Search results for "Algorithms"
showing 10 items of 1716 documents
MMGBSA As a Tool To Understand the Binding Affinities of Filamin–Peptide Interactions
2013
Filamins (FLN) are large dimeric proteins that cross-link actin and work as important scaffolds in human cells. FLNs consist of an N-terminal actin-binding domain followed by 24 immunoglobulin-like domains (FLN1-24). FLN domains are divided into four subgroups based on their amino acid sequences. One of these subgroups, including domains 4, 9, 12, 17, 19, 21, and 23, shares a similar ligand-binding site between the β strands C and D. Several proteins, such as integrins β2 and β7, glycoprotein Ibα (GPIbα), and migfilin, have been shown to bind to this site. Here, we computationally estimated the binding free energies of filamin A (FLNa) subunits with bound peptides using the molecular mechan…
Machine learning techniques to estimate the degree of binder activity of reclaimed asphalt pavement
2022
Part of this research was funded by the project RTI2018-096224-J-I00 that has been cofounded by the Spanish Ministry of Science and Innovation, inside the National Program for Fostering Excellence in Scientific and Technical Research, National Subprogram of Knowledge Generation, 2018 call, in the framework of the Spanish National Plan for Scientific and Technical Research and Innovation 2017-2020, and by the European Union, through the European Regional Development Fund, with the main objective of Promoting technological development, innovation and quality research. Part of this work was financially supported by the Italian Ministry of University and Research with the research Grant PRIN 20…
IMFLer: A Web Application for Interactive Metabolic Flux Analysis and Visualization.
2021
Increasing genome-wide data in biological sciences and medicine has contributed to the development of a variety of visualization tools. Several automatic, semiautomatic, and manual visualization tools have already been developed. Some even have integrated flux balance analysis (FBA), but in most cases, it depends on separately installed third party software that is proprietary and does not allow customization of its functionality and has many restrictions for easy data distribution and analysis. In this study, we present an interactive metabolic flux analyzer and visualizer (IMFLer)-a static single-page web application that enables the reading and management of metabolic model layout maps, …
Data mining-based statistical analysis of biological data uncovers hidden significance: clustering Hashimoto’s thyroiditis patients based on the resp…
2014
The pathogenesis of Hashimoto's thyroiditis includes autoimmunity involving thyroid antigens, autoantibodies, and possibly cytokines. It is unclear what role plays Hsp60, but our recent data indicate that it may contribute to pathogenesis as an autoantigen. Its role in the induction of cytokine production, pro- or anti-inflammatory, was not elucidated, except that we found that peripheral blood mononucleated cells (PBMC) from patients or from healthy controls did not respond with cytokine production upon stimulation by Hsp60 in vitro with patterns that would differentiate patients from controls with statistical significance. This "negative” outcome appeared when the data were pooled and ana…
Determination of metabolite concentrations in human brain tumour biopsy samples using HR-MAS and ERETIC measurements.
2009
Accurate determination of the concentration of the metabolites contained in intact human biopsies of 10 glioblastoma multiforme samples was achieved using one-dimensional 1H high-resolution magic angle spinning (HR-MAS) NMR combined with ERETIC™ (electronic reference to in vivo concentrations) measurements. The amount of sample used ranged from 6.8 to 12.9 mg. Metabolite concentrations were measured in each sample using two methods: with DSS (2,2-dimethyl-2-silapentane-5-sulfonate sodium salt) as an internal reference and with ERETIC™ as an external electronically generated reference. The ERETIC™ signal was shown to be highly reproducible and did not affect the spectral quality. The concent…
Interactions of pharmaceutical companies with world countries, cancers and rare diseases from Wikipedia network analysis
2019
AbstractUsing the English Wikipedia network of more than 5 million articles we analyze interactions and interlinks between the 34 largest pharmaceutical companies, 195 world countries, 47 rare renal diseases and 37 types of cancer. The recently developed algorithm using a reduced Google matrix (REGOMAX) allows us to take account both of direct Markov transitions between these articles and also of indirect transitions generated by the pathways between them via the global Wikipedia network. This approach therefore provides a compact description of interactions between these articles that allows us to determine the friendship networks between them, as well as the PageRank sensitivity of countr…
Formal verification of a Cooperative Automatic Repeat reQuest MAC protocol
2012
Author's version of an article published in the journal: Computer Standards & Interfaces. Also available from the publisher at: http://dx.doi.org/10.1016/j.csi.2011.12.001 Cooperative communications, in which a relay node helps the source node to deliver its packets to the destination node, are able to obtain significant benefits in terms of transmission reliability, coverage extension and energy efficiency. A Cooperative Automatic Repeat reQuest (C-ARQ) MAC protocol has been recently proposed to exploit cooperative diversity at the MAC layer. in this paper, we validate the integrity and the validity of the C-ARQ protocol using formal methods. The protocol logic is modeled in SDL and implem…
Nonadiabatic transitions between lambda-doubling states in the capture of a diatomic molecule by an ion
2008
The low-energy capture of a dipolar diatomic molecule in an adiabatically isolated electronic state with a good quantum number Hund’s coupling case a by an ion occurs adiabatically with respect to rotational transitions of the diatom. However, the capture dynamics may be nonadiabatic with respect to transitions between the pair of the -doubling states belonging to the same value of the intrinsic angular momentum j. In this work, nonadiabatic transition probabilities are calculated which define the -doubling j-specific capture rate coefficients. It is shown that the transition from linear to quadratic Stark effect in the ion-dipole interaction, which damps the T �1/2 divergence of the captur…
A non-parametric segmentation methodology for oral videocapillaroscopic images
2014
We aim to describe a new non-parametric methodology to support the clinician during the diagnostic process of oral videocapillaroscopy to evaluate peripheral microcirculation. Our methodology, mainly based on wavelet analysis and mathematical morphology to preprocess the images, segments them by minimizing the within-class luminosity variance of both capillaries and background. Experiments were carried out on a set of real microphotographs to validate this approach versus handmade segmentations provided by physicians. By using a leave-one-patient-out approach, we pointed out that our methodology is robust, according to precision-recall criteria (average precision and recall are equal to 0.9…
Measurement of high order Kerr refractive index of major air components
2009
International audience; We measure the instantaneous electronic nonlinear refractive index of N2 , O2 , and Ar at room temperature for a 90 fs and 800 nm laser pulse. Measurements are calibrated by post-pulse molecular alignment through a polarization technique. At low intensity, quadratic coefficients n2 are determined. At higher intensities, a strong negative contribution with a higher nonlinearity appears, which leads to an overall negative nonlinear Kerr refractive index in air above 26 TW/cm2 .