Search results for "Bioinformatics"

Analysis of Lipid Experiments (ALEX): A Software Framework for Analysis of High-Resolution Shotgun Lipidomics Data

2013

Global lipidomics analysis across large sample sizes produces high-content datasets that require dedicated software tools supporting lipid identification and quantification, efficient data management and lipidome visualization. Here we present a novel software-based platform for streamlined data processing, management and visualization of shotgun lipidomics data acquired using high-resolution Orbitrap mass spectrometry. The platform features the ALEX framework designed for automated identification and export of lipid species intensity directly from proprietary mass spectral data files, and an auxiliary workflow using database exploration tools for integration of sample information, computat…

An open-source computational and data resource to analyze digital maps of immunopeptidomes

2015

We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the de…

A Knowledge Based Decision Support System for Bioinformatics and System Biology

2011

In this paper, we present a new Decision Support System for Bioinformatics and System Biology issues. Our system is based on a Knowledge base, representing the expertise about the application domain, and a Reasoner. The Reasoner, consulting the Knowledge base and according to the user’s request, is able to suggest one or more strategies in order to resolve the selected problem. Moreover, the system can build, at different abstraction layers, a workflow for the current problem on the basis of the user’s choices, freeing the user from implementation details and assisting him in the correct configuration of the algorithms. Two possible application scenarios will be introduced: the analysis of …

A knowledge-based decision support system in bioinformatics: An application to protein complex extraction

2013

Abstract Background We introduce a Knowledge-based Decision Support System (KDSS) in order to face the Protein Complex Extraction issue. Using a Knowledge Base (KB) coding the expertise about the proposed scenario, our KDSS is able to suggest both strategies and tools, according to the features of input dataset. Our system provides a navigable workflow for the current experiment and furthermore it offers support in the configuration and running of every processing component of that workflow. This last feature makes our system a crossover between classical DSS and Workflow Management Systems. Results We briefly present the KDSS' architecture and basic concepts used in the design of the knowl…

Thromboinflammation and Vascular Dysfunction.

2018

Thromboinflammation and vascular dysfunction are inseparably combined with the innate and the adaptive immune response. While the role of this interplay has gained considerable attention in the arena of atherosclerosis/atherothrombosis and in deep vein thrombosis, its role in other forms of vascular disease and risk factors is currently emerging. In this brief review, we will focus on thromboinflammation with regard to cytokine signalling as well as on the novel role of a vascular coagulation-inflammatory circuit in arterial hypertension.Thrombo-Inflammation und vaskuläre Dysfunktion sind untrennbar mit dem angeborenen und dem erworbenen Immunsystem verbunden. Dieses Zusammenspiel wurde im …

Détection automatique des repères visuels associés à la dépression

2018

Depression is the most prevalent mood disorder worldwide having a significant impact on well-being and functionality, and important personal, family and societal effects. The early and accurate detection of signs related to depression could have many benefits for both clinicians and affected individuals. The present work aimed at developing and clinically testing a methodology able to detect visual signs of depression and support clinician decisions.Several analysis pipelines were implemented, focusing on motion representation algorithms, including Local Curvelet Binary Patterns-Three Orthogonal Planes (LCBP-TOP), Local Curvelet Binary Patterns- Pairwise Orthogonal Planes (LCBP-POP), Landma…

Method and apparatus using selected superparamagnetic labels for rapid quantification of immunochromatographic tests

2009

Mika PA Laitinen1, Jari Salmela2, Leona Gilbert1, Risto Kaivola1, Topi Tikkala2, Christian Oker-Blom1, Jukka Pekola3, Matti Vuento11Department of Biological and Environmental Science; 2Department of Physics, University of Jyväskylä, Jyväskylä, Finland; 3Low Temperature Laboratory, Helsinki University of Technology, Helsinki, FinlandAbstract: A rapid method and instrumentation for quantification of immunochromatographic tests (ICT) are described. The principle and performance of the method was demonstrated by measuring the levels of human chorionic gonadotropin (hCG) present in urine. The test format was a sandwich assay using two distinct monoclonal antib…

Gene therapy for type 1 diabetes: is it ready for the clinic?

1999

This review, in addition to updating the growing list of type 1 diabetes- relevant gene therapies, offers an outline of short-term objectives that can readily be met to move, at least, adenoviral and adeno-associated viral-based protocols into the clinic, first as a means of facilitating islet allografts as well as platforms with which to introduce immunoregulatory transgenes. A wide array of genes have been tested to restore insulin production, to drive the differentiation of insulin-producing progenitors, and to confer immunosuppression in an antigen- and tissue-restricted manner.

Attenuated mucopolysaccharidosis: are you missing this debilitating condition?

2011

Liver fibrosis: Common mechanisms and antifibrotic therapies

2015

Liver fibrosis and in particular cirrhosis have become major endpoints in clinical trials of patients with chronic liver diseases. Here, viral hepatitis, alcoholic and non-alcoholic steatohepatitis have become the major etiologies. We have made great progress in our understanding of the mechanisms and the cell biology of liver fibrosis and have already made the transition from preclinical testing of antifibrotic agents and strategies towards clinical translation. There continues to be an urgent need for specific antifibrotic therapies, despite the advent of highly potent antiviral agents that can even induce regression of advanced fibrosis. This review addresses central mechanisms and cells…