1,720,969 research outputs found
The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events
Get PDFInternational audienceAbstractBackgroundWater buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types.ResultsThe SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction.ConclusionsAnalysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations
No full textBACKGROUND: An understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution.RESULTS: We compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure.CONCLUSIONS: WGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.<br/
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Three-dimensional regulation: Establishing novel linkages between non-coding genetic variation and target genes
Get PDFIn the human genome, 98% of the DNA is in non-gene coding regions. While these regions do not express genes, a mounting number of studies have shown that they are crucial to the maintenance of chromosome structure and in the regulation of gene expression. Although large epigenomics projects were established to functionally annotate non-coding regions, the comprehensive linkages between these regions and their target genes remain unknown. The human genome folds into hierarchical three-dimensional (3D) structure, bringing distantly regulatory elements into close proximity, leading to the formation of 3D chromatin physical interactions and playing an important role in the complex gene regulation network. Using chromatin interaction information, we can connect functional non-coding regions to their target genes to reveal novel regulation mechanisms. In Chapter 1, we reviewed current existing approaches to prioritise functional interactions from Hi-C data, the state-of-the-art data type used to study chromatin interactions, and categorised them into three classifications, including structuralbased methods, statistical model-based methods and data integration methods. Chapter 2 described the computational procedures of analysing Hi-C datasets, and introduced: HiC-QC, a tool that extracting summary statistics to perform quality control with Hi-C libraires; HiC-interactionmap and integration-tracks plot, tools to offer visualisation for Hi-C data integration. Additionally, aligners BWA and Bowtie2, were compared for their performance of mapping Hi-C data. Using type 1 diabetes (T1D) and regulatory T cells (Treg) as a disease-cell type model, based on data integration of Treg-specific Hi-C interactions and other epigenomics information, Chapter 3 established a filtering workflow called 3DFAACT-SNPs to link genetic variants that are associated with T1D to the loss of immune tolerance in Treg. Using this workflow, we identified 36 SNPs with plausible Treg-specific mechanisms of action contributing to T1D, linking 119 novel interacting regions. We demonstrated that it is possible to prioritise SNPs that contribute to disease based on regulatory function and illustrate the power of using chromatin interactions to connect non-coding SNPs to disease mechanisms. Lastly, Chapters 4 and 5 launch the statistically significant interaction profiling of 51 human cell lines and primary tissues from 173 public Hi-C datasets using a statistical model from MaxHiC, followed by investigating the uniqueness, distancing preference and the associated genes of the cell/tissue-specific interactions. We also identified interaction “hot zones”, regions with chromatin interactions observed across many cells and tissues. Using global and local enrichment analysis and a comparison to frequent interacting regions, we demonstrated the structural and regulatory functionality of the hot zones. We further comprehensively annotated chromatin interactions into 66 interaction classes, cataloguing potentially regulatory functional interactions for different cells and tissues. Finally, we revealed cell/tissue-specific 3D regulatory regions that are enriched with super-enhancers and overlapped with expression quantitative trait loci (eQTLs). Overall, using data integration and statistical models to prioritise functional chromatin interactions, this work produced novel computational tools and pipelines and generated valuable resource for the investigation of genome structure, demonstrating the power of using chromatin interactions to discover novel mechanisms in the genome and revealing novel linkages between noncoding DNA to traits/diseases.Thesis (Ph.D.) -- University of Adelaide, Adelaide Medical School, 202
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