Search results for " tool"
showing 10 items of 687 documents
Nanoscale Engineering of Designer Cellulosomes.
2016
Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an…
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…
Automated selection of homologs to track the evolutionary history of proteins
2018
Background The selection of distant homologs of a query protein under study is a usual and useful application of protein sequence databases. Such sets of homologs are often applied to investigate the function of a protein and the degree to which experimental results can be transferred from one organism to another. In particular, a variety of databases facilitates static browsing for orthologs. However, these resources have a limited power when identifying orthologs between taxonomically distant species. In addition, in some situations, for a given query protein, it is advantageous to compare the sets of orthologs from different specific organisms: this recursive step-wise search might give …
ParDRe: faster parallel duplicated reads removal tool for sequencing studies
2016
This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record [insert complete citation information here] is available online at: https://doi.org/10.1093/bioinformatics/btw038 [Abstract] Summary: Current next generation sequencing technologies often generate duplicated or near-duplicated reads that (depending on the application scenario) do not provide any interesting biological information but can increase memory requirements and computational time of downstream analysis. In this work we present ParDRe , a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of S…
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 [...]
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…
Vacuolated PAS-Positive Lymphocytes on Blood Smear: An Easy Screening Tool and a Possible Biomarker for Monitoring Therapeutic Responses in Late Onse…
2018
Background: Primary aim was to investigate the diagnostic value of PAS-positive vacuolated lymphocytes on blood smear in Late Onset Pompe Disease (LOPD) patients and, secondly, to evaluate its potential utility in monitoring treatment effects.Methods: We examined blood smear of 26 LOPD patients. We evaluated 10 treated and 16 untreated LOPD patients. Among the latter group, 7 patients later initiated ERT and were tested again 6 months after start. Blood smear was also sampled from 82 controls and 19 patients with other muscle glycogenoses (MGSDs). PAS staining was used to evaluate: (1) presence of lymphocytes with glycogen-filled vacuoles, (2) quantification of vacuolated lymphocytes.Result…
Relative validity of a short food frequency questionnaire assessing adherence to the Norwegian dietary guidelines among colorectal cancer patients
2018
Background: The Norwegian food-based dietary guidelines (FBDG) aim at reducing the risk of developing chronic diseases and promote overall health. We studied the effect of the Norwegian FBDG in colorectal cancer (CRC) patients. There is a need for a time-efficient dietary assessment tool measuring adherence to these guidelines in patients treated for dietary dependent cancer, such as CRC patients. Objective: To evaluate a new short food frequency questionnaire (NORDIET-FFQ), developed to estimate adherence to the Norwegian FBDG among CRC patients. Design: Eighty-one CRC patients from both study groups in the Norwegian Dietary Guidelines and Colorectal Cancer Survival study, an ongoing dieta…
Visualizing Human Protein‐Protein Interactions and Subcellular Localizations on Cell Images Through CellMap
2020
Visualizing protein data remains a challenging and stimulating task. Useful and intuitive visualization tools may help advance biomolecular and medical research; unintuitive tools may bar important breakthroughs. This protocol describes two use cases for the CellMap (http://cellmap.protein.properties) web tool. The tool allows researchers to visualize human protein-protein interaction data constrained by protein subcellular localizations. In the simplest form, proteins are visualized on cell images that also show protein-protein interactions (PPIs) through lines (edges) connecting the proteins across the compartments. At a glance, this simultaneously highlights spatial constraints that prot…
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…