Search results for "Information"
showing 10 items of 14916 documents
QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computati…
2017
Background In previous reports, Marrero-Ponce et al. proposed algebraic formalisms for characterizing topological (2D) and chiral (2.5D) molecular features through atom- and bond-based ToMoCoMD-CARDD (acronym for Topological Molecular Computational Design-Computer Aided Rational Drug Design) molecular descriptors. These MDs codify molecular information based on the bilinear, quadratic and linear algebraic forms and the graph-theoretical electronic-density and edge-adjacency matrices in order to consider atom- and bond-based relations, respectively. These MDs have been successfully applied in the screening of chemical compounds of different therapeutic applications ranging from antimalarials…
Identification of control targets in Boolean molecular network models via computational algebra
2015
Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The pot…
Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs
2017
Detecting higher-order epistatic interactions in Genome-Wide Association Studies (GWAS) remains a challenging task in the fields of genetic epidemiology and computer science. A number of algorithms have recently been proposed for epistasis discovery. However, they suffer from a high computational cost since statistical measures have to be evaluated for each possible combination of markers. Hence, many algorithms use additional filtering stages discarding potentially non-interacting markers in order to reduce the overall number of combinations to be examined. Among others, Mutual Information Clustering (MIC) is a common pre-processing filter for grouping markers into partitions using K-Means…
A detailed experimental study of a DNA computer with two endonucleases
2017
Abstract Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro’s group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity – increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effe…
Biomolecular computers with multiple restriction enzymes
2017
Abstract The development of conventional, silicon-based computers has several limitations, including some related to the Heisenberg uncertainty principle and the von Neumann “bottleneck”. Biomolecular computers based on DNA and proteins are largely free of these disadvantages and, along with quantum computers, are reasonable alternatives to their conventional counterparts in some applications. The idea of a DNA computer proposed by Ehud Shapiro’s group at the Weizmann Institute of Science was developed using one restriction enzyme as hardware and DNA fragments (the transition molecules) as software and input/output signals. This computer represented a two-state two-symbol finite automaton t…
Bacterial antisense RNAs are mainly the product of transcriptional noise
2015
Most of the antisense transcripts in bacteria are the product of transcriptional noise derived from spurious promoters.
Pursuing softer urban mobility behaviors through game-based apps
2020
Cities are currently engaged through their urban policies in pushing people towards less environmentally impacting mobility modalities: therefore, cycling and walking are strongly promoted, especially by means of new and wider limited traffic and no-cars zones. In this paper, the effectiveness of the new smartphones and apps-based technologies in modifying the mobility behaviors of citizens towards more sustainable choices has been investigated. Specifically, the potential of a smartphone app, directly involving citizens by means of a game rewarding the most sustainable trips, has been tested on a university commuters' group. These latter, starting from their current mobility situation, wer…
Changes in the international wine market competitiveness
2017
This study offers a contribution to understanding the complexity of the international wine trade analysing the specialisation patterns of 14 among the most important wine world actors in the period 2007â2016, in order to verify if the patterns of comparative advantages for the trade of this countries have experienced significant changes. Using the Lafay index, as a comparative advantage measure, our results reveal deep changes in the global wine market exchange. Our result constitutes a base element for the future development of the competitive scenario and provides some both theoretical and practical implications. In the baseline projection, the maintenance of the competitive position is…
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters
2016
Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data par…
Closed-Locked and Apo-Resting State Structures of the Human α7 Nicotinic Receptor: A Computational Study
2018
International audience; Nicotinic acetylcholine receptors, belonging to the Cys-loop super-family of ligand-gated ion channels (LGICs), are membrane proteins present in neurons and at neuromuscular junctions. They are responsible for signal transmission, and their function is regulated by neurotransmitters, agonists and antagonists drugs. A detailed knowledge of their conformational transition in response to ligand binding is critical to understand the basis of ligand-receptor interaction, in view of new pharmacological approaches to control receptor activity. However, the scarcity of experimentally derived structures of human channels makes this perspective extremely challenging. To contri…