Automatic classification of enzyme family in protein annotation

Most of the tasks in genome annotation can be at least partially automated. Since this annotation is time-consuming, facilitating some parts of the process - thus freeing the specialist to carry out more valuable tasks - has been the motivation of many tools and annotation environments. In particular, annotation of protein function can benefit from knowledge about enzymatic processes. The use of sequence homology alone is not a good approach to derive this knowledge when there are only a few homologues of the sequence to be annotated. The alternative is to use motifs. This paper uses a symbolic machine learning approach to derive rules for the classification of enzymes according to the Enzyme Commission (EC). Our results show that, for the top class, the average global classification error is 3.13%. Our technique also produces a set of rules relating structural to functional information, which is important to understand the protein tridimensional structure and determine its biological function. © 2009 Springer Berlin Heidelberg.

Classification of intact fresh plums according to sweetness using time-domain nuclear magnetic resonance and chemometrics

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Land cover classification of Lago Grande de Curuai floodplain (Amazon, Brazil) using multi-sensor and image fusion techniques

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Automated system of seedling image analysis (SVIS) and electrical conductivity to assess sun hemp seed vigor

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Environmental Fate of Neonicotinoids and Classification of Their Potential Risks to Hypogean, Epygean, and Surface Water Ecosystems in Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A classification of Pepper yellow mosaic virus isolates into pathotypes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Self-Organizing Maps as a New Tool for Classification of Plants at Lower Hierarchical Levels

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Detection and classification of voltage disturbances using a Fuzzy-ARTMAP-wavelet network

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Critical analysis of the international classification of headache disorders diagnostic criteria (ICHD I-1988) and (ICHD II-2004), for migraine in children and adolescents

The present study analyzed the (ICHD I-1988) and ( ICHD II-2004) diagnostic criteria in children and adolescents. Our population consisted of 496 patients of the Headache Outpatient Ward for Children and Adolescents retrospectively studied from 1992 to 2002. Individuals were classified according to three diagnostic groups: Intuitive Clinical Diagnosis ( Gold Standard), ICHD I-1988 and ICHD II-2004. They were statistically compared using the variables: Sensitivity ( S), Specificity (Sp), Positive Predictive Value (PPV), Negative Predictive Value (NPV). When ICHD I-1988 was used, the sensitivity of migraine without and with aura was 21% and 27%, respectively, whereas in ICHD II-2004 it changed to 53% and 71% without affecting specificity. As a conclusion, the current classification criteria ( ICHD II-2004) showed greater sensitivity and high specificity for migraine than ICHD I-1988, although it improved migraine diagnosis in children and adolescents, the sensitivity remains poor.

A Brazilian registry of juvenile dermatomyositis: onset features and classification of 189 cases

ObjectiveTo describe onset features, classification and treatment of juvenile dermatomyositis (JDM) and juvenile polymyositis (JPM) from a multicentre registry.MethodsInclusion criteria were onset age lower than 18 years and a diagnosis of any idiopathic inflammatory myopathy (IIM) by attending physician. Bohan & Peter (1975) criteria categorisation was established by a scoring algorithm to define JDM and JPM based oil clinical protocol data.ResultsOf the 189 cases included, 178 were classified as JDM, 9 as JPM (19.8: 1) and 2 did not fit the criteria; 6.9% had features of chronic arthritis and connective tissue disease overlap. Diagnosis classification agreement occurred in 66.1%. Medial? onset age was 7 years, median follow-up duration was 3.6 years. Malignancy was described in 2 (1.1%) cases. Muscle weakness occurred in 95.8%; heliotrope rash 83.5%; Gottron plaques 83.1%; 92% had at least one abnormal muscle enzyme result. Muscle biopsy performed in 74.6% was abnormal in 91.5% and electromyogram performed in 39.2% resulted abnormal in 93.2%. Logistic regression analysis was done in 66 cases with all parameters assessed and only aldolase resulted significant, as independent variable for definite JDM (OR=5.4, 95%CI 1.2-24.4, p=0.03). Regarding treatment, 97.9% received steroids; 72% had in addition at least one: methotrexate (75.7%), hydroxychloroquine (64.7%), cyclosporine A (20.6%), IV immunoglobulin (20.6%), azathioprine (10.3%) or cyclophosphamide (9.6%). In this series 24.3% developed calcinosis and mortality rate was 4.2%.ConclusionEvaluation of predefined criteria set for a valid diagnosis indicated aldolase as the most important parameter associated with de, methotrexate combination, was the most indicated treatment.

Concordance between macroinvertebrate communities and the typological classification of white and clear-water streams in Western Brazilian Amazonia

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Branch formation in Pulvinularia suecica (Nostocales, Cyanoprokaryota) and considerations on the classification of dichotomously and pseudodichotomously branched genera

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Classification of normal swallowing and oropharyngeal dysphagia using wavelet

Oropharyngeal dysphagia is characterized by any alteration in swallowing dynamics which may lead to malnutrition and aspiration pneumonia. Early diagnosis is crucial for the prognosis of patients with dysphagia, and the best method for swallowing dynamics assessment is swallowing videofluoroscopy, an exam performed with X-rays. Because it exposes patients to radiation, videofluoroscopy should not be performed frequently nor should it be prolonged. This study presents a non-invasive method for the pre-diagnosis of dysphagia based on the analysis of the swallowing acoustics, where the discrete wavelet transform plays an important role to increase sensitivity and specificity in the identification of dysphagic patients. (C) 2008 Elsevier B.V. All rights reserved.

Classification of states in S0(8) proton-neutron pairing model

lsoscalar (T = 0) plus isovector (T = 1) pairing Hamiltonian in LS-coupling. which is important for heavy N = Z nuclei, is solvable in terms of a SO(8) Lie algebra for three special values of the mixing parameter that measures the competition between the T = 0 aid T = 1 pairing. The SO(8) algebra is generated, amongst others, by the S = 1, T = 0 and S = 0, T = 1 pair creation and annihilation operators and corresponding to the three values of the mixing parameter, there are three chains of subalgebras: SO(8) superset of SOST (6) superset of SOS(3) circle times SOT(3), SO(8) superset of [SOS(5) superset of SOS(3)] circle times SOT(3) and SO(8) superset of [SOT(5) superset of SOT(3)] circle times SOS(3). Shell model Lie algebras, with only particle number conserving generators, that are complementary to these three chains of subalgebras are identified and they are used in the classification of states for a given number of nucleons. The classification problem is solved explicitly tor states with SO(8) seniority nu = 0, 1, 2, 3 and 4. Using them, hand structures in isospin space are identified for states with nu = 0, 1, 2 and 3. (c) 2005 Elsevier B.V. All rights reserved.