1,720,973 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Full text linkWe 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
Investigation of genetic characteristics of Streptococcus suis Isolates Recovered from Sick and Healthy Nursery Pigs
Full text linkThe aim of this study was to characterize genomic features in S. suis isolates recovered from systemic and non-systemic sites of sick and healthy pigs and their association to S. suis disease. A total of 273 S. suis isolates were subjected to whole-genome sequencing. Twenty-one S. suis serotypes were identified in the collection with serotypes 9 (13.9%) and 2 (8.4%) as the most prevalent, while 19.4% of the isolate remained untypable. Virulence-associated factor (VAF) genes were found to be abundant but there was a higher frequency of VAF genes in systemic (p<0.001) and non-systemic (p<0.001) isolates from sick pigs compared to isolates from healthy pigs. Additionally, 98% of the isolates were found to carry at least one antimicrobial resistance (AMR) gene with tetO and ermB as most the prevalent. Interestingly, several AMR genes and VAF genes were found in mobile genetic elements such as integrative and conjugative elements, and phages.Ontario PorkOntario Ministry of Agriculture, Food and Rural AffairsSwine Innovation PorcCanada First Research Excellence FundFood from Though
Investigating the Plasmid Uptake of Salmonella enterica in the Presence of Gastrointestinal Stressors
No full textThe human gastrointestinal tract has been described as a “mixing pot” for dissemination of genetic elements due to the variety of organisms in the intrinsic gut microbiome and its ability to act as a genetic reservoir. Genes are often transferred via conjugation but few studies to date have examined the frequency of plasmid transfer in the environmental conditions of the gastrointestinal tract. Salmonella enterica carries many different families of plasmids, which have varying transmission dynamics. We observed how S. enterica plasmid transfer dynamics are affected by environmental factors (including pH, bile acids, the presence of a microbiota) consistent with transit through the gastrointestinal (GI) tract. We determined that S. enterica’s response to stress, and S. enterica's ability as a recipient, were strain specific. Furthermore, the majority of S. enterica strains studied were more efficient recipients after an acid-shock.Food from ThoughtUniversity of Guelp
Acidification as an Alternative to Antibiotics in Laying hens: Insights from Experimental and Commercial Studies
No full textThis thesis explores the effects of water and feed acidification, combined with omega-3 supplementation, on gut microbiota, short-chain fatty acid (SCFA) profiles, productivity, and susceptibility to Avian Pathogenic Escherichia coli (APEC) in laying hens. Water acidification reduced fecal microbial diversity and altered cecal gut SCFA profiles, while omega-3 supplementation enhanced fecal gut microbial diversity and increased beneficial SCFAs, such as n-butyric acid. Egg production was highest and most stable in the control group, with acidifiers partially mitigating the decline seen in omega-3-fed hens. Structural egg characteristics remained unaffected across treatments. APEC colonization varied, with higher APEC abundance with acidification than with omega-3 supplementation alone. These findings highlight the potential of acidifiers and omega-3 diets to optimize gut health and productivity while reducing antibiotic reliance. However, targeted strategies are essential to balance pathogen dynamics and performance outcomes
Enrichment of Gammaproteobacteria from metagenomic samples using Readfish adaptive sequencing can be achieved without prior knowledge of target species
No full textGammaproteobacteria contain several key pathogens for both human and animal health. Yet, surveillance strategies for these bacteria and reporting their resistance genes have been costly and time-consuming for metagenomic samples due to their low abundance combined with the high diversity of organisms. In this work, a broad non-specific on-target reference made up of Gammaproteobacteria is used in conjunction with a broad non-specific off-target reference. These references were used to test the effect of reference specificity on the sequencing output and enrichment of Gammaproteobacteria in a ZymoBIOMICS Gut Microbiome standard, as well as dairy cattle manure. We determined that the Readfish software could accommodate a reference library of at least 6 GB without significantly increasing the time to decision. On-target enrichment was at least 13-fold in reads longer than 8 kb compared to the overall relative abundance and resistance genes from on-target reads could be identified in both samples.Canadian Institutes of Health Researc
Statistical Methods for High-Dimensional Complex Data with Application for Microbiome Studies
No full textAdvancements in high-throughput technologies have enabled the generation of modern, large-scale, and multi-dimensional datasets. However, analyzing such complex data poses considerable challenges. As high-dimensional data becomes increasingly prevalent, traditional statistical methods often prove inadequate. The presence of more predictors than observations complicates statistical learning, leading to model inaccuracies and potential generalization issues. This thesis addresses these challenges by focussing on advanced statistical techniques for high-dimensional datasets, with a particular emphasis on microbiome studies. The research provides guidelines for selecting the appropriate models and offers practical solutions for two common scenarios encountered in biological data: repeated measurements and variations in library size encountered in amplicon sequencing. In the first study, COVID-19 data is analyzed to assess sphericity and intra-individual variability in cases where the sample size exceeds the number of variables (n > p). By examining repeated measurements of cytokines, chemokines, and acute-phase proteins in COVID-19 patients, the model aims to predict the course of the disease progression. The second and third studies focus on scenarios where the number of variables exceeds the sample size (n < p), with an emphasis on amplicon sequencing data. Generalized linear mixed models (GLMMs) are applied to 16S rRNA sequencing data to analyze the vaginal microbiome of sows, accounting for repeated measurements and data compositionality. This approach reveals dynamic changes in microbial diversity and taxonomic abundance throughout gestation, and significant associations with gestational age and parity. Additionally, a latent topic model, inspired by natural language processing, is employed to identify sub-communities within the vaginal microbiome. These microbiota clusters are correlated with vaginal discharge and reproductive outcomes in gilts, offering new insights into microbiome-host interactions.
This thesis demonstrates the effectiveness of both traditional and advanced machine learning algorithms in identifying patterns for classification and prediction. It provides comprehensive guidelines for model selection and presents practical tools for managing the complexities of high-dimensional biological data.Natural Sciences and Engineering Research Council of CanadaOntario Por
Understanding the Relationship Between the Tonsil Microbiota and Clinical Streptococcus suis Infection in Nursery Pigs
Full text linkThe objective of this study was to determine if the tonsillar microbiota is different in nursery pigs with Streptococcus suis disease compared with that of healthy pigs. Fifty-six pigs from 9 farms were classified as confirmed cases, probable cases and healthy controls. Illumina MiSeq-sequencing of the 16S V3-V4 hypervariable region was done to assess the microbiota composition and the mothur pipeline was used for clustering and taxonomical assignment. Overall, 453, 600 and 334 different taxa were identified in confirmed cases, probable cases and controls, respectively. The beta diversity differed significantly between the farms (p=0.035). Alpha diversity differed between probable cases and control (p<0.001) and tended to be different between confirmed and probable cases (p=0.088). The inverse Simpson tended to be different between confirmed cases and controls (p=0.083). Phylogenetic analysis demonstrated no differences between the microbiota of nursery pigs with clinical S. suis infection and that of heathy animals.Canada First Research Excellence Fun
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