Pre-processing for noise detection in gene expression classification data

Due to the imprecise nature of biological experiments, biological data is often characterized by the presence of redundant and noisy data. This may be due to errors that occurred during data collection, such as contaminations in laboratorial samples. It is the case of gene expression data, where the equipments and tools currently used frequently produce noisy biological data. Machine Learning algorithms have been successfully used in gene expression data analysis. Although many Machine Learning algorithms can deal with noise, detecting and removing noisy instances from the training data set can help the induction of the target hypothesis. This paper evaluates the use of distance-based pre-processing techniques for noise detection in gene expression data classification problems. This evaluation analyzes the effectiveness of the techniques investigated in removing noisy data, measured by the accuracy obtained by different Machine Learning classifiers over the pre-processed data.

A phylogenetic analysis of Brycon and Henochilus (Characiformes, Characidae, Bryconinae) based on the mitochondrial gene 16S rRNA

The genus Brycon, the largest subunit of the Bryconinae, has 42 valid species distributed from southern Mexico to the La Plata River in Argentina. Henochilus is a monotypic genus, comprising a single species (H. wheatlandii) found in the upper Rio Doce basin. In the present study, partial sequences of the mitochondrial gene 16S were obtained for fifteen species of Brycon and for Henochilus wheatlandii. The results showed that the genus Brycon is paraphyletic, since Henochilus is the sister-group of B. ferox and B. insignis. The most basal species analyzed were the trans-Andean species B. henni, B. petrosus, and B. chagrensis.

Descriptor-and fragment-based QSAR models for a series of Schistosoma mansoni purine nucleoside inhibitors

The enzyme purine nucleoside phosphorylase from Schistosoma mansoni (SmPNP) is an attractive molecular target for the treatment of major parasitic infectious diseases, with special emphasis on its role in the discovery of new drugs against schistosomiasis, a tropical disease that affects millions of people worldwide. In the present work, we have determined the inhibitory potency and developed descriptor- and fragment-based quantitative structure-activity relationships (QSAR) for a series of 9-deazaguanine analogs as inhibitors of SmPNP. Significant statistical parameters (descriptor-based model: r² = 0.79, q² = 0.62, r²pred = 0.52; and fragment-based model: r² = 0.95, q² = 0.81, r²pred = 0.80) were obtained, indicating the potential of the models for untested compounds. The fragment-based model was then used to predict the inhibitory potency of a test set of compounds, and the predicted values are in good agreement with the experimental results

Enzyme kinetics, structural analysis and molecular modeling studies on a series of Schistosoma mansoni PNP inhibitors

The enzyme purine nucleoside phosphorylase from Schistosoma mansoni (SmPNP) is an attractive molecular target for the development of novel drugs against schistosomiasis, a neglected tropical disease that affects about 200 million people worldwide. In the present work, enzyme kinetic studies were carried out in order to determine the potency and mechanism of inhibition of a series of SmPNP inhibitors. In addition to the biochemical investigations, crystallographic and molecular modeling studies revealed important molecular features for binding affinity towards the target enzyme, leading to the development of structure-activity relationships (SAR).

Stress distribution in the cervical region of an upper central incisor in a 3D finite element model

The aim of this study was to evaluate the stress distribution in the cervical region of a sound upper central incisor in two clinical situations, standard and maximum masticatory forces, by means of a 3D model with the highest possible level of fidelity to the anatomic dimensions. Two models with 331,887 linear tetrahedral elements that represent a sound upper central incisor with periodontal ligament, cortical and trabecular bones were loaded at 45º in relation to the tooth's long axis. All structures were considered to be homogeneous and isotropic, with the exception of the enamel (anisotropic). A standard masticatory force (100 N) was simulated on one of the models, while on the other one a maximum masticatory force was simulated (235.9 N). The software used were: PATRAN for pre- and post-processing and Nastran for processing. In the cementoenamel junction area, tensile forces reached 14.7 MPa in the 100 N model, and 40.2 MPa in the 235.9 N model, exceeding the enamel's tensile strength (16.7 MPa). The fact that the stress concentration in the amelodentinal junction exceeded the enamel's tensile strength under simulated conditions of maximum masticatory force suggests the possibility of the occurrence of non-carious cervical lesions such as abfractions.

Sublimação e pulsão de morte: a desfusão pulsional

Com o advento do segundo dualismo pulsional freudiano, surge uma série de mudanças no entendimento da sublimação. Essa passa a se apresentar como a causa por excelência da desfusão das pulsões, o que nos leva a um paradoxo: ao mesmo tempo em que a sublimação é a base da cultura, ela é também causa da destrutividade no seio dessa mesma cultura. A pulsão de morte resultante da desfusão das pulsões, por sua vez, teria consequências tanto em cada indivíduo quanto na cultura como um todo, tal como o que se observa em relação ao primado da imagem na sociedade contemporânea. Este artigo busca discutir alguns dos efeitos da pulsão de morte desfusionada, entendida como resultado da sublimação, principalmente no que tange à sublimação implicada na criação literária.

Some aspects of acetylation of untreated and mercerized sisal cellulose

We report here on some aspects of the acetylation in LiCl/N,N-dimethylacetamide, DMAc, of untreated and mercerized sisal cellulose, hereafter designated as sisal and M-sisal, respectively. Fiber mercerization by NaOH solution has resulted in the following changes: 29.9% decrease in the index of crystallinity; 16.2% decrease in the degree of polymerization and 9.3% increase in α-cellulose content. A light scattering study of solutions of sisal, M-sisal, microcrystalline and cotton celluloses in LiCl/DMAc has shown that they are present as aggregates, with (an apparent) average aggregation numbers of 5.2, 3.2, 9.8, and 35.3, respectively. The presence of these aggregates affects the accessibility of cellulose during its functionalization. A study of the evolution of the degree of substitution, DS, of cellulose acetate as a function of reaction time showed an increase up to 5 h, followed by a decrease at 7 h. Possible reasons for this decrease are discussed. As expected, M-sisal gave a higher DS that its untreated counterpart.

Metabólitos secundários das esponjas Aplysina fistularis e Dysidea sp. e atividade antituberculose da 11-cetofistularina-3

The present investigation reports the isolation of aeroplysinin-2, 2-(3,5-dibromo-4-methoxyphenyl)-N,N,N-trimethyletanamonium, 7,9-dibromo-10-hydroxy-8-methoxy-1-oxa-2-azaspiro[4.5]deca-2,6,8-trien-3-carboxylic acid and its methyl ester, 11-oxoaerothionin, aerothionin, 11-keto-12-hydroxyaerothionin, 11-ketofistularin-3 and fistularin-3 from Aplysina fistularis, as well as of furodysinin lactone and 9α,11α-epoxicholest-7-en-3β,5α,6α,10-tetrol-6-acetate from Dysidea sp. Although the extracts of both sponges displayed antituberculosis activity, only 11-ketofistularin-3 isolated from A. fistularis displayed antimycobacterial activity against Mycobacterium tuberculosis H34Rv, with MIC at 16 μg/mL and SI of 40, a result that reinforce that fistularin-3 derivatives are interesting leads for the development of antituberculosis drugs.

On-line identification of minor flavones from sugarcane juice by LC/UV/MS and post-column derivatization

This work describes the on-line characterization of minor flavones from sugarcane (Saccharum officinarum) juice by high-performance liquid chromatography coupled to diode array UV detection and mass spectrometry (LC/UV/MS) using atmospheric pressure chemical ionization-collision-induced dissociation (APCI-CID-MS/MS) and post-column derivatization using UV shift reagents. HPLC-UV analysis with shift reagents provided information about the substitution pattern in the flavonoid skeleton and, combined with MS data, these techniques allowed for the on-line identification of five "garapa" flavones: luteolin-8-C-glucosyl-7-O-glucuronide; tricin-7-O-neohesperoside-4'-O-rhamnoside; tricin-7-O-methylglucuronate-4'-O-rhamnoside; tricin-7-O-methylglucuronide; swertisin, while four other compounds were partially identified as glycosylflavones. Only swertisin (7-O-methylapigenin-6-C-glucoside) was reported previously in sugarcane molasses.

Solvation simplified

The effects of solvents on chemical phenomena is complex because there are various solute-solvent interaction mechanisms. Solvatochromism refers to the effects of solvents on the spectra of probes. The study of this phenomenon sheds light on the relative importance of the solvation mechanisms. Solvation in pure solvents is quantitatively analyzed in terms of a multi-parameter equation. In binary solvent mixtures, solvation is analyzed by considering the organic solvent, S, water, W, and a 1:1 hydrogen bonded species (S-W). The applications of solvatochromism to understand distinct chemical phenomena, reactivity and swelling of cellulose, is briefly discussed.

Alameda Glette, 463, sede do Curso de Química da Universidade de São Paulo no período 1939-1965

As the foundation of the University of São Paulo completes 75 years, this article describes the history of a mansion at 463 Glette Boulevard, in São Paulo city, where several undergraduate courses of the University's Philosophy, Sciences and Letters Faculty operated until 1969. The first building of the school of Chemistry was erected there, 70 years ago. A brief retrospective of the Department of Chemistry at that place is given. The mansion was torn down by the middle of the 1970s, but it remained as a symbol of the school identity in the memory of all those who studied there.

On the name of the lepidophagous characid fish Roeboexodon guyanensis (Puyo) (Teleostei: Characiformes: Characidae)

The arguments for the usage of the names Gnathoplax, Roeboexodon, R. geryi, and R. guyanensis are revised. Based on the literature and museum specimens, we recommend that the neotype of Exodon guyanensis should be considered valid; that the genus Gnathoplax should be considered an objective junior synonym of Roeboexodon; and that Roeboexodon geryi should be considered an objective junior synonym of Exodonguyanensis.

Butterflies (Lepidoptera, Papilionoidea and Hesperioidea) of the "Baixada Santista" region, coastal São Paulo, southeastern Brazil

Butterflies (Lepidoptera, Papilionoidea and Hesperioidea) of the "Baixada Santista" region, coastal São Paulo, southeastern Brazil. A list with 538 species of butterflies recorded in the Baixada Santista, São Paulo ( SE Brazil) is presented. Standard sampling protocols (i.e. with entomological nets) were followed. Baited traps were installed for fruit feeding species. Data from the literature and entomological collections were also considered in the total estimated species richness. The species richness recorded in the Baixada Santista region represents about 16% of the Brazilian butterfly fauna, and 34% of the known butterfly fauna for the state of São Paulo. The present list contains an appreciably higher number of species in comparison to other lists from similar biomes farther south, such as Blumenau in Santa Catarina, and Maquiné in Rio Grande do Sul.

Mortalidade cardiovascular por sexo e faixa etária em São Paulo, Brasil: 1996 a 1998 e 2003 a 2005

FUNDAMENTO: O conhecimento da evolução da mortalidade cardiovascular é importante para levantar hipóteses sobre a sua ocorrência e subsidiar medidas de prevenção e controle. OBJETIVOS: Comparar a mortalidade pelo conjunto das doenças cardiovasculares e seus principais subgrupos: doença isquêmica do coração e cerebrovasculares (DIC e DCBV), no município de São Paulo, por sexo e idade, de 1996 a 1998 e 2003 a 2005. MÉTODOS: Foram usados dados de óbitos do Programa de Aprimoramento das Informações de Mortalidade para o Município (PROAIM) e estimativas populacionais da Fundação Sistema Estadual de Análise de Dados (SEADE) do Estado de São Paulo. A magnitude na mortalidade e as mudanças entre os triênios foram medidas pela descrição de coeficientes e variação percentual relativa. O modelo de regressão de Poisson foi usado também para estimar a mudança na mortalidade entre os períodos. RESULTADOS: Observou-se redução importante da mortalidade cardiovascular. Os coeficientes aumentam com a idade em ambos os sexos. Também são mais elevados na população masculina, na faixa a partir dos 70 anos. Os coeficientes de mortalidade por DIC são maiores que aqueles por DCBV, tanto nos homens como nas mulheres de 50 anos ou mais. O declínio pelo conjunto das doenças cardiovasculares foi maior em mulheres de 20 a 29 anos (-30%) e em homens de 30 a 39 anos (-26%). CONCLUSÃO: A força da intensidade da mortalidade cardiovascular diminuiu entre 1996 e 1998, a 2003 e 2005. Ainda assim há diferenças entre os grupos. Essa redução pode significar, em parte, um maior acesso aos métodos diagnósticos e terapêuticos.

Epidemiological study on leishmaniasis in an area of environmental tourism and ecotourism, State of Mato Grosso do Sul, 2006-2007

The aims of this study were to carry out a serological survey of canine leishmaniasis and identify the phlebotomine fauna in the urban area of Bonito, Mato Grosso do Sul. The serological survey was conducted on a sample of 303 dogs, by means of the indirect immunofluorescence test. Phlebotomines were captured using automated light traps. The serological survey found that 30% of the dogs were seropositive, both from the center and from all districts of the town. A total of 2,772 specimens of phlebotomines were caught and the species most found was Lutzomyia longipalpis (90.4%), which corroborated its role as the vector of for canine visceral leishmaniasis in the region. Phlebotomines of the species Bichromomyia flaviscutellata (the main vector for Leishmania (Leishmania) amazonensis) and Nyssomyia whitmani (the vector for Leishmania (Viannia) brasiliensis) were also caught. The findings indicate the need for continuous epidemiological surveillance, with attention towards diminishing the vector breeding sites and the transmission of these diseases in that region.