1,721,002 research outputs found
Comparative phylogeography of six Highland Ethiopian passerines in the eastern Afromontane biodiversity hotspot
No full textTopographically complex montane regions in the tropics harbor high biodiversity and drive diversification. Located within the East Africa Biodiversity Hotspot, the Ethiopian Highlands are one such montane region of high species diversity but disproportionately undescribed genetic diversity. Montane habitats of the Ethiopian Highlands are divided by lowland barriers including the Blue Nile Valley (BNV) and Great Rift Valley (GRV). These lowland barriers have shaped phylogeographic patterns in sedentary taxa like frogs and rodents but the relative effects of the GRV and BNV have not been assessed in dispersive taxa such as birds. We used whole genome resequencing data from six codistributed highland songbirds to assess comparative patterns of phylogeographic structure in our focal species and how those compare to patterns in other taxonomic groups. Generally, we found that populations separated by the GRV are more differentiated than populations separated by the BNV, but also that species appeared to respond idiosyncratically. The phylogeographic structure found in these taxa have similarities and differences with previous work in frogs and rodents, but overall, no single pattern is consistent across taxonomic groups. Within taxa, genetic diversity was broadly consistent across localities and was explained by harmonic mean NE through time, although there were noticeable reductions in one population each of two species. Here, we showed that highland topography impacts the diversification of even the most dispersive Ethiopian taxa by quantifying population genetic variation of six avian species in the East Africa Biodiversity Hotspot.Embargo status: Restricted until 06/2024. To request the author grant access, click on the PDF link
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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
Fine-scale spatial variation shape fecal microbiome diversity and composition in black-tailed prairie dogs (Cynomys ludovicianus)
Get PDFHost-associated gut microbiota is important in understanding the coevolution of host-microbe, its causes, and consequences that may help the wildlife population to adapt to its rapid climatic changes. Mammalian gut microbiota composition and diversity may be affected by a variety of factors including geographic variation, seasonal variation in diet, habitat disturbance, environmental conditions, age, and sex. However, there have been few studies that have examined how ecological and environmental factors influence gut microbiota composition in animals' natural environments. In this study, we explore how host habitat, geographical location, and environmental factors affect the fecal microbiota of Cynomys ludovicianus at a small spatial scale. We collected fecal samples from five geographically distinct locations in Texas Panhandle occupying habitats classified as urban and rural areas using high throughput 16S gene amplicon sequencing. The results showed that the microbiota of fecal samples was largely dominated by phylum Bacteroidetes. Fecal microbiome diversity and composition differed significantly across sampling sites and habitats. Prairie dogs inhabiting urban areas showed reduced fecal diversity due to a more homogenous environment and anthropogenic disturbance. Urban prairie dog colonies displayed greater phylogenetic variation than those in rural habitats. Differentially abundant analysis revealed that bacterial species pathogenic to humans and animals were highly abundant in urban areas which indicates that host health and fitness might be negatively affected. The random forest model identified Alistipes shahii as the important species driving the changes in fecal microbiome composition. Despite the effects of habitat and geographic location of the host, we found a strong correlation with environmental factors- the average maximum temperature was the best predictor of prairie dog fecal microbial diversity. Our findings suggest that reduction in alpha diversity in conjunction with greater dispersion in beta diversity could be indicative of declining host health in urban areas which could help determine future conservation efforts. Moreover, several bacterial species pathogenic to humans and other animals detected highly abundant in urban areas may adversely affect host phenotype and fitness.Embargo status: Restricted until 09/2023. To request the author grant access, click on the PDF link to the left
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
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
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
Novel HiC modification to study biofilms in polymicrobial infections
No full textTraditionally, studies performed to evaluate polymicrobial infections have focused on single species which are free floating planktonic cells in in vitro culture, but these microorganisms actually tend to exist in multispecies biofilms during chronic infection. Unlike the planktonic state, biofilms consist of bacteria aggregated in a matrix composed of polysaccharides, proteins, and extracellular DNA (eDNA). In this state, cells may grow and accumulate mutations within the context of interactions between neighboring cells in the biofilm. To understand polymicrobial (biofilm) infections, including the spatial context driving ecological and evolutionary dynamics, a new method is required – one not involving isolation and culturing, but instead involving in situ metagenomics or meta-transcriptomics. This project developed and tested a new method that attempts to solve this problem through modifying an existing next generation sequencing (NGS) technique called HiC, which is based on chromosomal conformation capture. The modification centers on a novel process that involves in situ cell lysis preceding DNA cross-linking in HiC. This will effectively bind chromatin of neighboring cells together prior to ligation and sequencing. Ultimately, uncovering the neighboring cell structure to answer questions on how biofilm spatial context impacts cell populations and microevolution and co-evolution by revealing biofilm micro- geography. Additionally, this project developed a new method to visualize and characterize eDNA in the biofilm matrix to enable, for the first time, the assignment of this DNA to different species. The new approach involved creating florescence in situ hybridization (FISH) probes that bind to short repetitive genomic sequences that are distinct to each species. The goal is to help determine which organisms contribute crucial eDNA that stabilizes the biofilm matrix. Lysis-HiC was performed with varying lysis times and strategies for (1) an artificial polymicrobial community consisting of Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli, and (2) mouse wound biofilm obtained after inoculation with P. aeruginosa and S. aureus. Results for Lysis-HiC produced a large number of high-quality sequencing reads for six samples, but bioinformatic analysis with HiC-Pro software suggested limited success in ligation of chimeric fragments, with a large fraction of invalid pairs consisting of dangling ends, likely due to incomplete dNTPs and biotin incorporation between cross-linked chromatin. Suggested improvements for future include increased lysis, biotin incorporation and ligation times and additional controls to confirm ligation of chimers. Results for repeats FISH showed success of the bioinformatic pipeline, with 8 repeat probes created and tested on three species. Four of these probes were specific and effective for intact cells of the target species, while all eight probes were effective and bound specifically to their target species free DNA. Future improvements will involve different methods to ensure probes penetrate Pseudomonas aeruginosa cell walls to interact with intact cells
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