1,720,972 research outputs found
Development of RNAcall, a Nextflow-based pipeline for somatic variant calling from RNA-seq data and its application in a multi-omics study on T-Cell Prolymphocytic Leukemia
No full textMulti-omics approaches integrate various biological data layers, including genomics, transcriptomics, and proteomics, to provide a comprehensive understanding of cellular functions and disease mechanisms. Transcriptome data play a pivotal role in multimodal data integration by capturing dynamic gene and non-coding RNAs expression profiles but also somatic variants enabling to disclose different levels of biological information from a single source. To achieve this, RNAcall has been developed, an innovative pipeline designed for the detection of bona fide somatic variants from paired-end Illumina RNA sequencing (RNA-Seq) data employing Nextflow and Docker for efficient workflow management and containerization. RNAcall utilizes a comprehensive approach to variant calling from transcriptomic data by employing STAR in a two-pass mode. It incorporates SplitNCigar to split splice junction reads, uses RNAIndel, an optimized tool for detecting InDels in RNA-Seq data, and annotates variants that occur in editing sites and splicing regions. A systematic benchmarking of filtering parameters was conducted across three different cancer types to optimize the overlap of common variants with those identified from Whole Exome Sequencing (WES) data, regarded as ground truth. Variants located at editing sites, splice junctions and within five bases, as well as those with alleles’ quality issues in RNA-seq data, do not significantly reduce the number of common variants detected by the two methodologies. Their removal enhances the performance metrics of the pipeline, thus categorizing them as spurious variants and suggesting their exclusion from the RNA-call results as a default filter. A comparison of variant allele frequencies (VAF) between WES and RNA-Seq revealed an overestimation of VAF from RNA-Seq, likely attributable to the phenomenon of allele-specific expression. Motivated by the need to elucidate the molecular characteristics of T-cell prolymphocytic leukemia (T-PLL), a rare and aggressive malignancy, a multi-omics study was established. In this study, RNA-seq profiling of 10 T-PLL samples and CD4+ cells from 5 healthy donors allowed us to report gene expression, non coding, antisense and circular RNA expression but also genomic variants identification. T-PLL gene expression dysregulation displayed activation of several oncogenic pathways, in addition to the suppression of healthy T-cellactivities and escape of multiple cell death mechanisms. Interestingly, tumor suppressor lncRNAs (NEAT1, MIAT and LUCAT1) with reduced expression, and several upregulated oncogenic pro-proliferative lncRNAs (FIRRE, TERC, XIST and PVT1) were identified. Our first account of circRNAome dysregulation of T-PLL could open new lines of investigation showing the ectopically expression of oncogenic circRNAs (circPVT1, circFKBP5, circFIRRE) in T-PLL. Furthermore, focusing on five (STAT5B, JAK3, ATM, KMT2C, and ARID1A) genes with validated oncogenic variants, previously detected via RNA-seq variant calling, recurrent in our cohort, we investigated genotype/phenotype relations in T-PLL, using a multiple predictor linear model to define the link between the five driver variants and alteration of gene and circRNA expression profiles. Overall, our pilot study disclosed three different expression profiles linked to the mutational status of the patients: mutations of STAT5B, JAK3, and KMT2C were linked to similar expression patterns, ATM to mild changes, and ARID1A to a peculiar profile. Notable genes whose expression could be altered specifically in link with each of these lesions, may be therapeutic targets and deserve further investigation
Dynamics of cell recruitment and transfection by gene activated matrices: Implications for tissue regeneration
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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
Lichen striatus: a review
No full textIntroduction: Lichen striatus (LS) is an acquired blaschkitis, with typical linear and unilateral distribution. It occurs mainly in children and is self-resolving, yet its etiopathogenesis remains widely unknown. Evidence acquisition: A review of the literature on LS cases was performed using the keyword "lichen striatus" to retrieve all relevant articles through PubMed and Google Scholar. Evidence synthesis: A total of 27 articles describing 440 LS patients were included in the present review. Mean age of patients was 3.8 years; male: female: ratio was 1:1.9. The present review confirms LS as a primarily pediatric condition, mainly affecting females. Dysregulation of the immune system might be involved in its pathogenesis, with cytotoxic T-cells attacking mosaic keratinocytes after loss of immune tolerance. The review confirms LS is mainly diagnosed clinically (80%) based on its clinical characteristics: erythematous (70%) or hypopigmented (24%) papules, distributed along the lines of Blashko. The benignity of this clinical entity is suggested by the rather short duration of disease (9.5 months on average) and by the uncommonness of therapy, adopted in only 20% of cases, and when needed, administered topically. Conclusions: This review examines the complexities of LS but acknowledges limitations in data sources and calls for further research
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