1,720,965 research outputs found
The healthy control landscape of the human gut microbiota by using ITS1 DNA metabarcoding data
No full textDisentangling the human gut microbiota composition is a pre-requisite to unveil its involvement in physiological and pathological host states. The human gut microbiota is composed by Prokaryotes (Archaea and Eubacteria), Viruses and small Eukaryotes such as Fungi and Protista. Over the last two decades, analysis of 16S DNA by metabarcoding allowed the convenient and effective investigation of the gut Bacteria populations, unveiling several insights about their compositional and functional features [1]. By contrast, only in recent years the interest in the Eukaryotic microorganisms of the human gut microbiota has begun to emerge. Aim of this work is therefore to deepen the knowledge about the Eukaryotic community of the gut microbiota, with a particular focus on mycobiota, exploiting the metabarcoding data of healthy control samples in publicly available NCBI BioProjects. For this investigation the (Internal Transcribed Spacer) ITS1 DNA barcode was selected because of its superior reliability in comparison with ITS2 [2]. Then, a compositional profile was obtained. Also, a focus about KEGG [3] pathways potentially associated with investigated microbiota was performed
kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes
No full textThe advent of high-throughput sequencing (HTS) technologies unlocked the complexity of the microbial world through the development of metagenomics, which now provides an unprecedented and comprehensive overview of its taxonomic and functional contribution in a huge variety of macro- and micro-ecosystems. In particular, shotgun metagenomics allows the reconstruction of microbial genomes, through the assembly of reads into MAGs (metagenome-assembled genomes). In fact, MAGs represent an information-rich proxy for inferring the taxonomic composition and the functional contribution of microbiomes, even if the relevant analytical approaches are not trivial and still improvable. In this regard, tools like CAMITAX and GTDBtk have implemented complex approaches, relying on marker gene identification and sequence alignments, requiring a large processing time. With the aim of deploying an effective tool for fast and reliable MAG taxonomic classification, we present here kMetaShot, a taxonomy classifier based on k-mer/minimizer counting. We benchmarked kMetaShot against CAMITAX and GTDBtk by using both in silico and real mock communities and demonstrated how, while implementing a fast and concise algorithm, it outperforms the other tools in terms of classification accuracy. Additionally, kMetaShot is an easy-to-install and easy-to-use bioinformatic tool that is also suitable for researchers with few command-line skills. It is available and documented at https://github.com/gdefazio/kMetaShot
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
Exome sequencing data management and variant filtering in azoospermic and testicular germ cell tumor patients
No full textNon-obstructive azoospermia (NOA) and Testicular Germ Cell Tumors (TGCT) are pathological conditions affecting men in their reproductive age. NOA is the absence of spermatozoa in the ejaculate. The etiology of NOA remains unknown in about 40% of cases and it is likely that yet unknown genetic factors are playing a major role [1]. In the literature, an increased susceptibility of NOA subjects to develop TGCT and other malignant tumors has been reported [2]. With the advent of high throughput sequencing platforms the exome analysis of these patients may allow the identification of pathogenic variants in genes implicated in NOA and TGCT [3]. However, the large amount of data generated by variant calling algorithms can make variant filtering and prioritization a difficult and time-consuming task particularly in case of manual management. To address this issue an automated procedure has been proposed
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
Treatment with antidepressant drugs and hyponatremia: a network meta-analysis
No full textObjective: To evaluate the risk of hyponatremia during therapy with antidepressant drugs, in particular by investigating whether there is a different risk profile depending on the class or single active principles. Methods: A meta-analysis was performed including all studies in which the risk of hyponatremia in subjects with or without antidepressant treatment was assessed. An extensive Medline, Embase and Cochrane search was performed, to retrieve all studies published up to February 5th 2024, using the following words: hyponatremia and antidepressant. Results: Of 409 retrieved articles, 10 studies satisfied the inclusion criteria encompassing a total of 1,026,870 patients with 89,403 hyponatremic subjects. Treatments with selective serotonin reuptake inhibitors (OR = 3.31 [2.41;4.56], p < 0.01), serotonin-noradrenaline reuptake inhibitors (OR = 5.79 [1.27;26.49], p = 0.02) and tricyclic antidepressants (OR = 3.01 [1.27;7.14], p = 0.01) were found to be significantly associated with an increased risk of hyponatremia, whereas treatment with noradrenaline and specific serotonergic antidepressants was not. A network meta-analysis indicated that treatments with venlafaxine (OR = 5.99 [2.39;14.99], p < 0.01), paroxetine (OR = 4.93 [2.01;12.12], p < 0.01), sertraline (OR = 4.15 [1.98;8.70], p < 0.01), citalopram (OR = 3.49 [1.54;7.9], p < 0.01), escitalopram (OR = 3.49 [1.49;8.19], p < 0.01), fluoxetine (OR = 3.40 [1.13;10.21], p = 0.03) and mirtazapine (OR = 2.83 [1.16;6.92], p = 0.02) were found to be significantly associated with an increased risk of hyponatremia with a progressively decreasing OR. Clomipramine (OR = 4.50 [0.97;20.93], p = 0.05) also showed a trend towards a greater risk of hyponatremia. Otherwise, treatments with fluvoxamine, imipramine, maprotiline, amitriptyline and mianserin were not associated with an increased risk of hyponatremia. Conclusions: These data appear useful on clinical grounds, in order to increase the awareness regarding the possibility that antidepressants induce hyponatremia and to encourage regular serum sodium monitoring
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
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