Search results for "tools"
showing 10 items of 360 documents
miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal
2017
Abstract Hundreds of bioinformatics tools have been developed for MicroRNA (miRNA) investigations including those used for identification, target prediction, structure and expression profile analysis. However, finding the correct tool for a specific application requires the tedious and laborious process of locating, downloading, testing and validating the appropriate tool from a group of nearly a thousand. In order to facilitate this process, we developed a novel database portal named miRToolsGallery. We constructed the portal by manually curating > 950 miRNA analysis tools and resources. In the portal, a query to locate the appropriate tool is expedited by being searchable, filterable and …
FragClust and TestClust, two informatics tools for chemical structure hierarchical clustering analysis applied to lipidomics. The example of Alzheime…
2016
Lipidomic analysis is able to measure simultaneously thousands of compounds belonging to a few lipid classes. In each lipid class, compounds differ only by the acyl radical, ranging between C10:0 (capric acid) and C24:0 (lignoceric acid). Although some metabolites have a peculiar pathological role, more often compounds belonging to a single lipid class exert the same biological effect. Here, we present a lipidomics workflow that extracts the tandem mass spectrometry data from individual files and uses them to group compounds into structurally homogeneous clusters by chemical structure hierarchical clustering analysis (CHCA). The case-to-control peak area ratios of the metabolites are then a…
A novel community driven software for functional enrichment analysis of extracellular vesicles data
2017
Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture "what the community needs in a tool". Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes. Remarkably, with the enthusiastic participation of the community, we were able to implement 90% of the requested feat…
Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes
2018
Modification of SMN2 exon 7 (E7) splicing is a validated therapeutic strategy against spinal muscular atrophy (SMA). However, a target-based approach to identify small-molecule E7 splicing modifiers has not been attempted, which could reveal novel therapies with improved mechanistic insight. Here, we chose as a target the stem-loop RNA structure TSL2, which overlaps with the 5′ splicing site of E7. A small-molecule TSL2-binding compound, homocarbonyltopsentin (PK4C9), was identified that increases E7 splicing to therapeutic levels and rescues downstream molecular alterations in SMA cells. High-resolution NMR combined with molecular modelling revealed that PK4C9 binds to pentaloop conformati…
Exosomal Chaperones and miRNAs in Gliomagenesis: State-of-Art and Theranostics Perspectives
2018
Gliomas have poor prognosis no matter the treatment applied, remaining an unmet clinical need. As background for a substantial change in this situation, this review will focus on the following points: (i) the steady progress in establishing the role of molecular chaperones in carcinogenesis; (ii) the recent advances in the knowledge of miRNAs in regulating gene expression, including genes involved in carcinogenesis and genes encoding chaperones; and (iii) the findings about exosomes and their cargo released by tumor cells. We would like to trigger a discussion about the involvement of exosomal chaperones and miRNAs in gliomagenesis. Chaperones may be either targets for therapy, due to their…
Editorial for the Special Issue “Extracellular Chaperones and Related miRNA as Diagnostic Tools of Chronic Diseases”
2021
Molecular chaperones are a family of proteins that are highly conserved during phylogenesis [...]
Tracking zoonotic pathogens using blood-sucking flies as 'flying syringes'
2017
About 60% of emerging infectious diseases in humans are of zoonotic origin. Their increasing number requires the development of new methods for early detection and monitoring of infectious agents in wildlife. Here, we investigated whether blood meals from hematophagous flies could be used to identify the infectious agents circulating in wild vertebrates. To this aim, 1230 blood-engorged flies were caught in the forests of Gabon. Identified blood meals (30%) were from 20 vertebrate species including mammals, birds and reptiles. Among them, 9% were infected by different extant malaria parasites among which some belonged to known parasite species, others to new parasite species or to parasite …
Field performance of HBsAg rapid diagnostic tests in rural Ethiopia.
2020
Abstract Point-of-care rapid diagnostic tests (POC-RDTs) are widely used to screen and diagnose hepatitis B virus (HBV) infection and are often the only available diagnostic tools in resource-limited settings. The aim of this study was to evaluate the validity of three hepatitis B surface antigen (HBsAg) POC-RDTs (Healgen®, Advanced Quality™ and Determine™) in an area with high prevalence of HBV in eastern Ethiopia. Results were compared with a commercial enzyme linked immunosorbent assay (ELISA) as gold standard. Quantification of HBsAg was performed in false negative samples. A total of 511 subjects were screened, of whom 81 (15.9 %) were HBsAg-positive with the gold standard. All three P…
Integrating risk management tools for regional forest planning: an interactive multiobjective value-at-risk approach
2018
In this paper, we present an approach employing multiobjective optimization to support decision making in forest management planning under risk. The primary objectives are biodiversity and timber cash flow, evaluated from two perspectives: the expected value and the value-at-risk (VaR). In addition, the risk level for both the timber cash flow and biodiversity values are included as objectives. With our approach, we highlight the trade-off between the expected value and the VaR, as well as between the VaRs of the two objectives of interest. We employ an interactive method in which a decision maker iteratively provides preference information to find the most preferred management plan and le…
Discordances in Ascriptions of Agency and Reflectivity in the First Psychotherapy Session
2018
We analyzed the first sessions of nine long-term individual psychotherapies with a model of ten discursive tools of agency ascription and studied discursive discordances, sequences of two talk turns in which the therapeutic dyad was misaligned in terms of how they ascribed agency to the client. We also studied how the clients’ agency self-ascriptions in the turn immediately following the discordances changed from the first turn. Classifying these discordance sequences, eight different types of sequences were found. One, in which the clients’ reflective agency constructions were missed by the therapists, was subjected to a detailed analysis. peerReviewed