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Epidemiological inference from pathogen genome data
Full text linkThe use of whole genome sequencing in infectious disease diagnostics generated an unprecedented amount and resolution of information. Large-scale sequencing of pathogens requires scalable methods in species identification, outbreak clustering, virulence phenotyping, antimicrobial resistance profiling, and epidemic modeling. This dissertation presents a new approach in defining species membership using a pangenome framework explicitly applied to the whole genome sequences of the genus Hungatella which effectively identified a misclassified reference strain. Genomic epidynamics is a phylogenetic free approach in epidemiological inference, particularly the disease transmission parameter reproductive number (R). This approach offers a scalable process in elucidating heterogeneous transmission of genomic variants of SARS-CoV-2. Genomic epidynamics bridges pathogen population genomics and epidemic modeling. A genome-first approach to antimicrobial resistance definition combines automated machine learning rank resistance genes and phenotypic data thru genomic MICs. This approach was applied to a multidrug-resistant serotype of Salmonella enterica subsp. enterica serovar Dublin (S. Dublin). Machine learning-based approach to genome-wide association study revealed allelic variants of porA in Campylobacter jejuni leading to an abortive phenotype when the organism is invasive from the gut and resides in the reproductive system
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Metatranscriptomic Insights into the Microbiomes of Canine and Feline Struvite Uroliths and Investigation of the Oral–Urolith Axis
Full text linkStruvite urolithiasis remains a significant clinical concern in companion animals, with recurrent cases frequently observed in both dogs and cats. While struvite stones from dogs have long been associated with bacterial urinary tract infections (UTIs), the microbial contribution to struvite formation remains largely uncharacterized. To address this gap, we hypothesized that struvite stones harbor a microbiome that actively contributes to ammonia production via urease activity. To test this, we applied shotgun metatranscriptomics to characterize the transcriptionally active microbial communities within struvite stones from dogs and cats.Stones from dogs harbored a robustly active and complex microbial community with predominantly active taxa being Staphylococcus, Enterococcus, Porphyromonas, and Bacillus. Functional analyses revealed active expression of key pathways involved in ammonia production, derived from microbial metabolism via urease, the arginine deiminase (ADI) pathway, and deamination of nitrogenous substrates. Notably, Staphylococcus actively expressed urease, which accounted for 28.3% of its total ammonia-related gene expression with other metabolic routes being 17.5% (Arginine Deaminase Pathway) and 54.3% (deamination routes). Among the ammonia-producing pathways, deamination emerged as the dominant mechanism across all predominant taxa. Other constituents that enable struvite formation including phosphate mobilization and biofilm formation were actively expressed by multiple taxa. Unexpectedly, Porphyromonas was active in stones in dogs, which prompted the investigation of the oral/stone axis. This analysis found that many organisms were shared between the two sites, suggesting a plausible relationship between the oral cavity and the urinary stone microbiome that warrants further investigation. Together, these findings highlight the functional complexity of the dog stone microbiome and suggest that polymicrobial metabolic activity plays a central role in shaping the biochemical conditions that drive struvite stone formation that in part was derived from organisms commonly associated with the oral cavity.Struvite uroliths from cats have historically been considered sterile due to their propensity to yield negative results on standard aerobic urine cultures. To evaluate this long-standing assumption, we applied metatranscriptomics to examine the activity of the microbiome from these stones. We extended our analysis to compare the stone microbiome with those of both healthy and FCGS-affected oral cavities. Despite negative culture results in some cases, all feline stone samples exhibited robust microbial activity. We found that a complex and active microbiome existed within cat struvite stones that contained a diverse microbial membership. Staphylococcus and Enterococcus dominated the active members of the microbiome; however, a broad range of taxa were observed in the stone microbiome. Importantly, extensive microbial overlap was observed between the stone and oral microbiomes, with the stone community showing greater compositional similarity to that of FCGS-affected individuals than to the microbiome of the healthy cohort. Functional analyses demonstrated active expression of ammonia-generating, phosphate-liberating, and biofilm-formation pathways. Microbial expression of genes associated urease, the ADI pathway, and deamination of nitrogenous substrates, were observed in multiple genera. Urease gene expression occurred exclusively in Staphylococcus and comprised 34.1% of all ammonia-producing pathways expressed by this genus. Again, oral organisms were found in the stone microbiome, including Pasteurella multocida, an organism associated with the oral cavity, was found in the struvite stones. Cat stones were not sterile and contained a very robust and active microbiome that produced ammonia from multiple biochemical routes. As with dogs, the oral/stone axis was observed with healthy and FCGS cats.Collectively, this study found that struvite stones from two different animal species contained a robust microbiome that was active and produces transcripts the transduce ammonia production via multiple routes. These observations challenge the paradigm that struvite uroliths—especially in cats—are sterile and provide evidence that the microbial community is cooperating to produce multiple constituents in struvite formation. Both dog and cat stones harbored polymicrobial communities whose combined metabolic activity was responsive to the local biochemical environment to produce ammonia via multiple routes along with expression of genes needed for phosphate liberation and biofilm formation that collectively provided the substrates and pH needed for struvite formation. Additionally, these results strongly support the existence of an oral–stone microbial axis in both animal species. However, different oral bacteria are important in stones between dogs and cats. This work extends our understanding of microbial contributions to struvite stone formation, underscores the limitations of culture-based diagnostics in detecting relevant organisms, and expands the biochemical routes that can lead to struvite formation beyond urease alone
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
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe 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
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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