1,720,961 research outputs found
Molecular markers and bioinformatics in species detection: two case studies in Pelophylax spp. (Amphibia, Ranidae) and in a novel bacterial endosymbiont, in ciliate protista
Get PDFSpecies detection is one of the older problems encountered by science. This detection implicitly needs the identification of several features that are peculiar of a group, or taxa, such that their cumulative presence or absence defines the category of the target. Initially, taxonomies were based on morphological characters, with some limitations as there are species lacking the needed informative features, as prokaryotic or cryptic species. From the discovery of genotype, sequences have proven as powerful features to be used to infer taxonomy and phylogenetic trees. A sample can be affiliated to a taxonomy by finding a homology to an already taxonomically classified sequence present in a public database. However, if the target sequence does not have a match, then a phylogenetic tree constructed together with the found similar sequences can be used to infer their relationships. This type of taxonomy annotation can be challenging as there is not a consensus about how much distant two taxa have to be to be considered of different species.
In this PhD thesis I consider two taxonomically challenging case studies, the first involving a complex of morphologically cryptic interbreeding Anuran species, the second a bacterial endosymbiont of a ciliate protozoa.
The first case is focused on Pelophylax, a genus of morphologically cryptic anuran species that show a form of sexual parasitism, called hybridogenesis, where inter-species mate produces viable offspring. Some species can be identified on a bio-acoustic basis, but the presence of hybrids makes the detection unaffordable. The identification is more precisely performed using mitochondrial DNA (mtDNA) and Short Tandem Repeats (STR) markers. I coupled these two techniques to classify animals sampled in the Po Valley, near Pavia, where two autochthonous taxa can be found together with allochthonous. A correct detection of these species is important to assess the conservation status of the local taxa and the impact of the allochthonous ones.
The second case is focused on the study if a prokaryotic endosymbiont of a ciliate Protista, where morphological traits are virtually useless to determinate the taxonomy. Due to differences between host and symbionts, it is possible to use molecular traits to discern the species, as using 16s rRNA for Bacteria and 18s rRNA for Eukaryotes. However, this approach may only provide species identification, not genomic information, which is needed to get a functional understanding of the symbiotic system, as also of the endosymbiotic species, which may be unknown. With this purpose, both organisms are sequenced together by using Whole Genome Sequencing (WGS) with Next Generation Sequencing (NGS) technologies. However, this procedure allows to obtain portion of the genomes fragmented into different contigs, which than have to be deconvolved to obtain separate genomes. We then decided to develop a fully automated tool, called SeqDex, able to deconvolve host-endosymbiont dataset by coupling partial taxonomic affiliations (homology derived) to composition analysis to predict the affiliations of all the sequences
4
using state of the art machine learning algorithms. The second case study is composed by three Spirostomum samples, which showed evidence of presence of a Neisseriales bacterium inside the ciliate cells. I have used SeqDex to deconvolve this dataset to reconstruct partially the endosymbionts genomes and perform functional analysis to infer their role and the nature of the relationship that bound the hosts and the bacteria
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
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
First report of <em>Bufo bufo</em> (Linnaeus, 1758) from Sardinia (Italy)
Get PDFThe Common toad Bufo bufo (Linneaus, 1758) was found for the first time in Sardinia in 2016 during herpetological surveys. The species appears to be well established in the finding area. Many adults and juveniles, tadpoles at different developmental stages, and eggs have been found during repeated monitoring. In order to infer the geographic origin of the Sardinian population, we amplified two mitochondrial markers (16S, cytb) and compared sequences with those available for the species across its natural range. We also screened samples for the presence of Bd pathogen to assess the risk of infection mediated by the species in the area. Results suggest that Sardinian individuals are genetically close to the Central Italian populations, although they show a unique distinct haplotype. Though the species should be considered allochthonous to the Island, further molecular and ecological data are urgently needed to assess the genetic structure and the possible impact on the local fauna, which is largely composed by endemic taxa. Particularly, possible interactions with other native amphibians like the green toad Bufo balearicus (Boettger, 1880), also present in the area, should be investigated, both in terms of competition for breeding sites and genetic pollution, as these species are already known to hybridize in the wild
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
- …
