐development, the ability to review issues crucially, awareness of their own mental functions, ability to make decision [sic] and being empowered when they had mastered the art of reflective practice and the more deeply analytical reflective writing. (p.84 EBLIP (the journal tries to incorporate elements of reflection within the articles we publish. While we clearly believe in the need for our profession to do quality research and publish that research so that it can be accessible to practitioners, we also know that research cannot be looked at in isolation. Our evidence summaries are one way of reflecting critically on previously published research, and in the same vein, our classics bring older research studies back to the foreground. This work needs to continue to be discussed and looked at for its impact on our profession.More directly, the Using

  13. Oral health students as reflective practitioners: changing patterns of student clinical reflections over a period of 12 months.

    Science.gov (United States)

    Tsang, Annetta K L

    2012-01-01

    The purpose of this study was to determine the levels of reflection shown by bachelor of oral health students in relation to their clinical and professional practice. Reflective learning was embedded as a topic in the oral health curriculum within the discipline of dental hygiene practice. Reflective journal writing was integrated with clinical practice and linked with assessment requirements. Students' reflective writing was analyzed thematically to elucidate levels of reflection based on Boud's 4 Rs of Reflection (review, react, relate and respond) over a period of 12 months. Differences in the levels of reflection at different time intervals were examined. Students' ability to critically reflect improved over the period of 12 months. The predominant level of reflection changed from primarily descriptive and superficial at the start of the academic year to primarily critical and relational by the end. As expected, the highest level of critical reflection (respond) occurred infrequently, although it became more frequent as the academic year progressed. Bachelor of oral health students do reflect critically. Regular reflective writing contributed to the development of critical reflective skills in the context of clinical and professional development.

  14. Context as a Spurious Concept

    CERN Document Server

    Hirst, G

    1997-01-01

    I take issue with AI formalizations of context, primarily the formalization by McCarthy and Buvac, that regard context as an undefined primitive whose formalization can be the same in many different kinds of AI tasks. In particular, any theory of context in natural language must take the special nature of natural language into account and cannot regard context simply as an undefined primitive. I show that there is no such thing as a coherent theory of context simpliciter -- context pure and simple -- and that context in natural language is not the same kind of thing as context in KR. In natural language, context is constructed by the speaker and the interpreter, and both have considerable discretion in so doing. Therefore, a formalization based on pre-defined contexts and pre-defined `lifting axioms' cannot account for how context is used in real-world language.

  15. Stereotypes in a context

    Directory of Open Access Journals (Sweden)

    Hnilica, Karel

    2017-07-01

    Full Text Available In the study we tested some hypotheses concerning the influence of a context on stereotypes. Our first hypothesis concerns explicit stereotypes. According to it Czech respondents will ascribe to their own category more positive attributes if a list of categories will include only Czech and Roma people than when it will include also some categories which are more positively evaluated than Czechs. The next hypothesis concerns implicit stereotypes. According to it when using IAT (Implicit Association Test; Greenwald et al., 1998, where there are compared two categories, we will ascertain a more profound difference between attitudes to Czech and Roma people than when we use BFP (Bona Fide Pipeline; Fazio et al., 1995, in which there is no such a comparison. Our next two hypotheses concern consensual stereotypes. According to one of them the content of a consensual stereotype will overlap with content of a no personal stereotype. According to the other, the valences of consensual stereotypes will be more polarized than the mean valences of personal stereotypes. The context will have similar influences on consensual and personal stereotypes. In our two researches there took part two samples (N1 = 86, N2 = 201 of adult members. To ascertain the content of explicit stereotypes we used an open-form technique. The first sample adduced attributes of members of two categories, the second sample adduced attributes of members of twelve categories. We define the consensual stereotype as a set of ten most often cited attributes. To measure implicit stereotypes, we used IAT and BFP. Results show that responses of the respondents were influenced by context in the directions expected. The content of no personal stereotype overlapped with the content of any consensual stereotype. The context had influence on both explicit and implicit measures. At the same time it was found that context had on personal and consensual stereotypes similar, but not identical

  16. Translational genomics

    Directory of Open Access Journals (Sweden)

    Martin Kussmann

    2014-09-01

    Full Text Available The term “Translational Genomics” reflects both title and mission of this new journal. “Translational” has traditionally been understood as “applied research” or “development”, different from or even opposed to “basic research”. Recent scientific and societal developments have triggered a re-assessment of the connotation that “translational” and “basic” are either/or activities: translational research nowadays aims at feeding the best science into applications and solutions for human society. We therefore argue here basic science to be challenged and leveraged for its relevance to human health and societal benefits. This more recent approach and attitude are catalyzed by four trends or developments: evidence-based solutions; large-scale, high dimensional data; consumer/patient empowerment; and systems-level understanding.

  17. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  18. Hippocampal place cells, context, and episodic memory.

    Science.gov (United States)

    Smith, David M; Mizumori, Sheri J Y

    2006-01-01

    Although most observers agree that the hippocampus has a critical role in learning and memory, there remains considerable debate about the precise functional contribution of the hippocampus to these processes. Two of the most influential accounts hold that the primary function of the hippocampus is to generate cognitive maps and to mediate episodic memory processes. The well-documented spatial firing patterns (place fields) of hippocampal neurons in rodents, along with the spatial learning impairments observed with hippocampal damage support the cognitive mapping hypothesis. The amnesia for personally experienced events seen in humans with hippocampal damage and the data of animal models, which show severe memory deficits associated with hippocampal lesions, support the episodic memory account. Although an extensive literature supports each of these hypotheses, a specific contribution of place cells to episodic memory has not been clearly demonstrated. Recent data from our laboratory, together with previous findings, indicate that hippocampal place fields and neuronal responses to task-relevant stimuli are highly sensitive to the context, even when the contexts are defined by abstract task demands rather than the spatial geometry of the environment. On the basis of these findings, it is proposed that place fields reflect a more general context processing function of the hippocampus. Hippocampal context representations could serve to differentiate contexts and prime the relevant memories and behaviors. Since episodic memories, by definition, include information about the time and place where the episode occurred, contextual information is a necessary prerequisite for any episodic memory. Thus, place fields contribute importantly to episodic memory as part of the needed context representations. Additionally, recent findings indicate that hippocampal neurons differentiate contexts at progressively finer levels of detail, suggesting a hierarchical coding scheme which

  19. Genome Mapping in Plant Comparative Genomics.

    Science.gov (United States)

    Chaney, Lindsay; Sharp, Aaron R; Evans, Carrie R; Udall, Joshua A

    2016-09-01

    Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics.

  20. Ontology for Genome Comparison and Genomic Rearrangements

    Directory of Open Access Journals (Sweden)

    Anil Wipat

    2006-04-01

    Full Text Available We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.

  1. Enabling functional genomics with genome engineering.

    Science.gov (United States)

    Hilton, Isaac B; Gersbach, Charles A

    2015-10-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.

  2. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.

    Science.gov (United States)

    Shaffer, H Bradley; Minx, Patrick; Warren, Daniel E; Shedlock, Andrew M; Thomson, Robert C; Valenzuela, Nicole; Abramyan, John; Amemiya, Chris T; Badenhorst, Daleen; Biggar, Kyle K; Borchert, Glen M; Botka, Christopher W; Bowden, Rachel M; Braun, Edward L; Bronikowski, Anne M; Bruneau, Benoit G; Buck, Leslie T; Capel, Blanche; Castoe, Todd A; Czerwinski, Mike; Delehaunty, Kim D; Edwards, Scott V; Fronick, Catrina C; Fujita, Matthew K; Fulton, Lucinda; Graves, Tina A; Green, Richard E; Haerty, Wilfried; Hariharan, Ramkumar; Hernandez, Omar; Hillier, LaDeana W; Holloway, Alisha K; Janes, Daniel; Janzen, Fredric J; Kandoth, Cyriac; Kong, Lesheng; de Koning, A P Jason; Li, Yang; Literman, Robert; McGaugh, Suzanne E; Mork, Lindsey; O'Laughlin, Michelle; Paitz, Ryan T; Pollock, David D; Ponting, Chris P; Radhakrishnan, Srihari; Raney, Brian J; Richman, Joy M; St John, John; Schwartz, Tonia; Sethuraman, Arun; Spinks, Phillip Q; Storey, Kenneth B; Thane, Nay; Vinar, Tomas; Zimmerman, Laura M; Warren, Wesley C; Mardis, Elaine R; Wilson, Richard K

    2013-03-28

    We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing. Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.

  3. The Policy Context.

    Science.gov (United States)

    Bell, Les; Bush, Tony

    This document is a chapter in "The Principles and Practice of Educational Management," which aims to provide a systematic and analytical introduction to the study of educational management. The structure of the book reflects the main substantive areas of educational leadership and management, and most of the major themes are covered in the…

  4. Genome interplay in the grain transcriptome of hexaploid bread wheat.

    Science.gov (United States)

    Pfeifer, Matthias; Kugler, Karl G; Sandve, Simen R; Zhan, Bujie; Rudi, Heidi; Hvidsten, Torgeir R; Mayer, Klaus F X; Olsen, Odd-Arne

    2014-07-18

    Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type-specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type- and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome. Copyright © 2014, American Association for the Advancement of Science.

  5. Hellbender genome sequences shed light on genomic expansion at the base of crown salamanders.

    Science.gov (United States)

    Sun, Cheng; Mueller, Rachel Lockridge

    2014-07-01

    Among animals, genome sizes range from 20 Mb to 130 Gb, with 380-fold variation across vertebrates. Most of the largest vertebrate genomes are found in salamanders, an amphibian clade of 660 species. Thus, salamanders are an important system for studying causes and consequences of genomic gigantism. Previously, we showed that plethodontid salamander genomes accumulate higher levels of long terminal repeat (LTR) retrotransposons than do other vertebrates, although the evolutionary origins of such sequences remained unexplored. We also showed that some salamanders in the family Plethodontidae have relatively slow rates of DNA loss through small insertions and deletions. Here, we present new data from Cryptobranchus alleganiensis, the hellbender. Cryptobranchus and Plethodontidae span the basal phylogenetic split within salamanders; thus, analyses incorporating these taxa can shed light on the genome of the ancestral crown salamander lineage, which underwent expansion. We show that high levels of LTR retrotransposons likely characterize all crown salamanders, suggesting that disproportionate expansion of this transposable element (TE) class contributed to genomic expansion. Phylogenetic and age distribution analyses of salamander LTR retrotransposons indicate that salamanders' high TE levels reflect persistence and diversification of ancestral TEs rather than horizontal transfer events. Finally, we show that relatively slow DNA loss rates through small indels likely characterize all crown salamanders, suggesting that a decreased DNA loss rate contributed to genomic expansion at the clade's base. Our identification of shared genomic features across phylogenetically distant salamanders is a first step toward identifying the evolutionary processes underlying accumulation and persistence of high levels of repetitive sequence in salamander genomes.

  6. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  7. Creation, Identity and Reflection

    Directory of Open Access Journals (Sweden)

    Alina Beatrice Cheşcă

    2015-05-01

    Full Text Available The paper “Creation, Identity and Reflection” approaches the identification in the “mirror” of reality with creation, in other words seeking the authors’ identity in the reflected images. Reflection means attempting to find oneself, the mirror being the main principle of creation. Many characters become interesting only when they step into the world beyond the mirror, when their faces are doubled by the other self or when their selves are returned by other characters. The narcissistic concept of the mirror, i.e. the reflection in the mirror and the representation of the mirror itself, is a recurrent one in literature, but the reflection of the self which is not the self (as it is a reflection does not necessarily appear in a mirror or in a photograph or portrait. Sometimes, the not-self is returned to the self by another person or character. As far as Oscar Wilde’s theories are concerned, the main idea is that people are interesting for their masks, not for their inner nature. What Wilde calls “inner nature” is the characters’ un-reflected self and the mask is the reflection, the self in the mirror. Some characters’ relationships develop within a fiction that they dramatically try to preserve and protect with the risk of suffering. They refuse to take off the masks which define them in the others’ minds and hearts; the narcissistic individuals (both artists and characters seek and love their own image which they project upon facts, thus creating a fictive realm.

  8. Public attitudes towards genomic risk profiling as a component of routine population screening.

    Science.gov (United States)

    Nicholls, S G; Wilson, B J; Craigie, S M; Etchegary, H; Castle, D; Carroll, J C; Potter, B K; Lemyre, L; Little, J

    2013-10-01

    Including low penetrance genomic variants in population-based screening might enable personalization of screening intensity and follow up. The application of genomics in this way requires formal evaluation. Even if clinically beneficial, uptake would still depend on the attitudes of target populations. We developed a deliberative workshop on two hypothetical applications (in colorectal cancer and newborn screening) in which we applied stepped, neutrally-framed, information sets. Data were collected using nonparticipant observation, free-text comments by individual participants, and a structured survey. Qualitative data were transcribed and analyzed using thematic content analysis. Eight workshops were conducted with 170 individuals (120 colorectal cancer screening and 50 newborn screening for type 1 diabetes). The use of information sets promoted informed deliberation. In both contexts, attitudes appeared to be heavily informed by assessments of the likely validity of the test results and its personal and health care utility. Perceived benefits included the potential for early intervention, prevention, and closer monitoring while concerns related to costs, education needs regarding the probabilistic nature of risk, the potential for worry, and control of access to personal genomic information. Differences between the colorectal cancer and newborn screening groups appeared to reflect different assessments of potential personal utility, particularly regarding prevention.

  9. Static context model for context aware E-Learning

    Directory of Open Access Journals (Sweden)

    Minu. M. Das

    2010-06-01

    Full Text Available Context aware E-Learning systems provide learning content according to a learner’s context. In order to determine a learner’s context, the parameters that constitute the context and the values of these parameters in the current learner’s situation have to be found. There are several existing context aware E-Learning systems and each of these are taking care of some of the context parameters - like learning styles, learner preferences etc. But, a standardized static context model that helps to capture a learner’s context in its ntirety is not available. This paper proposes a static context model that helps to capture a learner’s context. The static context model is developed by consolidating the various context parameters used in the existing context aware E-Learning systems and organizing them into an appropriate structure. The structure of the static context model along with the parameters that constitute the context is explained in the paper

  10. Translating genomics in cancer care.

    Science.gov (United States)

    Bombard, Yvonne; Bach, Peter B; Offit, Kenneth

    2013-11-01

    NGS technologies into health care. It concludes that significant evidentiary gaps remain in translating genomic technologies into routine clinical practice, particularly in efficacy, health outcomes, cost-effectiveness, and health services research. These caveats are especially germane in the context of NGS, wherein efforts are underway to translate NGS results despite their limited accuracy, lack of proven efficacy, and significant computational and counseling challenges. Further research across these domains is critical to inform the effective, efficient, and equitable translation of genomics into cancer care.

  11. Genomic Medicine

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-04-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence.  The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others. There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine.  For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc.. Legal aspects are also present in this new conception of medicine.  For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others. We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the

  12. GENOMIC MEDICINE

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-03-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence. The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others.There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine. For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc..Legal aspects are also present in this new conception of medicine. For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others.We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the disease

  13. Genomic alterations in pancreatic cancer and their relevance to therapy

    Institute of Scientific and Technical Information of China (English)

    Erina; Takai; Shinichi; Yachida

    2015-01-01

    Pancreatic cancer is a highly lethal cancer type, for which there are few viable therapeutic options. But, with the advance of sequencing technologies for global genomic analysis, the landscape of genomic alterations in pancreatic cancer is becoming increasingly well understood. In this review, we summarize current knowledge of genomic alterations in 12 core signaling pathways or cellular processes in pancreatic ductal adenocarcinoma, which is the most common type of malignancy in the pancreas, including four commonly mutated genes and many other genes that are mutated at low frequencies. We also describe the potential implications of these genomic alterations for development of novel therapeutic approaches in the context of personalized medicine.

  14. A práxis do agente comunitário de saúde no contexto do programa saúde da família: reflexões estratégicas The community health agent's praxis in the context of the family health program: strategic reflections

    Directory of Open Access Journals (Sweden)

    Karine de Oliveira Gomes

    2009-12-01

    Full Text Available O Programa Saúde da Família (PSF surgiu no cenário brasileiro como estratégia de superação do modelo assistencial centrado na doença e no cuidado médico individualizado. Nesse contexto, os agentes comunitários de saúde (ACS têm sido considerados atores-chave na implantação de políticas voltadas para a reorientação do modelo de atenção à saúde. O objetivo deste estudo foi analisar as concepções e percepções sobre o SUS e o PSF que norteiam as ações dos ACS, refletindo sobre sua função e formação profissional. O trabalho fundamentou-se na pesquisa quali-quantitativa, foi realizado em Cajuri-MG e foram entrevistados todos os ACS (n=11 que trabalhavam no PSF. Os resultados demonstraram que a maioria dos ACS (72,7% residia na comunidade em que atuava, trabalhava há mais de cinco anos no PSF e acompanhava a quantidade de famílias recomendada. Entre as principais funções, destacaram-se visitas domiciliares, busca ativa e educação em saúde, que na maioria das vezes acontecia de forma individualizada e centrada no reforço da assistência médica e na prevenção de riscos específicos. Em relação à capacitação, 54,6% dos ACS receberam orientação antes de iniciar o trabalho e 81,8% participaram de cursos depois que já estavam trabalhando. Apenas 27,3% dos ACS souberam conceituar o SUS e 36,4% demonstraram entendimento adequado sobre PSF. Esses resultados demonstram a necessidade de maiores esforços para melhorar a capacitação do ACS, visando adequar seu nível de apreensão e conhecimento dos princípios do SUS e PSF, para que ele possa atuar segundo as diretrizes desse sistema e contribuir efetivamente para sua consolidação.Programa Saúde da Família (PSF - Family Health Program appeared in the Brazilian scenario as a strategy to overcome an assistance model that is centered on disease and on individualized medical care. In this context, the agentes comunitários de saúde (ACS - community health agents

  15. Between Two Fern Genomes

    OpenAIRE

    Sessa, Emily B.; Banks, Jo; Michael S Barker; Der, Joshua P; Duffy, Aaron M; Graham, Sean W.; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D; Kathleen M. Pryer; Rothfels, Carl J.; Roux, Stanley J.; Salmi, Mari L; Sigel, Erin M.

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense divers...

  16. Genome organization, instabilities, stem cells, and cancer

    Directory of Open Access Journals (Sweden)

    Senthil Kumar Pazhanisamy

    2009-01-01

    Full Text Available It is now widely recognized that advances in exploring genome organization provide remarkable insights on the induction and progression of chromosome abnormalities. Much of what we know about how mutations evolve and consequently transform into genome instabilities has been characterized in the spatial organization context of chromatin. Nevertheless, many underlying concepts of impact of the chromatin organization on perpetuation of multiple mutations and on propagation of chromosomal aberrations remain to be investigated in detail. Genesis of genome instabilities from accumulation of multiple mutations that drive tumorigenesis is increasingly becoming a focal theme in cancer studies. This review focuses on structural alterations evolve to raise a variety of genome instabilities that are manifested at the nucleotide, gene or sub-chromosomal, and whole chromosome level of genome. Here we explore an underlying connection between genome instability and cancer in the light of genome architecture. This review is limited to studies directed towards spatial organizational aspects of origin and propagation of aberrations into genetically unstable tumors.

  17. Genomes and evolutionary genomics of animals

    Institute of Scientific and Technical Information of China (English)

    Luting SONG; Wen WANG

    2013-01-01

    Alongside recent advances and booming applications of DNA sequencing technologies,a great number of complete genome sequences for animal species are available to researchers.Hundreds of animals have been involved in whole genome sequencing,and at least 87 non-human animal species' complete or draft genome sequences have been published since 1998.Based on these technological advances and the subsequent accumulation of large quantity of genomic data,evolutionary genomics has become one of the most rapidly advancing disciplines in biology.Scientists now can perform a number of comparative and evolutionary genomic studies for animals,to identify conserved genes or other functional elements among species,genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation.This review deals with the current genomic and evolutionary research on non-human animals,and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals.It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom [Current Zoology 59 (1):87-98,2013].

  18. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  19. Genome Maps, a new generation genome browser

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  20. Cue conflicts in context

    DEFF Research Database (Denmark)

    Boeg Thomsen, Ditte; Poulsen, Mads

    2015-01-01

    When learning their first language, children develop strategies for assigning semantic roles to sentence structures, depending on morphosyntactic cues such as case and word order. Traditionally, comprehension experiments have presented transitive clauses in isolation, and crosslinguistically...... in discourse-pragmatically felicitous contexts. Our results extend previous findings of preschoolers’ sensitivity to discourse-contextual cues in sentence comprehension (Hurewitz, 2001; Song & Fisher, 2005) to the basic task of assigning agent and patient roles....

  1. Sounds in context

    DEFF Research Database (Denmark)

    Weed, Ethan

    are colored by contextual information. This can be longterm contextual information, such as knowledge of phonological or emotional categories, but can also be short-term local expectancies, such as the previous sound heard. In this paper, I present original electrophysiological data illustrating the early...... auditory processing of emotional speech was modulated by an accompanying visual context. I then discuss these results in terms of their implication for how we conceive of the auditory processing stream....

  2. Reading the African context

    Directory of Open Access Journals (Sweden)

    Musonda Bwalya

    2012-12-01

    Full Text Available There is so much alienation, pain and suffering in our today�s world. In this vein, African Christianity, a voice amongst many voices, should seek to be a transformational religion for the whole of life, affecting all facets of human life towards a fuller life of all in Africa. This article sought to highlight and point to some of the major societal challenges in the African context which African Christianity, as a life-affirming religion, should continue to embrace, re-embrace and engage with, if it has to be relevant to the African context. In this vein, the article argued that a correct reading of the African context would lead to a more relevant theory and praxis of African Christianity for the benefit of all African peoples and their global neighbours. The contention of this article was that African Christianity has a significant role to play in the re-shaping of the African society and in the global community of humans, only that this role must be executed inclusively, responsibly and appropriately, together with all those who seek the holistic development of Africa towards one common destiny.

  3. Invisibility via reflecting coating

    CERN Document Server

    Burdzy, Krzysztof

    2012-01-01

    We construct a subset $A$ of the unit disc with the following properties. (i) The set $A$ is the finite union of disjoint line segments. (ii) The shadow of $A$ is arbitrarily close to the shadow of the unit disc in "most" directions. (iii) If the line segments are considered to be mirrors reflecting light according to the classical law of specular reflection then most light rays hitting the set emerge on the other side of the disc moving along a parallel line and shifted by an arbitrarily small amount. We also construct a set which reflects almost all light rays coming from one direction to another direction but its shadow is arbitrarily small in other directions, except for an arbitrarily small family of directions.

  4. Comparative Genomic and Phylogenomic Analyses Reveal a Conserved Core Genome Shared by Estuarine and Oceanic Cyanopodoviruses

    Science.gov (United States)

    Huang, Sijun; Zhang, Si; Jiao, Nianzhi; Chen, Feng

    2015-01-01

    Podoviruses are among the major viral groups that infect marine picocyanobacteria Prochlorococcus and Synechococcus. Here, we reported the genome sequences of five Synechococcus podoviruses isolated from the estuarine environment, and performed comparative genomic and phylogenomic analyses based on a total of 20 cyanopodovirus genomes. The genomes of all the known marine cyanopodoviruses are highly syntenic. A pan-genome of 349 clustered orthologous groups was determined, among which 15 were core genes. These core genes make up nearly half of each genome in length, reflecting the high level of genome conservation among this cyanophage type. The whole genome phylogenies based on concatenated core genes and gene content were highly consistent and confirmed the separation of two discrete marine cyanopodovirus clusters MPP-A and MPP-B. The genomes within cluster MPP-B grouped into subclusters mainly corresponding to Prochlorococcus or Synechococcus host types. Auxiliary metabolic genes tend to occur in a specific phylogenetic group of these cyanopodoviruses. All the MPP-B phages analyzed here encode the photosynthesis gene psbA, which are absent in all the MPP-A genomes thus far. Interestingly, all the MPP-B and two MPP-A Synechococcus podoviruses encode the thymidylate synthase gene thyX, while at the same genome locus all the MPP-B Prochlorococcus podoviruses encode the transaldolase gene talC. Both genes are hypothesized to have the potential to facilitate the biosynthesis of deoxynucleotide for phage replication. Inheritance of specific functional genes could be important to the evolution and ecological fitness of certain cyanophage genotypes. Our analyses demonstrate that cyanopodoviruses of estuarine and oceanic origins share a conserved core genome and suggest that accessory genes may be related to environmental adaptation. PMID:26569403

  5. Comparative Genomic and Phylogenomic Analyses Reveal a Conserved Core Genome Shared by Estuarine and Oceanic Cyanopodoviruses.

    Directory of Open Access Journals (Sweden)

    Sijun Huang

    Full Text Available Podoviruses are among the major viral groups that infect marine picocyanobacteria Prochlorococcus and Synechococcus. Here, we reported the genome sequences of five Synechococcus podoviruses isolated from the estuarine environment, and performed comparative genomic and phylogenomic analyses based on a total of 20 cyanopodovirus genomes. The genomes of all the known marine cyanopodoviruses are highly syntenic. A pan-genome of 349 clustered orthologous groups was determined, among which 15 were core genes. These core genes make up nearly half of each genome in length, reflecting the high level of genome conservation among this cyanophage type. The whole genome phylogenies based on concatenated core genes and gene content were highly consistent and confirmed the separation of two discrete marine cyanopodovirus clusters MPP-A and MPP-B. The genomes within cluster MPP-B grouped into subclusters mainly corresponding to Prochlorococcus or Synechococcus host types. Auxiliary metabolic genes tend to occur in a specific phylogenetic group of these cyanopodoviruses. All the MPP-B phages analyzed here encode the photosynthesis gene psbA, which are absent in all the MPP-A genomes thus far. Interestingly, all the MPP-B and two MPP-A Synechococcus podoviruses encode the thymidylate synthase gene thyX, while at the same genome locus all the MPP-B Prochlorococcus podoviruses encode the transaldolase gene talC. Both genes are hypothesized to have the potential to facilitate the biosynthesis of deoxynucleotide for phage replication. Inheritance of specific functional genes could be important to the evolution and ecological fitness of certain cyanophage genotypes. Our analyses demonstrate that cyanopodoviruses of estuarine and oceanic origins share a conserved core genome and suggest that accessory genes may be related to environmental adaptation.

  6. Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.

    Science.gov (United States)

    Smokvina, Tamara; Wels, Michiel; Polka, Justyna; Chervaux, Christian; Brisse, Sylvain; Boekhorst, Jos; van Hylckama Vlieg, Johan E T; Siezen, Roland J

    2013-01-01

    Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its "pan-genome". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon) are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis, in order to link

  7. Biology Reflective Assessment Curriculum

    Science.gov (United States)

    Bayley, Cheryl Ann

    Often students and educators view assessments as an obligation and finality for a unit. In the current climate of high-stakes testing and accountability, the balance of time, resources and emphasis on students' scores related to assessment have been slanted considerably toward the summative side. This tension between assessment for accountability and assessment to inform teaching strains instruction and educators' ability to use that information to design learning opportunities that help students develop deeper conceptual understanding. A substantive body of research indicates that formative and reflective assessment can significantly improve student learning. Biology Reflective Assessment Curriculum (BRAC) examines support provided for high school science students through assessment practices. This investigation incorporates the usage of reflective assessments as a guiding practice for differentiated instruction and student choice. Reflective assessment is a metacognitive strategy that promotes self-monitoring and evaluation. The goals of the curriculum are to promote self-efficacy and conceptual understanding in students learning biology through developing their metacognitive awareness. BRAC was implemented in a high school biology classroom. Data from assessments, metacognitive surveys, self-efficacy surveys, reflective journals, student work, a culminating task and field notes were used to evaluate the effectiveness of the curriculum. The results suggest that students who develop their metacognitive skills developed a deeper conceptual understanding and improved feelings of self-efficacy when they were engaged in a reflective assessment unit embedded with student choice. BRAC is a tool for teachers to use assessments to assist students in becoming metacognitive and to guide student choice in learning opportunities.

  8. Teacher Reflections and Praxis: A Case Study of Indian Teachers of English as a Foreign Language

    Science.gov (United States)

    Makarani, Sakilahmed A. R.

    2012-01-01

    This case study engaged Gujarati English as Foreign Language (EFL) teachers in video-based reflection with the goal of increasing their reflective abilities and uncovering their understandings about reflective teaching practices in the Indian pedagogical and cultural context. The study aimed to explore, and gain a deeper understanding of how…

  9. Teaching Reflective Social Work Practice in Health Care: Promoting Best Practices

    Science.gov (United States)

    McCoyd, Judith L. M.; Kerson, Toba S.

    2013-01-01

    Reflection on case material is traditionally believed to promote better clinical practice; recent neurobiological understandings explain why reflection consolidates learning and allows professional heuristics to develop. Here, we describe a practice in context (PIC) framework that requires reflection on the contextual and decisional aspects of a…

  10. Student Reflective Writing: Cognition and Affect before, during, and after Study Abroad

    Science.gov (United States)

    Savicki, Victor; Price, Michele V.

    2015-01-01

    Reflective thinking is an important feature of study-abroad learning, yet research on reflection in this context is sparse. The current study examined student reflection on 3 content areas (Academic Expectations, Cultural Expectations, and Psychological Issues) at 3 times (before, during, and after study abroad). A content analysis approach with…

  11. Teaching Reflective Social Work Practice in Health Care: Promoting Best Practices

    Science.gov (United States)

    McCoyd, Judith L. M.; Kerson, Toba S.

    2013-01-01

    Reflection on case material is traditionally believed to promote better clinical practice; recent neurobiological understandings explain why reflection consolidates learning and allows professional heuristics to develop. Here, we describe a practice in context (PIC) framework that requires reflection on the contextual and decisional aspects of a…

  12. Reflecting telescope optics

    CERN Document Server

    Wilson, Raymond N

    2004-01-01

    R.N. Wilson's two-volume treatise on reflecting telescope optics has become a classic in its own right. It is intended to give a complete treatment of the subject, addressing professionals in research and industry as well as students of astronomy and amateur astronomers. This first volume, Basic Design Theory and its Historical Development, is devoted to the theory of reflecting telescope optics and systematically recounts the historical progress. The author's approach is morphological, with strong emphasis on the historical development. The book is richly illustrated including spot-diagrams a

  13. Acoustic Bottom Reflectivity

    Science.gov (United States)

    1986-12-01

    Calculates the reflection loss as function of frequency. ---PLOTV/ PLOTF ---Plots loss and phase as function of angle or frequency. ---QUIT--- ENTER YOUR...34Y" if you want to leave PLOTV or PLOTF and return to the HELP MENU. A similar procedure to plot results as a function of frequency is contained in... PLOTF and works in the same way. Figures A-1 and A-2 show the results for an 18-layer sample input file, FLOOR18.DAT, giving the reflection loss as a

  14. Reflecting on a room of one reflectance.

    Science.gov (United States)

    Ruppertsberg, Alexa I; Bloj, Marina

    2007-10-30

    We present a numerical analysis of rendered pairs of rooms, in which the spectral power distribution of the illuminant in one room matched the surface reflectance function in the other room, and vice versa. We ask whether distinction between the rooms is possible and on what cues this discrimination is based. Using accurately rendered three-dimensional (3D) scenes, we found that room pairs can be distinguished based on indirect illumination, as suggested by A. L. Gilchrist and A. Jacobsen (1984). In a simulated color constancy scenario, we show that indirect illumination plays a pivotal role as areas of indirect illumination undergo a smaller appearance change than areas of direct illumination. Our study confirms that indirect illumination can play a critical role in surface color recovery and shows how computer rendering programs, which model the light-object interaction according to the laws of physics, are valuable tools that can be used to analyze and explore what image information is available to the visual system from 3D scenes.

  15. Integral representation of Skorokhod reflection

    CERN Document Server

    Anantharam, Venkat

    2010-01-01

    We show that a certain integral representation of the one-sided Skorokhod reflection of a continuous bounded variation function characterizes the reflection in that it possesses a unique maximal solution which solves the Skorokhod reflection problem.

  16. Reflection in learning at work

    DEFF Research Database (Denmark)

    Pedersen, Steen Høyrup

    2006-01-01

    Three domains and approaches of learning - adult learning, problem-solving and cirtical reflection theory are used as different lenses through which the question: what is reflection and how is reflection related to learning, - are interpreted....

  17. Chlamydia genomics: providing novel insights into chlamydial biology.

    Science.gov (United States)

    Bachmann, Nathan L; Polkinghorne, Adam; Timms, Peter

    2014-08-01

    Chlamydiaceae are obligate intracellular pathogens that have successfully evolved to colonize a diverse range of hosts. There are currently 11 described species of Chlamydia, most of which have a significant impact on the health of humans or animals. Expanding chlamydial genome sequence information has revolutionized our understanding of chlamydial biology, including aspects of their unique lifecycle, host-pathogen interactions, and genetic differences between Chlamydia strains associated with different host and tissue tropisms. This review summarizes the major highlights of chlamydial genomics and reflects on the considerable impact these have had on understanding the biology of chlamydial pathogens and the changing nature of genomics tools in the 'post-genomics' era.

  18. Principles of proteome allocation are revealed using proteomic data and genome-scale models

    DEFF Research Database (Denmark)

    Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.

    2016-01-01

    , prediction errors for growth rate and metabolic fluxes were 69% and 14% lower, respectively. The sector-constrained ME model thus represents a generalist ME model reflecting both growth rate maximization and "hedging" against uncertain environments and stresses, as indicated by significant enrichment...... of these sectors for the general stress response sigma factor sigma(S). Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally......Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked...

  19. Context-specific metabolic networks are consistent with experiments.

    Directory of Open Access Journals (Sweden)

    Scott A Becker

    2008-05-01

    Full Text Available Reconstructions of cellular metabolism are publicly available for a variety of different microorganisms and some mammalian genomes. To date, these reconstructions are "genome-scale" and strive to include all reactions implied by the genome annotation, as well as those with direct experimental evidence. Clearly, many of the reactions in a genome-scale reconstruction will not be active under particular conditions or in a particular cell type. Methods to tailor these comprehensive genome-scale reconstructions into context-specific networks will aid predictive in silico modeling for a particular situation. We present a method called Gene Inactivity Moderated by Metabolism and Expression (GIMME to achieve this goal. The GIMME algorithm uses quantitative gene expression data and one or more presupposed metabolic objectives to produce the context-specific reconstruction that is most consistent with the available data. Furthermore, the algorithm provides a quantitative inconsistency score indicating how consistent a set of gene expression data is with a particular metabolic objective. We show that this algorithm produces results consistent with biological experiments and intuition for adaptive evolution of bacteria, rational design of metabolic engineering strains, and human skeletal muscle cells. This work represents progress towards producing constraint-based models of metabolism that are specific to the conditions where the expression profiling data is available.

  20. Self-face recognition in social context.

    Science.gov (United States)

    Sugiura, Motoaki; Sassa, Yuko; Jeong, Hyeonjeong; Wakusawa, Keisuke; Horie, Kaoru; Sato, Shigeru; Kawashima, Ryuta

    2012-06-01

    The concept of "social self" is often described as a representation of the self-reflected in the eyes or minds of others. Although the appearance of one's own face has substantial social significance for humans, neuroimaging studies have failed to link self-face recognition and the likely neural substrate of the social self, the medial prefrontal cortex (MPFC). We assumed that the social self is recruited during self-face recognition under a rich social context where multiple other faces are available for comparison of social values. Using functional magnetic resonance imaging (fMRI), we examined the modulation of neural responses to the faces of the self and of a close friend in a social context. We identified an enhanced response in the ventral MPFC and right occipitoparietal sulcus in the social context specifically for the self-face. Neural response in the right lateral parietal and inferior temporal cortices, previously claimed as self-face-specific, was unaffected for the self-face but unexpectedly enhanced for the friend's face in the social context. Self-face-specific activation in the pars triangularis of the inferior frontal gyrus, and self-face-specific reduction of activation in the left middle temporal gyrus and the right supramarginal gyrus, replicating a previous finding, were not subject to such modulation. Our results thus demonstrated the recruitment of a social self during self-face recognition in the social context. At least three brain networks for self-face-specific activation may be dissociated by different patterns of response-modulation in the social context, suggesting multiple dynamic self-other representations in the human brain.

  1. Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing

    NARCIS (Netherlands)

    Abdolrasouli, A.; Rhodes, J.; Beale, M.A.; Hagen, F.; Rogers, T.R.; Chowdhary, A.; Meis, J.F.G.M.; Armstrong-James, D.; Fisher, M.C.

    2015-01-01

    A rapid and global emergence of azole resistance has been observed in the pathogenic fungus Aspergillus fumigatus over the past decade. The dominant resistance mechanism appears to be of environmental origin and involves mutations in the cyp51A gene, which encodes a protein targeted by triazole

  2. Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing

    NARCIS (Netherlands)

    Abdolrasouli, A.; Rhodes, J.; Beale, M.A.; Hagen, F.; Rogers, T.R.; Chowdhary, A.; Meis, J.F.G.M.; Armstrong-James, D.; Fisher, M.C.

    2015-01-01

    A rapid and global emergence of azole resistance has been observed in the pathogenic fungus Aspergillus fumigatus over the past decade. The dominant resistance mechanism appears to be of environmental origin and involves mutations in the cyp51A gene, which encodes a protein targeted by triazole anti

  3. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  4. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  5. Understanding the industrial application potential of lactic acid bacteria through genomics.

    Science.gov (United States)

    Zhu, Yan; Zhang, Yanping; Li, Yin

    2009-06-01

    Lactic acid bacteria (LAB) are a heterogeneous group of bacteria contributing to various industrial applications, ranging from food and beverage fermentation, bulk and fine chemicals production to pharmaceuticals manufacturing. Genome sequencing is booming; hitherto, 25 genomes of LAB have been published and many more are in progress. Based on genomic content of LAB, this review highlights some findings related to applications revealed by genomics and functional genomics analyses. Finally, this review summarizes mathematical modeling strategies of LAB in the context of genomics, to further our understanding of industrial related features.

  6. The integrated microbial genomes (IMG) system in 2007: datacontent and analysis tool extensions

    Energy Technology Data Exchange (ETDEWEB)

    Markowitz, Victor M.; Szeto, Ernest; Palaniappan, Krishna; Grechkin, Yuri; Chu, Ken; Chen, I-Min A.; Dubchak, Inna; Anderson, Iain; Lykidis, Athanasios; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2007-08-01

    The Integrated Microbial Genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov.

  7. Lights, Camera, Reflection!

    Science.gov (United States)

    Mourlam, Daniel

    2013-01-01

    There are many ways to critique teaching, but few are more effective than video. Personal reflection through the use of video allows one to see what really happens in the classrooms--good and bad--and provides a visual path forward for improvement, whether it be in one's teaching, work with a particular student, or learning environment. This…

  8. Value reflected health education

    DEFF Research Database (Denmark)

    Wistoft, Karen; Nordentoft, Helle Merete

    2011-01-01

    This article examines the impact of a value-reflected approach in health education by demonstrating the nature of professional competence development connected to this approach. It is based on findings from two three-year health educational development projects carried out by school health nurses...... develop pedagogical competences in health education improving school childrens’ health....

  9. Self-Reflection

    DEFF Research Database (Denmark)

    Fausing, Bent

    Reflecting has a double meaning, mirroring and thinking. The seminar will investigate how these two meanings intervene in each other. As we perceive we are already in pre-refectory state, and thinking involves a lot of not only thoughts, but also of senses and sensing, wherefrom our thoughts star...

  10. Wave Reflection Model Tests

    DEFF Research Database (Denmark)

    Burcharth, H. F.; Larsen, Brian Juul

    The investigation concerns the design of a new internal breakwater in the main port of Ibiza. The objective of the model tests was in the first hand to optimize the cross section to make the wave reflection low enough to ensure that unacceptable wave agitation will not occur in the port. Secondly...

  11. Changes Brought by Reflection

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    Feng: A number of changes have taken place in Europe after reflection, such as specific anti-terrorist measures, progress in the construction of integration, changes in the structure of political forces and adjustments in the EU foreign policy. Would you make some comments first, Dr. Sun?

  12. Self-Reflection

    DEFF Research Database (Denmark)

    Fausing, Bent

    2016-01-01

    Reflecting has a double meaning, mirroring and thinking. The seminar will investigate how these two meanings intervene in each other. As we perceive we are already in pre-refectory state, and thinking involves a lot of not only thoughts, but also of senses and sensing, wherefrom our thoughts star...

  13. Clinical Linguistics: Conversational Reflections

    Science.gov (United States)

    Crystal, David

    2013-01-01

    This is a report of the main points I made in an informal "conversation" with Paul Fletcher and the audience at the 14th ICPLA conference in Cork. The observations arose randomly, as part of an unstructured 1-h Q&A, so they do not provide a systematic account of the subject, but simply reflect the issues which were raised by the conference…

  14. Reflections: Children and Literature.

    Science.gov (United States)

    And Others; Cianciolo, Patricia J.

    1980-01-01

    Six educational leaders--Patricia J. Cianciolo, Lee Bennett Hopkins, Nancy Larrick, Alan C. Purves, Morton Schindel, and James R. Squire--offer reflections on signficiant developments in children's literature during the 1970s, their hopes for the 1980s, and references that constitute required reading for elementary language arts teachers. (ET)

  15. Reflection by Porro Prisms

    Science.gov (United States)

    Greenslade, Thomas B.

    2010-04-01

    Students all know that reflection from a plane mirror produces an image that is reversed right to left and so cannot be read by anyone but Leonardo da Vinci, who kept his notes in mirror writing. A useful counter-example is the Porro prism, which produces an image that is not reversed.

  16. Reflecting on Data

    Science.gov (United States)

    Kraus, Rudolf V.

    2014-01-01

    This article describes a two-day optics laboratory activity that investigates the scientific phenomenon of reflection, which students are generally familiar with but usually have not studied in depth. This investigation can be used on its own or as part of a larger unit on optics. This lesson encourages students to think critically and…

  17. Supporting Authentic Learning Contexts Beyond Classroom Walls

    Science.gov (United States)

    Herrington, Jan; Specht, Marcus; Brickell, Gwyn; Harper, Barry

    At the classroom level, contexts for learning are often limited in the experiential component. Teachers and trainers feel overwhelmed by the difficulty of inventing authentic learning contexts, and creating tasks that truly reflect the way knowledge would be used in the real world (Herrington et al. 2004). However, there are growing numbers of examples of how such authentic learning environments are being used in schools, higher education, and professional development in a variety of contexts and discipline areas, such as in literacy education (Ferry et al. 2006), in physical activity fitness and health (Rice et al. 1999), in Indigenous education (Marshall et al. 2001), in evaluation (Agostinho 2006), in multimedia and ICT (Bennett et al. 2001), in literature (Fitzsimmons 2006), and in business writing (Pennell et al. 1997). Teachers and trainers who subscribe to this approach to learning can be very inventive in developing learner perceptions of authentic contexts, but often financial, situational and time constraints limit the experiential elements of authentic learning settings.

  18. Context-free multilanguages

    CERN Document Server

    Knuth, Donald E

    2008-01-01

    This article is a sketch of ideas that were once intended to appear in the author's famous series, "The Art of Computer Programming". He generalizes the notion of a context-free language from a set to a multiset of words over an alphabet. The idea is to keep track of the number of ways to parse a string. For example, "fruit flies like a banana" can famously be parsed in two ways; analogous examples in the setting of programming languages may yet be important in the future. The treatment is informal but essentially rigorous.

  19. Context-free multilanguages

    OpenAIRE

    Knuth, Donald E.

    1991-01-01

    This article is a sketch of ideas that were once intended to appear in the author's famous series, "The Art of Computer Programming". He generalizes the notion of a context-free language from a set to a multiset of words over an alphabet. The idea is to keep track of the number of ways to parse a string. For example, "fruit flies like a banana" can famously be parsed in two ways; analogous examples in the setting of programming languages may yet be important in the future. The treatment is in...

  20. THE MUMMY in context

    OpenAIRE

    Richard Freeman

    2009-01-01

    This article examines the literary and cinematic antecedents of a cinema icon, The Mummy, produced by Universal Pictures in 1932.  It looks at the sources in Victorian and Edwardian literature to see if any of the ideas found their way into the film.  Similarly, the silent cinema is surveyed to see if the 1932 film was a collection of previously filmed stories remoulded.  The context of the Great Depression and its effects on Universal Studios will be shown to have a significant influence on ...

  1. Sounds in context

    DEFF Research Database (Denmark)

    Weed, Ethan

    A sound is never just a sound. It is becoming increasingly clear that auditory processing is best thought of not as a one-way afferent stream, but rather as an ongoing interaction between interior processes and the environment. Even the earliest stages of auditory processing in the nervous system...... time-course of contextual influence on auditory processing in three different paradigms: a simple mismatch negativity paradigm with tones of differing pitch, a multi-feature mismatch negativity paradigm in which tones were embedded in a complex musical context, and a cross-modal paradigm, in which...

  2. French grammar in context

    CERN Document Server

    Jubb, Margaret

    2013-01-01

    Instructors' edition without answer keysDiscount of 20% offered when 10 ebooks are sold- e.g. they will be sold for 263.60/ £151.90 instead of 329.50/£189.90French Grammar in Context presents a unique and exciting approach to learning grammar. Authentic texts from a rich variety of sources, literary and journalistic, are used as the starting point for the illustration and explanation of key areas of French grammar. Each point is consolidated with a wide range of written and spoken exercises. Grammar is presented not as an end in itself, but as a

  3. Context in place

    DEFF Research Database (Denmark)

    Nordentoft, Helle Merete; Thomsen, Rie

    specifically argue for a more grounded approach to the conception of context - a topographic approach - in which the physical setting - i.e. 'the place' becomes an inevitable part of analyses of guidance practices in order to understand participants' sense-making processes. In the paper we draw on two case...... studies on interdisciplinary clinical supervision and work place guidance in which there appears to be a mismatch between intended outcomes and actual events. The analyses demonstrate and support that 'the place' seems - to influence partipants' responses in the guidance sessions and, therefore, must...

  4. PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    Wasnick Michael

    2008-03-01

    Full Text Available Abstract Background The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes. Results PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function. Conclusion PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any

  5. Using articulation and inscription as catalysts for reflection: Design principles for reflective inquiry

    Science.gov (United States)

    Loh, Ben Tun-Bin

    2003-07-01

    The demand for students to engage in complex student-driven and information-rich inquiry investigations poses challenges to existing learning environments. Students are not familiar with this style of work, and lack the skills, tools, and expectations it demands, often forging blindly forward in the investigation. If students are to be successful, they need to learn to be reflective inquirers, periodically stepping back from an investigation to evaluate their work. The fundamental goal of my dissertation is to understand how to design learning environments to promote and support reflective inquiry. I have three basic research questions: how to define this mode of work, how to help students learn it, and understanding how it facilitates reflection when enacted in a classroom. I take an exploratory approach in which, through iterative cycles of design, development, and reflection, I develop principles of design for reflective inquiry, instantiate those principles in the design of a software environment, and test that software in the context of classroom work. My work contributes to the understanding of reflective inquiry in three ways: First, I define a task model that describes the kinds of operations (cognitive tasks) that students should engage in as reflective inquirers. These operations are defined in terms of two basic tasks: articulation and inscription, which serve as catalysts for externalizing student thinking as objects of and triggers for reflection. Second, I instantiate the task model in the design of software tools (the Progress Portfolio). And, through proof of concept pilot studies, I examine how the task model and tools helped students with their investigative classroom work. Finally, I take a step back from these implementations and articulate general design principles for reflective inquiry with the goal of informing the design of other reflective inquiry learning environments. There are three design principles: (1) Provide a designated work space

  6. Being a reflective teacher——reflection on group management

    Institute of Scientific and Technical Information of China (English)

    Pan; Lehui

    2015-01-01

    <正>Introduction According to Pollard and Triggs(1997),reflective teaching is a process through which the capacity to make such professional judgments can be developed and maintained.Then what is a reflective teacher?Reflective teacher is someone who reflects systematically on her practice in a constant attempt to improve

  7. Regulating genomics in the 21st century: from logos to pathos?

    Science.gov (United States)

    Gottweis, Herbert

    2005-03-01

    There is currently an important change in the governance of genomics. In the past, much of the regulatory discussion about genomics has focused on issues of risk. Today, a new discussion is evolving that emphasizes the uncertainties involved in the development and diffusion of genomics into society. The increasing importance of emotional language and the focus on trust in the discussion about genomics reflects the attempt to substitute for the shortcomings of logos with ethos and pathos.

  8. The amphioxus genome and the evolution of the chordate karyotype

    Energy Technology Data Exchange (ETDEWEB)

    Putnam, Nicholas H.; Butts, Thomas; Ferrier, David E.K.; Furlong, Rebecca F.; Hellsten, Uffe; Kawashima, Takeshi; Robinson-Rechavi, Marc; Shoguchi, Eiichi; Terry, Astrid; Yu, Jr-Kai; Benito-Gutierrez, Elia; Dubchak, Inna; Garcia-Fernandez, Jordi; Gibson-Brown, Jeremy J.; Grigoriev, Igor V.; Horton, Amy C.; de Jong, Pieter J.; Jurka, Jerzy; Kapitonov, Vladimir; Kohara, Yuji; Kuroki, Yoko; Lindquist, Erika; Lucas, Susan; Osoegawa, Kazutoyo; Pennacchio, Len A.; Salamov, Asaf A.; Satou, Yutaka; Sauka-Spengler, Tatjana; Schmutz[, Jeremy; Shin-I, Tadasu; Toyoda, Atsushi; Bronner-Fraser, Marianne; Fujiyama, Asao; Holland, Linda Z.; Holland, Peter W. H.; Satoh, Nori; Rokhsar, Daniel S.

    2008-04-01

    Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage with a fossil record dating back to the Cambrian. We describe the structure and gene content of the highly polymorphic {approx}520 million base pair genome of the Florida lancelet Branchiostoma floridae, and analyze it in the context of chordate evolution. Whole genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets, and vertebrates), and allow reconstruction of not only the gene complement of the last common chordate ancestor, but also a partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.

  9. Harnessing CRISPR-Cas systems for bacterial genome editing.

    Science.gov (United States)

    Selle, Kurt; Barrangou, Rodolphe

    2015-04-01

    Manipulation of genomic sequences facilitates the identification and characterization of key genetic determinants in the investigation of biological processes. Genome editing via clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) constitutes a next-generation method for programmable and high-throughput functional genomics. CRISPR-Cas systems are readily reprogrammed to induce sequence-specific DNA breaks at target loci, resulting in fixed mutations via host-dependent DNA repair mechanisms. Although bacterial genome editing is a relatively unexplored and underrepresented application of CRISPR-Cas systems, recent studies provide valuable insights for the widespread future implementation of this technology. This review summarizes recent progress in bacterial genome editing and identifies fundamental genetic and phenotypic outcomes of CRISPR targeting in bacteria, in the context of tool development, genome homeostasis, and DNA repair.

  10. Evolution and genome architecture in fungal plant pathogens.

    Science.gov (United States)

    Möller, Mareike; Stukenbrock, Eva H

    2017-08-07

    The fungal kingdom comprises some of the most devastating plant pathogens. Sequencing the genomes of fungal pathogens has shown a remarkable variability in genome size and architecture. Population genomic data enable us to understand the mechanisms and the history of changes in genome size and adaptive evolution in plant pathogens. Although transposable elements predominantly have negative effects on their host, fungal pathogens provide prominent examples of advantageous associations between rapidly evolving transposable elements and virulence genes that cause variation in virulence phenotypes. By providing homogeneous environments at large regional scales, managed ecosystems, such as modern agriculture, can be conducive for the rapid evolution and dispersal of pathogens. In this Review, we summarize key examples from fungal plant pathogen genomics and discuss evolutionary processes in pathogenic fungi in the context of molecular evolution, population genomics and agriculture.

  11. Goal-Driven Context-aware Service Composition

    DEFF Research Database (Denmark)

    Yu, Lian; Glenstrup, Arne John; Zhang, Yang;

    2011-01-01

    Two important aspects are associated with service composition. One is to understand the needs and constraints for a new added-value composite service, and otherwise it would lead to an ad-hoc effort for service composition. The second is to reflect the changes of computing environment...... to the service composition to catch up the on-demand of users. This paper introduces a goal-driven approach to specify the user requirements and demands that guides the service composition, and proposes context awareness to adapt to a dynamically changing environment. Computing contexts, including physical...... context, user profile and computed results, are gathered by various services, and imported into an ontology based a context repository. A Goal Description Language, Context Condition/Effect are designed to describe the dynamic semantics of goal requirements and service capability. A planner is designed...

  12. Mindfulness in cultural context.

    Science.gov (United States)

    Kirmayer, Laurence J

    2015-08-01

    Mindfulness meditation and other techniques drawn from Buddhism have increasingly been integrated into forms of psychotherapeutic intervention. In much of this work, mindfulness is understood as a mode of awareness that is present-centered and nonevaluative. This form of awareness is assumed to have intrinsic value in promoting positive mental health and adaptation by interrupting discursive thoughts that give rise to suffering. However, in the societies where it originated, mindfulness meditation is part of a larger system of Buddhist belief and practice with strong ethical and moral dimensions. Extracting techniques like mindfulness meditation from the social contexts in which they originate may change the nature and effects of the practice. The papers in this issue of Transcultural Psychiatry explore the implications of a cultural and contextual view of mindfulness for continued dialogue between Buddhist thought and psychiatry. This introductory essay considers the meanings of mindfulness meditation in cultural context and the uses of mindfulness as a therapeutic intervention in contemporary psychiatry and psychology.

  13. Context Construction Through Competition

    DEFF Research Database (Denmark)

    Kjær, Poul F.

    2015-01-01

    This article examines the relationship between the evolution of statehood and competition in the European context. To begin with, a particular take on the evolution of modern political power in the state form in Europe is developed. Against this background, the article reconstructs how the instit......This article examines the relationship between the evolution of statehood and competition in the European context. To begin with, a particular take on the evolution of modern political power in the state form in Europe is developed. Against this background, the article reconstructs how...... the institutionalization of competition as a specific type of policy tool has been used by emerging modern states to establish their authority vis-à-vis competing claims to public authority in society. The article, furthermore, engages in an examination of (neo-)corporatist and governance-based attempts both to curb...... and to expand the use of competition as a tool for organizing social processes, and the implications of these attempts for the state of statehood....

  14. Ethical reflection and psychotherapy.

    Science.gov (United States)

    Vyskocilová, Jana; Prasko, Jan

    2013-01-01

    Theories of ethics and ethical reflection may be applied to both theory and practice in psychotherapy. There is a natural affinity between ethics and psychotherapy. Psychotherapy practice is concerned with human problems, dilemmas and emotions related to both one's own and other people's values. Ethics is also concerned with dilemmas in human thinking and with how these dilemmas reflect other individuals' values. Philosophical reflection itself is not a sufficient basis for the ethics of psychotherapy but it may aid in exploring attitudes related to psychotherapy, psychiatry and health care. PubMed, Web of Science and Scopus databases were searched for articles containing the keywords "psychotherapy", "ethics", "therapeutic relationship" and "supervision". The search was conducted by repeating the terms in various combinations without language or time restrictions. Also included were data from monographs cited in reviews. The resulting text is a review with conclusions concerning ethical aspects of psychotherapy. The ability to behave altruistically, sense for justice and reciprocity and mutual help are likely to be genetically determined as dispositions to be later developed by upbringing or to be formed or deformed by upbringing. Early experiences lead to formation of ethical attitudes which are internalized and then applied to both one's own and other people's behavior. Altruistic behavior has a strong impact on an individual's health and its acceptance may positively influence the pathophysiological mechanisms underlying numerous diseases. Ethical theory and reflection, however, may be applied to both theory and practice of psychotherapy in a conscious, targeted and thoughtful manner. In everyday practice, psychotherapists and organizations must necessarily deal with conscious conflicts between therapeutic possibilities, clients' wishes, their own as well as clients' ideas and the real world. Understanding one's own motives in therapy is one of the aims of a

  15. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies. Usi

  16. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2003-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies. Usi

  17. Directed genome engineering for genome optimization.

    Science.gov (United States)

    D'Halluin, Kathleen; Ruiter, Rene

    2013-01-01

    The ability to develop nucleases with tailor-made activities for targeted DNA double-strand break induction at will at any desired position in the genome has been a major breakthrough to make targeted genome optimization feasible in plants. The development of site specific nucleases for precise genome modification has expanded the repertoire of tools for the development and optimization of traits, already including mutation breeding, molecular breeding and transgenesis.Through directed genome engineering technology, the huge amount of information provided by genomics and systems biology can now more effectively be used for the creation of plants with improved or new traits, and for the dissection of gene functions. Although still in an early phase of deployment, its utility has been demonstrated for engineering disease resistance, herbicide tolerance, altered metabolite profiles, and for molecular trait stacking to allow linked transmission of transgenes. In this article, we will briefly review the different approaches for directed genome engineering with the emphasis on double strand break (DSB)-mediated engineering to-wards genome optimization for crop improvement and towards the acceleration of functional genomics.

  18. Genomic Data Commons | Office of Cancer Genomics

    Science.gov (United States)

    The NCI’s Center for Cancer Genomics launches the Genomic Data Commons (GDC), a unified data sharing platform for the cancer research community. The mission of the GDC is to enable data sharing across the entire cancer research community, to ultimately support precision medicine in oncology.

  19. Behavioral Biases in Interpersonal Contexts

    NARCIS (Netherlands)

    N. Liu (Ning)

    2017-01-01

    markdownabstractThis thesis presents evidence suggesting that the same types of biases in individual decision making under uncertainty pertain in interpersonal contexts. The chapters above demonstrate in specific contexts how specific interpersonal factors attenuate, amplify, or replicate these bias

  20. The Commercialization of Genomic Research in Canada

    Science.gov (United States)

    Joly, Yann; Caulfield, Timothy; Knoppers, Bartha M.; Harmsen, Eef; Pastinen, Tomi

    2010-01-01

    The commercialization of academic research has been promoted by North American policy makers for over 30 years as a means of increasing university financing and to ensure that promising research would eventually find its way to the marketplace. The following issues paper constitutes a reflection on the impact of the Canadian commercialization framework on academic research in the field of genomics. It was written following two workshops and two independent studies organized by academic groups in Quebec (Centre of Genomics and Policy) and Alberta (Health Law Institute). The full sets of recommendations are available upon request to the authors. PMID:22043221

  1. Reflective Inverse Diffusion

    Directory of Open Access Journals (Sweden)

    Kenneth Burgi

    2016-11-01

    Full Text Available Phase front modulation was previously used to refocus light after transmission through scattering media. This process has been adapted here to work in reflection. A liquid crystal spatial light modulator is used to conjugate the phase scattering properties of diffuse reflectors to produce a converging phase front just after reflection. The resultant focused spot had intensity enhancement values between 13 and 122 depending on the type of reflector. The intensity enhancement of more specular materials was greater in the specular region, while diffuse reflector materials achieved a greater enhancement in non-specular regions, facilitating non-mechanical steering of the focused spot. Scalar wave optics modeling corroborates the experimental results.

  2. The Human Genome Project, and recent advances in personalized genomics

    Directory of Open Access Journals (Sweden)

    Wilson BJ

    2015-02-01

    Full Text Available Brenda J Wilson, Stuart G Nicholls Department of Epidemiology and Community Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada Abstract: The language of “personalized medicine” and “personal genomics” has now entered the common lexicon. The idea of personalized medicine is the integration of genomic risk assessment alongside other clinical investigations. Consistent with this approach, testing is delivered by health care professionals who are not medical geneticists, and where results represent risks, as opposed to clinical diagnosis of disease, to be interpreted alongside the entirety of a patient's health and medical data. In this review we consider the evidence concerning the application of such personalized genomics within the context of population screening, and potential implications that arise from this. We highlight two general approaches which illustrate potential uses of genomic information in screening. The first is a narrowly targeted approach in which genetic profiling is linked with standard population-based screening for diseases; the second is a broader targeting of variants associated with multiple single gene disorders, performed opportunistically on patients being investigated for unrelated conditions. In doing so we consider the organization and evaluation of tests and services, the challenge of interpretation with less targeted testing, professional confidence, barriers in practice, and education needs. We conclude by discussing several issues pertinent to health policy, namely: avoiding the conflation of genetics with biological determinism, resisting the “technological imperative”, due consideration of the organization of screening services, the need for professional education, as well as informed decision making and public understanding. Keywords: genomics, personalized medicine, ethics, population health, evidence, education

  3. Clinical linguistics: conversational reflections.

    Science.gov (United States)

    Crystal, David

    2013-04-01

    This is a report of the main points I made in an informal "conversation" with Paul Fletcher and the audience at the 14th ICPLA conference in Cork. The observations arose randomly, as part of an unstructured 1-h Q&A, so they do not provide a systematic account of the subject, but simply reflect the issues which were raised by the conference participants during that time.

  4. Ubuntu feminism: Tentative reflections

    OpenAIRE

    Drucilla Cornell; Karin van Marle

    2015-01-01

    The starting-point for the article is to provide a brief background on the Ubuntu Project that Prof. Drucilla Cornell convened in 2003; most notably the interviews conducted in Khayamandi, the support of a sewing collective, and the continued search to launch an Ubuntu Women�s Centre. The article will reflect on some of the philosophical underpinnings of ubuntu, whereafter debates in Western feminism will be revisited. Ubuntu feminism is suggested as a possible response to these types of femi...

  5. Reflections and Interpretations

    DEFF Research Database (Denmark)

    Reflections and Interpretations is an anthology on The Freedom Writers’ methodology. It is an anthology for all those with a professional need for texts explaining, not only how The Freedom Writers’ tools are being used, but also why they work so convincingly well. It is not an anthology of guide...... of guidelines; it is an anthology of explanations based on theory. And it is an anthology written by Freedom Writer Teachers – who else could do it?...

  6. Interface between Context and Theory

    DEFF Research Database (Denmark)

    Chen, Cong; Wang, Daojuan; Zhang, Bin

    2017-01-01

    In this paper, we explores how to consider contextual factors in the development of paradigm theory by focusing on the application and development of agency theory in a cross context. Specifically, the interface between agency theory and context is established from two aspects. On one hand...... and PPC, which shows that the two forms of conflict co-exist in the Chinese context and that the primary or secondary status of either conflict is sensitive to the context....

  7. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  8. Genomic Data Commons launches

    Science.gov (United States)

    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.

  9. Reflection and teaching: a taxonomy

    NARCIS (Netherlands)

    Vos, Henk; Cowan, John

    2009-01-01

    A major problem in teaching reflection is that educational objectives for reflection in terms of student behaviour are lacking. Therefore a taxonomy of reflection has been developed based on Bloom’s taxonomy. Reflective assignments can then be better focused on any chosen educational objectives. The

  10. Parallel context-free languages

    DEFF Research Database (Denmark)

    Skyum, Sven

    1974-01-01

    The relation between the family of context-free languages and the family of parallel context-free languages is examined in this paper. It is proved that the families are incomparable. Finally we prove that the family of languages of finite index is contained in the family of parallel context......-free languages....

  11. Class-Based Context Quality Optimization For Context Management Frameworks

    DEFF Research Database (Denmark)

    Shawky, Ahmed; Olsen, Rasmus Løvenstein; Pedersen, Jens Myrup

    2012-01-01

    delay, packet drop probability, information dynamics and the access strategies taken. QoS classification and system configuration of context management traffic is in this aspect important in order to efficiently balance generated access traffic between network delay, packet loss probability, information......Context-awareness is a key requirement in many of today's networks, services and applications. Context Management systems are in this respect used to provide access to distributed, dynamic context information. The reliability of remotely accessed dynamic context information is challenged by network...... dynamics and reliability requirements to the information from the applications. In this paper we develop a QoS Control network concept for context management systems. The concept includes a soft realtime algorithm for model based context access configuration and QoS class assignment, and allows to put...

  12. Genomics of Sorghum

    OpenAIRE

    PATERSON, ANDREW H

    2008-01-01

    Sorghum (Sorghum bicolor (L.) Moench) is a subject of plant genomics research based on its importance as one of the world's leading cereal crops, a biofuels crop of high and growing importance, a progenitor of one of the world's most noxious weeds, and a botanical model for many tropical grasses with complex genomes. A rich history of genome analysis, culminating in the recent complete sequencing of the genome of a leading inbred, provides a foundation for invigorating progress toward relatin...

  13. Beyond the bounds of orthology: functional inference from metagenomic context.

    Science.gov (United States)

    Vey, Gregory; Moreno-Hagelsieb, Gabriel

    2010-07-01

    The effectiveness of the computational inference of function by genomic context is bounded by the diversity of known microbial genomes. Although metagenomes offer access to previously inaccessible organisms, their fragmentary nature prevents the conventional establishment of orthologous relationships required for reliably predicting functional interactions. We introduce a protocol for the prediction of functional interactions using data sources without information about orthologous relationships. To illustrate this process, we use the Sargasso Sea metagenome to construct a functional interaction network for the Escherichia coli K12 genome. We identify two reliability metrics, target intergenic distance and source interaction count, and apply them to selectively filter the predictions retained to construct the network of functional interactions. The resulting network contains 2297 nodes with 10 072 edges with a positive predictive value of 0.80. The metagenome yielded 8423 functional interactions beyond those found using only the genomic orthologs as a data source. This amounted to a 134% increase in the total number of functional interactions that are predicted by combining the metagenome and the genomic orthologs versus the genomic orthologs alone. In the absence of detectable orthologous relationships it remains feasible to derive a reliable set of predicted functional interactions. This offers a strategy for harnessing other metagenomes and homologs in general. Because metagenomes allow access to previously unreachable microorganisms, this will result in expanding the universe of known functional interactions thus furthering our understanding of functional organization.

  14. Developing and Understanding Intelligent Contexts for Playing and Learning

    DEFF Research Database (Denmark)

    Larsen, Lasse Juel; Helms, Niels Henrik

    2009-01-01

    This short paper outlines experiences and reflections on the research and development project “Octopus” in order to describe and illustrate how intelligent context facilitates and embody learning. The framework is a research and development project where we have tried to work with new kinds of ta...

  15. An Agenda for Designing Natural Interaction in a Museum Context

    DEFF Research Database (Denmark)

    Lund, Morten

    2012-01-01

    and information processing 3) Re-­‐understanding information in terms of presentation, representation, navigation, search & findability 4) Transgression of realities from virtual to real and real to virtual. These themes are in particular relevant to the context of museums as they reflect the dominant direction...

  16. The HFEA in context.

    Science.gov (United States)

    Franklin, Sarah

    2013-04-01

    While the regulatory role of the HFEA, its independence and its shortcomings are debated in the context of a fiscal economic crisis, the larger sociological importance of the Authority may be overlooked. Harder to calculate than its annual budget and more elusive than its technical remit as a licensing body, the cultural value of the HFEA as a historical and symbolic entity that was born out of a pioneering debate unique to the UK must be included in a discussion of its future role. Against its perceived shortcomings as an expensive and outdated quango is the importance of the Authority as a public instrument for enhancing the future of translational bioscience. From this point of view, the HFEA is crucial not only to ensuring the successful realization of a domestic bioscience agenda but also to protecting the international reputation of UK Plc as a best-practice model of publicly supported bioinnovation.

  17. Context effects in games

    Directory of Open Access Journals (Sweden)

    Ivo Vlaev

    2007-12-01

    Full Text Available We report an experiment exploring sequential context effects on strategy choices in one-shot Prisoner's Dilemma (PD game. Rapoport and Chammah (1965 have shown that some PDs are cooperative and lead to high cooperation rate, whereas others are uncooperative. Participants played very cooperative and very uncooperative games, against anonymous partners. The order in which these games were played affected their cooperation rate by producing perceptual contrast, which appeared only between the trials, but not between two separate sequences of games. These findings suggest that people may not have stable perceptions of absolute cooperativeness. Instead, they judge the cooperativeness of each fresh game only in relation to the previous game. The observed effects suggest that the principles underlying judgments about highly abstract magnitudes such as cooperativeness may be similar to principles governing the perception of sensory magnitudes.

  18. Celebrity and contemporary context

    Directory of Open Access Journals (Sweden)

    Paula Guimarães Simões

    2014-12-01

    Full Text Available This paper discusses the hermeneutic power of a celebrity (seen from the concept of event, seeking to understand what it reveals about the contemporary context. Based on this premise, we attempt to recognize some aspects of contemporary social life that emerge from the trajectory of a specific celebrity: the former soccer player Ronaldo Fenômeno. This analysis brings to light the hermeneutic power of Ronaldo, i.e., how his life story reveals characteristics of contemporary social life. Individualism, machismo, emphasis on a heteronormative ideal, shifts in the construction of romantic relationships, and the overlapping spheres of public and private life, are some important aspects of contemporary society revealed by this analysis.

  19. Context Construction through Competition

    DEFF Research Database (Denmark)

    Kjær, Poul F.

    This paper examines the relation between the evolution of statehood and institutionalised competition in the European context. The first half of the paper develops a historical-sociological view on the evolution of modern political power in the state form in Europe while the second half the paper...... reconstructs how the institutionalisation of competition as a specific type of policy tool which has been used by emerging modern states to establish its authority vis-à-vis competing claims to authority. It furthermore engages in an examination of corporatist and governance based attempts to respectively curb...... and expand the use of competition as a tool for organising social processes and the implications of the se attempts for the state of statehood....

  20. Discourse, Ideology and Context

    Directory of Open Access Journals (Sweden)

    Teun Van Dijk

    2003-12-01

    Full Text Available ideologi merupakan sistem kepercayaan, keyakinan dasar; menyangkut gagasan-gagasan, dan representasi sosial tentang sejumlah hal yang dijadikan acuan bersama dalam kelompok. Ia akan terekspresikan dalam struktur wacana dan mengontrol pengetahuan yang dimiliki dan, terdistribusi dalam kelompok. Pemahaman biasa tentang ideologi adalah dengan mengkaji efek ideologi pada bentuk-bentuk wacana dan makna. fdeologi jJositifatau negatiftergantung pada konsekuensinya dalam praktik sosial. Orang membentuk model mental tentang peristitwa yang dipercakapkan dan peristiwa di mana ia berpartisipasi. Model mental adalah memori personal yang bersifat episodik. Dan, orang tidak berada dalam ruang hampa. fa berada dalam sebuah kontkes, yakni situasi subjektifdi mana ia berada atau terlibat. Konteks itu sendiri tidak statis. secara terus-menerus akan direkonstruksi dalam mental para partisipan. Untuk mendeskripsikan wacana, sebagai alat analisis, kategori-kategori kotekstual berikut dapat digunakan: domain, global action, roles, sosial relations, dan context. interpretasi para partisipan dan peneliti yang dihasilkan tak terhindarkan pada bias ideologi tertentu yang dianut, sehingga bersifat subjektif.

  1. THE MUMMY in context

    Directory of Open Access Journals (Sweden)

    Richard Freeman

    2009-06-01

    Full Text Available This article examines the literary and cinematic antecedents of a cinema icon, The Mummy, produced by Universal Pictures in 1932.  It looks at the sources in Victorian and Edwardian literature to see if any of the ideas found their way into the film.  Similarly, the silent cinema is surveyed to see if the 1932 film was a collection of previously filmed stories remoulded.  The context of the Great Depression and its effects on Universal Studios will be shown to have a significant influence on the decision to make the film.  The film itself and its publicity is discussed, followed by its reception at the time, and its significance to writers since.

  2. Generalization as creative and reflective act

    DEFF Research Database (Denmark)

    Tateo, Luca

    2013-01-01

    It is argued that generalization in psychology is a creative, interpretative, and reflective act of thought, by accessing a higher level of abstraction from meaningful events. In the context of clarification of this claim, a fresh look at Lewin’s argumentation about the “Aristotelian” and “Galile...... in psychology can provide a relevant starting point to foster contemporary reflexivity in psychology. Scientific method provides conceptual artifacts, constraints, and norms of sharing that enable this particular type of sense-making process.......” and “Galileian” epistemologies will be useful. Lewin’s ideas illuminate the contemporary debate about individual cases, lawfulness, and theory in psychology. Finally, it is demonstrated how Lewin’s reasoning can still provide the ground for theoretical reflection in psychology. This science is indeed still...

  3. NAVIGATING LIVED EXPERIENCE: REFLECTIONS FROM THE FIELD.

    Directory of Open Access Journals (Sweden)

    Leah Farrall

    2015-09-01

    Full Text Available In this article I use an autoethnographic approach to reflect on my experiences in Egypt—in which I came to live alongside converts to Islam and interact with adherents to militant salafist belief systems, as well as those who had disengaged from them. I outline how I came to have these lived experiences before explaining how they caused me to reexamine my understanding of radicalization and deradicalization in the militant salafist context, and to consider radicalization as a form of conversion.

  4. National Human Genome Research Institute

    Science.gov (United States)

    ... the Director Organization Reports & Publications Español The National Human Genome Research Institute conducts genetic and genomic research, funds ... Landscape Social Media Videos Image Gallery Fact Sheets Human Genome Project Clinical Studies Genomic Careers DNA Day Calendar ...

  5. Personality and social context.

    Science.gov (United States)

    Webster, Mike M; Ward, Ashley J W

    2011-11-01

    There has been considerable interest among biologists in the phenomenon of non-human animal personality in recent years. Consistent variations among individuals in their behavioural responses to ecologically relevant stimuli, often relating to a trade-off between level of risk and reward, have been recorded in a wide variety of species, representing many animal taxa. Research into behavioural variation among individuals has major implications for our understanding of ecological patterns and processes at scales from the level of the individual to the level of the population. Until recently, however, many studies that have considered the broader ecological implications of animal personality have failed to take into account the crucial moderating effect of social context. It is well documented that social processes, such as conformity and facilitation, exert considerable influence on the behaviour of grouping animals and hence that isolated individuals may often behave in a qualitatively as well as quantitatively different manner to those in groups. Recently, a number of studies have begun to address aspects of this gap in our knowledge and have provided vital insights. In this review we examine the state of our knowledge on the relationship between individual personality and sociality. In doing so we consider the influence of the social context on individual personality responses, the interaction between the collective personalities of group members and the expression of those personalities in the individual, and the influence of the personalities of group members on group structure and function. We propose key areas of focus for future studies in order to develop our understanding of this fundamentally important area. © 2010 The Authors. Biological Reviews © 2010 Cambridge Philosophical Society.

  6. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  7. Chicken's Genome Decoded

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ After completing the work on mapping chicken genome sequence and chicken genome variation in early March, 2004, two international research consortiums have made significant progress in reading the maps, shedding new light on the studies into the first bird as well as the first agricultural animal that has its genome sequenced and analyzed in the world.

  8. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribut...

  9. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    2015-01-01

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribut...

  10. Exploration of plant genomes in the FLAGdb++ environment

    Directory of Open Access Journals (Sweden)

    Leplé Jean-Charles

    2011-03-01

    Full Text Available Abstract Background In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. Results The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. Conclusion Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features.

  11. Communication and nursing: a study-abroad student's reflections.

    Science.gov (United States)

    de Oliveira, Anna Karina Martins; Tuohy, Dympna

    Globalisation in the academic context provides the opportunity for sharing knowledge and innovations between institutions in different countries, through the creation of study abroad and academic mobility programmes. For nursing students, studying abroad facilitates the development of cultural sensitivity so that they may care appropriately for an increasingly multicultural patient population in their own countries. This article describes a Brazilian 'study abroad' student nurse's experience of studying a 'communication and therapeutic relationships' module in an Irish university. Johns' model of structured reflection was used to frame, describe and reflect on the experience. This reflection informs 'study abroad' students and their universities about the student experience through a personal account of one such student.

  12. [Genomics and functional genomics in microbiology].

    Science.gov (United States)

    Encarnación-Guevara, Sergio

    2006-01-01

    Functional genomics is changing our understanding of biology and changing our approach to biological research. It brings about concerted, high-throughput genetics with analyses of gene transcripts, proteins, and metabolites to answer the ultimate question posed by all genome-sequencing projects: what is the biological function of each and every gene? Functional genomics is stimulating a change in the research paradigm away from the analysis of single genes, proteins, or metabolites towards the analysis of each of these parameters on a global scale. By identifying and measuring several, if not the entire, molecular group of actors that take part in a given biological process, functional genomics offers the panorama of obtaining a truly holistic representation of life. Functional genomics methods are defined by high-throughput methods which are, not necessarily hypothesis-dependent. They offer insights into mRNA expression, protein expression, protein localization, and protein interactions and may cast light on the flow of information within signaling pathways. At its beginning, biology involved observing nature and experimenting on its isolated parts. Genomic research now generates new types of complex observational data derived from nature. This review describes the tools that are currently being used for functional genomics work and considers the impact that this new discipline on microbiology research.

  13. How to Use the Candida Genome Database.

    Science.gov (United States)

    Skrzypek, Marek S; Binkley, Jonathan; Sherlock, Gavin

    2016-01-01

    Studying Candida biology requires access to genomic sequence data in conjunction with experimental information that provides functional context to genes and proteins. The Candida Genome Database (CGD) integrates functional information about Candida genes and their products with a set of analysis tools that facilitate searching for sets of genes and exploring their biological roles. This chapter describes how the various types of information available at CGD can be searched, retrieved, and analyzed. Starting with the guided tour of the CGD Home page and Locus Summary page, this unit shows how to navigate the various assemblies of the C. albicans genome, how to use Gene Ontology tools to make sense of large-scale data, and how to access the microarray data archived at CGD.

  14. Inferences from Genomic Models in Stratified Populations

    DEFF Research Database (Denmark)

    Janss, Luc; de los Campos, Gustavo; Sheehan, Nuala

    2012-01-01

    Unaccounted population stratification can lead to spurious associations in genome-wide association studies (GWAS) and in this context several methods have been proposed to deal with this problem. An alternative line of research uses whole-genome random regression (WGRR) models that fit all markers...... are unsatisfactory. Here we address this problem and describe a reparameterization of a WGRR model, based on an eigenvalue decomposition, for simultaneous inference of parameters and unobserved population structure. This allows estimation of genomic parameters with and without inclusion of marker......-derived eigenvectors that account for stratification. The method is illustrated with grain yield in wheat typed for 1279 genetic markers, and with height, HDL cholesterol and systolic blood pressure from the British 1958 cohort study typed for 1 million SNP genotypes. Both sets of data show signs of population...

  15. How to use the Candida Genome Database

    Science.gov (United States)

    Skrzypek, Marek S.; Binkley, Jonathan; Sherlock, Gavin

    2016-01-01

    Summary Studying Candida biology requires access to genomic sequence data in conjunction with experimental information that provides functional context to genes and proteins. The Candida Genome Database (CGD) integrates functional information about Candida genes and their products with a set of analysis tools that facilitate searching for sets of genes and exploring their biological roles. This chapter describes how the various types of information available at CGD can be searched, retrieved, and analyzed. Starting with the guided tour of the CGD Home page and Locus Summary page, this unit shows how to navigate the various assemblies of the C. albicans genome, how to use Gene Ontology tools to make sense of large-scale data, and how to access the microarray data archived at CGD. PMID:26519061

  16. Drosophila as a Model for Context-Dependent Tumorigenesis

    OpenAIRE

    2014-01-01

    Drosophila can exhibit classic hallmarks of cancer, such as evasion of apoptosis, sustained proliferation, metastasis, prolonged survival, genome instability, and metabolic reprogramming, when cancer-related genes are perturbed. In the last two decades, studies in flies have identified several tumor suppressor and oncogenes. However, the greatest strength of the fly lies in its ability to model cancer hallmarks in a variety of tissue types, which enables the study of context-dependent tumorig...

  17. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.

    2009-01-01

    . RESULTS: We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide...... a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains...

  18. Effect of reference genome selection on the performance of computational methods for genome-wide protein-protein interaction prediction.

    Directory of Open Access Journals (Sweden)

    Vijaykumar Yogesh Muley

    Full Text Available BACKGROUND: Recent progress in computational methods for predicting physical and functional protein-protein interactions has provided new insights into the complexity of biological processes. Most of these methods assume that functionally interacting proteins are likely to have a shared evolutionary history. This history can be traced out for the protein pairs of a query genome by correlating different evolutionary aspects of their homologs in multiple genomes known as the reference genomes. These methods include phylogenetic profiling, gene neighborhood and co-occurrence of the orthologous protein coding genes in the same cluster or operon. These are collectively known as genomic context methods. On the other hand a method called mirrortree is based on the similarity of phylogenetic trees between two interacting proteins. Comprehensive performance analyses of these methods have been frequently reported in literature. However, very few studies provide insight into the effect of reference genome selection on detection of meaningful protein interactions. METHODS: We analyzed the performance of four methods and their variants to understand the effect of reference genome selection on prediction efficacy. We used six sets of reference genomes, sampled in accordance with phylogenetic diversity and relationship between organisms from 565 bacteria. We used Escherichia coli as a model organism and the gold standard datasets of interacting proteins reported in DIP, EcoCyc and KEGG databases to compare the performance of the prediction methods. CONCLUSIONS: Higher performance for predicting protein-protein interactions was achievable even with 100-150 bacterial genomes out of 565 genomes. Inclusion of archaeal genomes in the reference genome set improves performance. We find that in order to obtain a good performance, it is better to sample few genomes of related genera of prokaryotes from the large number of available genomes. Moreover, such a sampling

  19. Reflections on preventive medicine.

    Science.gov (United States)

    Miettinen, Olli S

    2014-10-01

    Having thought much about medicine in my career-long effort to understand it and the research for its advancement, I have come to views rather different form the now-prevailing ones in respect to what preventive medicine is about; what epidemiology is in relation to preventive medicine; what distinguishes preventive medicine in preventive healthcare at large; the relation of preventive medicine to public health; the concept of health promotion; and also the core principles of preventive medicine. All of these views I set forth in this article, for the readers' critical reflection.

  20. Reflective writing in medical education.

    Science.gov (United States)

    Song, Philip; Stewart, Rosalyn

    2012-01-01

    The teaching of reflection and the use of reflective writing assignments is commonplace in medical school education. There is a preponderance of research in medical education, which appraises and discusses new ways of teaching reflection. Students often complain about having to write about their experience with that patient. This work explores some of the reasoning between the variability of student acceptance of reflection in medical education. The method is based on available literature as well as a personal perspective regarding reflective writing in medical education. Reflection is a skill that requires teaching and practice. It is within the explicit process of teaching reflection in medical education that reflective learners can be developed. Reflection includes the take-home lesson from patient encounters. Its use can help learners become better physicians in terms of medical and humanistic effectiveness and support personal growth.