62 research outputs found
A genetic approach for building different alphabets for peptide and protein classification
<p>Abstract</p> <p>Background</p> <p>In this paper, it is proposed an optimization approach for producing reduced alphabets for peptide classification, using a Genetic Algorithm. The classification task is performed by a multi-classifier system where each classifier (Linear or Radial Basis function Support Vector Machines) is trained using features extracted by different reduced alphabets. Each alphabet is constructed by a Genetic Algorithm whose objective function is the maximization of the area under the ROC-curve obtained in several classification problems.</p> <p>Results</p> <p>The new approach has been tested in three peptide classification problems: HIV-protease, recognition of T-cell epitopes and prediction of peptides that bind human leukocyte antigens. The tests demonstrate that the idea of training a pool classifiers by reduced alphabets, created using a Genetic Algorithm, allows an improvement over other state-of-the-art feature extraction methods.</p> <p>Conclusion</p> <p>The validity of the novel strategy for creating reduced alphabets is demonstrated by the performance improvement obtained by the proposed approach with respect to other reduced alphabets-based methods in the tested problems.</p
How to find simple and accurate rules for viral protease cleavage specificities
<p>Abstract</p> <p>Background</p> <p>Proteases of human pathogens are becoming increasingly important drug targets, hence it is necessary to understand their substrate specificity and to interpret this knowledge in practically useful ways. New methods are being developed that produce large amounts of cleavage information for individual proteases and some have been applied to extract cleavage rules from data. However, the hitherto proposed methods for extracting rules have been neither easy to understand nor very accurate. To be practically useful, cleavage rules should be accurate, compact, and expressed in an easily understandable way.</p> <p>Results</p> <p>A new method is presented for producing cleavage rules for viral proteases with seemingly complex cleavage profiles. The method is based on orthogonal search-based rule extraction (OSRE) combined with spectral clustering. It is demonstrated on substrate data sets for human immunodeficiency virus type 1 (HIV-1) protease and hepatitis C (HCV) NS3/4A protease, showing excellent prediction performance for both HIV-1 cleavage and HCV NS3/4A cleavage, agreeing with observed HCV genotype differences. New cleavage rules (consensus sequences) are suggested for HIV-1 and HCV NS3/4A cleavages. The practical usability of the method is also demonstrated by using it to predict the location of an internal cleavage site in the HCV NS3 protease and to correct the location of a previously reported internal cleavage site in the HCV NS3 protease. The method is fast to converge and yields accurate rules, on par with previous results for HIV-1 protease and better than previous state-of-the-art for HCV NS3/4A protease. Moreover, the rules are fewer and simpler than previously obtained with rule extraction methods.</p> <p>Conclusion</p> <p>A rule extraction methodology by searching for multivariate low-order predicates yields results that significantly outperform existing rule bases on out-of-sample data, but are more transparent to expert users. The approach yields rules that are easy to use and useful for interpreting experimental data.</p
PMeS: Prediction of Methylation Sites Based on Enhanced Feature Encoding Scheme
Protein methylation is predominantly found on lysine and arginine residues, and carries many important biological functions, including gene regulation and signal transduction. Given their important involvement in gene expression, protein methylation and their regulatory enzymes are implicated in a variety of human disease states such as cancer, coronary heart disease and neurodegenerative disorders. Thus, identification of methylation sites can be very helpful for the drug designs of various related diseases. In this study, we developed a method called PMeS to improve the prediction of protein methylation sites based on an enhanced feature encoding scheme and support vector machine. The enhanced feature encoding scheme was composed of the sparse property coding, normalized van der Waals volume, position weight amino acid composition and accessible surface area. The PMeS achieved a promising performance with a sensitivity of 92.45%, a specificity of 93.18%, an accuracy of 92.82% and a Matthew’s correlation coefficient of 85.69% for arginine as well as a sensitivity of 84.38%, a specificity of 93.94%, an accuracy of 89.16% and a Matthew’s correlation coefficient of 78.68% for lysine in 10-fold cross validation. Compared with other existing methods, the PMeS provides better predictive performance and greater robustness. It can be anticipated that the PMeS might be useful to guide future experiments needed to identify potential methylation sites in proteins of interest. The online service is available at http://bioinfo.ncu.edu.cn/inquiries_PMeS.aspx
Magnetism in Dense Quark Matter
We review the mechanisms via which an external magnetic field can affect the
ground state of cold and dense quark matter. In the absence of a magnetic
field, at asymptotically high densities, cold quark matter is in the
Color-Flavor-Locked (CFL) phase of color superconductivity characterized by
three scales: the superconducting gap, the gluon Meissner mass, and the
baryonic chemical potential. When an applied magnetic field becomes comparable
with each of these scales, new phases and/or condensates may emerge. They
include the magnetic CFL (MCFL) phase that becomes relevant for fields of the
order of the gap scale; the paramagnetic CFL, important when the field is of
the order of the Meissner mass, and a spin-one condensate associated to the
magnetic moment of the Cooper pairs, significant at fields of the order of the
chemical potential. We discuss the equation of state (EoS) of MCFL matter for a
large range of field values and consider possible applications of the magnetic
effects on dense quark matter to the astrophysics of compact stars.Comment: To appear in Lect. Notes Phys. "Strongly interacting matter in
magnetic fields" (Springer), edited by D. Kharzeev, K. Landsteiner, A.
Schmitt, H.-U. Ye
Matter in Strong Magnetic Fields
The properties of matter are significantly modified by strong magnetic
fields, Gauss (), as are typically
found on the surfaces of neutron stars. In such strong magnetic fields, the
Coulomb force on an electron acts as a small perturbation compared to the
magnetic force. The strong field condition can also be mimicked in laboratory
semiconductors. Because of the strong magnetic confinement of electrons
perpendicular to the field, atoms attain a much greater binding energy compared
to the zero-field case, and various other bound states become possible,
including molecular chains and three-dimensional condensed matter. This article
reviews the electronic structure of atoms, molecules and bulk matter, as well
as the thermodynamic properties of dense plasma, in strong magnetic fields,
. The focus is on the basic physical pictures and
approximate scaling relations, although various theoretical approaches and
numerical results are also discussed. For the neutron star surface composed of
light elements such as hydrogen or helium, the outermost layer constitutes a
nondegenerate, partially ionized Coulomb plasma if , and may be in
the form of a condensed liquid if the magnetic field is stronger (and
temperature K). For the iron surface, the outermost layer of the
neutron star can be in a gaseous or a condensed phase depending on the cohesive
property of the iron condensate.Comment: 45 pages with 9 figures. Many small additions/changes. Accepted for
publication in Rev. Mod. Phy
The European language technology landscape in 2020 : language-centric and human-centric AI for cross-cultural communication in multilingual Europe
Multilingualism is a cultural cornerstone of Europe and firmly anchored in the European treaties including full language equality. However, language barriers impacting business, cross-lingual and cross-cultural communication are still omnipresent. Language Technologies (LTs) are a powerful means to break down these barriers. While the last decade has seen various initiatives that created a multitude of approaches and technologies tailored to Europe’s specific needs, there is still an immense level of fragmentation. At the same time, AI has become an increasingly important concept in the European Information and Communication Technology area. For a few years now, AI – including many opportunities, synergies but also misconceptions – has been overshadowing every other topic. We present an overview of the European LT landscape, describing funding programmes, activities, actions and challenges in the different countries with regard to LT, including the current state of play in industry and the LT market. We present a brief overview of the main LT-related activities on the EU level in the last ten years and develop strategic guidance with regard to four key dimensions
Relatório de estágio em farmácia comunitária
Relatório de estágio realizado no âmbito do Mestrado Integrado em Ciências Farmacêuticas, apresentado à Faculdade de Farmácia da Universidade de Coimbr
Extracting statistical parameters of extreme precipitation from a NWP model
Precipitation simulations on an 8×8 km grid using the PSU/NCAR Mesoscale Model MM5 are used to estimate the M5 and Ci statistical parameters in order to support the M5 map used for flood estimates by Icelandic engineers. It is known a priori that especially wind anomalies occur on a considerably smaller scale than 8 km. The simulation period used is 1962–2005 and 73 meteorological stations have records long enough in this period to provide a validation data set. Of these only one station is in the central highlands, so the highland values of the existing M5 map are estimates. A comparison between the simulated values and values based on station observations set shows an M5 average difference (observed-simulated) of −5 mm/24 h with a standard deviation of 17 mm, 3 outliers excluded. This is within expected limits, computational and observational errors considered. A suggested correction procedure brings these values down to 4mm and 11 mm, respectively
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