Search results for "soft"

Reactome pathway analysis: a high-performance in-memory approach

2016

Reactome aims to provide bioinformatics tools for visualisation, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education. Pathway analysis methods have a broad range of applications in physiological and biomedical research; one of the main problems, from the analysis methods performance point of view, is the constantly increasing size of the data samples. Here, we present a new high-performance in-memory implementation of the well-established over-representation analysis method. To achieve the target, the over-representation analysis method is divided in four different steps and, for each of them, specific data st…

2015

The University of Minnesota Biocatalysis/Biodegradation Database and Pathway Prediction System (UM-BBD/PPS) has been a unique resource covering microbial biotransformation pathways of primarily xenobiotic chemicals for over 15 years. This paper introduces the successor system, enviPath (The Environmental Contaminant Biotransformation Pathway Resource), which is a complete redesign and reimplementation of UM-BBD/PPS. enviPath uses the database from the UM-BBD/PPS as a basis, extends the use of this database, and allows users to include their own data to support multiple use cases. Relative reasoning is supported for the refinement of predictions and to allow its extensions in terms of previo…

Reactome graph database: Efficient access to complex pathway data

2018

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its qu…

A REST-based framework to support non-invasive and early coeliac disease diagnosis

2019

The health sector has traditionally been one of the early adopters of databases, from the most simple Electronic Health Record (formerly Computer-Based Patient Record) systems in use in general practice, hospitals and intensive care units to big data, multidata based systems used to support diagnosis and care decisions. In this paper we present a framework to support non-invasive and early diagnosis of coeliac disease. The proposed framework makes use of well-known technologies and techniques, both hardware and software, put together in a novel way. The main goals of our framework are: (1) providing users with a reliable and fast repository of a large amount of data; (2) to make such reposi…

Influence of supracrestal tissue attachment thickness on radiographic bone level around dental implants: A systematic review and meta-analysis.

2019

The present systematic review and meta-analysis was carried out to determine the extent to which supracrestal tissue attachment (STA) thickness affects marginal bone loss (MBL) around dental implants. An electronic search was conducted in PubMed (MEDLINE), EMBASE, and complementary sources covering the period up to June 2018. The studies were meta-analyzed based on implant position with respect to the alveolar bone crest (crestal/supracrestal). The MBL values were categorized according to STA width (thick/thin). Of the 1062 eligible titles, nine articles were included in the review. The implants were positioned crestal or supracrestal with respect to the alveolar ridge. The difference betwe…

A framework for data-driven adaptive GUI generation based on DICOM

2018

Computer applications for diagnostic medical imaging provide generally a wide range of tools to support physicians in their daily diagnosis activities. Unfortunately, some functionalities are specialized for specific diseases or imaging modalities, while other ones are useless for the images under investigation. Nevertheless, the corresponding Graphical User Interface (GUI) widgets are still present on the screen reducing the image visualization area. As a consequence, the physician may be affected by cognitive overload and visual stress causing a degradation of performances, mainly due to unuseful widgets. In clinical environments, a GUI must represent a sequence of steps for image investi…

Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding

2017

We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling we additionally perform steered molecular dynamics simulations and find excellen…

Fishing anti-inflammatories from known drugs: In silico repurposing, design, synthesis and biological evaluation of bisacodyl analogues

2017

Herein is described in silico repositioning, design, synthesis, biological evaluation and structure-activity relationship (SAR) of an original class of anti-inflammatory agents based on a polyaromatic pharmacophore structurally related to bisacodyl (BSL) drug used in therapeutic as laxative. We describe the potential of TOMOCOMD-CARDD methods to find out new anti-inflammatory drug-like agents from a diverse series of compounds using the total and local atom based bilinear indices as molecular descriptors. The models obtained were validated by biological studies, identifying BSL as the first anti-inflammatory lead-like using in silico repurposing from commercially available drugs. Several bi…

Drugs Polypharmacology by in Silico Methods: New Opportunities in Drug Discovery

2016

Background Polypharmacology, defined as the modulation of multiple proteins rather than a single target to achieve a desired therapeutic effect, has been gaining increasing attention since 1990s, when industries had to withdraw several drugs due to their adverse effects, leading to permanent injuries or death, with multi-billiondollar legal damages. Therefore, if up to then the "one drug one target" paradigm had seen many researchers interest focused on the identification of selective drugs, with the strong expectation to avoid adverse drug reactions (ADRs), very recently new research strategies resulted more appealing even as attempts to overcome the decline in productivity of the drug dis…

A deeper look into natural sciences with physics-based and data-driven measures

2021

Summary With the development of machine learning in recent years, it is possible to glean much more information from an experimental data set to study matter. In this perspective, we discuss some state-of-the-art data-driven tools to analyze latent effects in data and explain their applicability in natural science, focusing on two recently introduced, physics-motivated computationally cheap tools—latent entropy and latent dimension. We exemplify their capabilities by applying them on several examples in the natural sciences and show that they reveal so far unobserved features such as, for example, a gradient in a magnetic measurement and a latent network of glymphatic channels from the mous…