The discriminant power of RNA features for pre-miRNA recognition

Computational discovery of microRNAs (miRNA) is based on pre-determined sets of features from miRNA precursors (pre-miRNA). These feature sets used by current tools for pre-miRNA recognition differ in construction and dimension. Some feature sets are composed of sequence-structure patterns commonly found in pre-miRNAs, while others are a combination of more sophisticated RNA features. Current tools achieve similar predictive performance even though the feature sets used - and their computational cost - differ widely. In this work, we analyze the discriminant power of seven feature sets, which are used in six pre-miRNA prediction tools. The analysis is based on the classification performance achieved with these feature sets for the training algorithms used in these tools. We also evaluate feature discrimination through the F-score and feature importance in the induction of random forests. More diverse feature sets produce classifiers with significantly higher classification performance compared to feature sets composed only of sequence-structure patterns. However, small or non-significant differences were found among the estimated classification performances of classifiers induced using sets with diversification of features, despite the wide differences in their dimension. Based on these results, we applied a feature selection method to reduce the computational cost of computing the feature set, while maintaining discriminant power. We obtained a lower-dimensional feature set, which achieved a sensitivity of 90% and a specificity of 95%. Our feature set achieves a sensitivity and specificity within 0.1% of the maximal values obtained with any feature set while it is 34x faster to compute. Even compared to another feature set, which is the computationally least expensive feature set of those from the literature which perform within 0.1% of the maximal values, it is 34x faster to compute.Comment: Submitted to BMC Bioinformatics in October 25, 2013. The material to reproduce the main results from this paper can be downloaded from http://bioinformatics.rutgers.edu/Static/Software/discriminant.tar.g

Characterization of decavanadate and decaniobate solutions by Raman spectroscopy

The decaniobate ion, (Nb10 = [Nb10O28]6−) being isoelectronic and isostructural with the decavanadate ion (V10 = [V10O28]6−), but chemically and electrochemically more inert, has been useful in advancing the understanding of V10 toxicology and pharmacological activities. In the present study, the solution chemistry of Nb10 and V10 between pH 4 and 12 is studied by Raman spectroscopy. The Raman spectra of V10 show that this vanadate species dominates up to pH 6.45 whereas it remains detectable until pH 8.59, which is an important range for biochemistry. Similarly, Nb10 is present between pH 5.49 and 9.90 and this species remains detectable in solution up to pH 10.80. V10 dissociates at most pH values into smaller tetrahedral vanadate oligomers such as V1 and V2, whereas Nb10 dissociates into Nb6 under mildly (10 > pH > 7.6) or highly alkaline conditions. Solutions of V10 and Nb10 are both kinetically stable under basic pH conditions for at least two weeks and at moderate temperature. The Raman method provides a means of establishing speciation in the difficult niobate system and these findings have important consequences for toxicology activities and pharmacological applications of vanadate and niobate polyoxometalates

White matter abnormalities in the fornix are linked to cognitive performance in SZ but not in BD disorder: An exploratory analysis with DTI deterministic tractography

Background In psychosis, white matter (WM) microstructural changes have been detected previously; however, direct comparisons of findings between bipolar (BD) and schizophrenia (SZ) patients are scarce. In this study, we employed deterministic tractography to reconstruct WM tracts in BD and SZ patients. Methods Diffusion tensor imaging (DTI) data was carried out with n=32 euthymic BD type I patients, n=26 SZ patients and 30 matched healthy controls. Deterministic tractography using multiple indices of diffusion (fractional anisotropy (FA), tract volume (Vol), tract length (Le) and number of tracts (NofT)) were obtained from the fornix, the cingulum, the anterior thalamic radiation, and the corpus callosum bilaterally. Results We showed widespread WM microstructural changes in SZ, and changes in the corpus callosum, the left cingulum and the fornix in BD. Fornix fiber tracking scores were associated with cognitive performance in SZ, and with age and age at disease onset in the BD patient group. Limitations Although the influence of psychopharmacological drugs as biasing variables on morphological alterations has been discussed for SZ and BD, we did not observe a clear influence of drug exposure on our findings. Conclusions These results confirm the assumption that SZ patients have more severe WM changes than BD patients. The findings also suggest a major role of WM changes in the fornix as important fronto-limbic connections in the etiology of cognitive symptoms in SZ, but not in B

TOPOGRAFIA E MORFOLOGIA DAS VÍSCERAS DO PERIQUITO-AUSTRALIANO (Melopsittacus undulatus, SHAW 1805)

Em virtude da escassez de dados referentes à morfologia e topografia das aves em geral, o presente estudo teve como objetivo descrever a topografia e morfologia das vísceras do periquito-australiano (Melopsittacus undulatus), para assim proporcionar um conhecimento mais amplo sobre características específicas dessa espécie. Para a descrição da morfologia e topografia das vísceras foram utilizados dez periquitos, sendo cinco machos e cinco fêmeas. Os animais foram fixados com solução de formaldeído 10%, através de perfusão na musculatura e cavidade visceral. Macroscopicamente, as vísceras do periquito não apresentaram muitas diferenças comparadas a outras espécies de aves domésticas. Microscopicamente, a principal diferença estava na presença de mecanorreceptores (corpúsculos de Pacini) na língua, encontrados pela primeira vez nesta espécie de psitaciforme.  PALAVRAS-CHAVES: Melopsittacus undulatus, morfologia, topografia, vísceras

Identification of hereditary cancer in the general population: development and validation of a screening questionnaire for obtaining the family history of cancer

One of the challenges for Latin American countries is to include in their healthcare systems technologies that can be applied to hereditary cancer detection and management. The aim of the study is to create and validate a questionnaire to identify individuals with possible risk for hereditary cancer predisposition syndromes (HCPS), using different strategies in a Cancer Prevention Service in Brazil. The primary screening questionnaire (PSQ) was developed to identify families at-risk for HCPS. The PSQ was validated using discrimination measures, and the reproducibility was estimated through kappa coefficient. Patients with at least one affirmative answer had the pedigree drawn using three alternative interview approaches: in-person, by telephone, or letter. Validation of these approaches was done. Kappa and intraclass correlation coefficients were used to analyze data’s reproducibility considering the presence of clinical criteria for HCPS. The PSQ was applied to a convenience sample of 20,000 women of which 3121 (15.6%) answered at least one affirmative question and 1938 had their pedigrees drawn. The PSQ showed sensitivity and specificity scores of 94.4% and 75%, respectively, and a kappa of 0.64. The strategies for pedigree drawing had reproducibility coefficients of 0.976 and 0.850 for the telephone and letter approaches, respectively. Pedigree analysis allowed us to identify 465 individuals (24.0%) fulfilling at least one clinical criterion for HCPS. The PSQ fulfills its function, allowing the identification of HCPS at-risk families. The use of alternative screening methods may reduce the number of excluded at-risk individuals/families who live in locations where oncogenetic services are not established.Research supported by Barretos Cancer Hospital. EIP has a grant from FAPESP (FAPESP, SP, Brazil, #2013/24633-2). N Campacci is supported by a PhD fellowship from FAPESP (FAPESP, SP, Brazil, #2015/02444-9).info:eu-repo/semantics/publishedVersio

ZOOTAXA

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Relationship between the amount of AgNORs, proliferative activity and stage of placental development in horses

As Regiões Organizadoras de Nucléolo (NORs - nucleolar organizer regions) são utilizadas para descrever regiões de cromatina coradas por Nitrato de Prata e estão relacionados com a atividade de síntese de RNAr e com a agilidade e rapidez na proliferação celular nos tecidos estudados. O objetivo deste trabalho foi relacionar a quantidade de AgNORs, a atividade proliferativa e o estágio da gestação em equinos, utilizando a coloração de Nitrato de Prata. Os anexos embrionários foram coletados, fixados em solução de formaldeído tamponado 10%, emblocadas em paraplast e submetidos à coloração de Nitrato de Prata. Os grupos foram determinados de acordo com a idade gestacional. A quantidade de NORs encontrada no cório no começo da gestação indica início da atividade celular e na medida em que a gestação avança, a quantidade de NORs aumenta, sugerindo maior atividade de síntese e aumento da sua importância na manutenção do feto. Ao contrário do que ocorre no cório, a quantificação das NORs foram maiores no final da gestação do que no inicio, sugerindo a estabilização destas membranas no final da gestação. A cinta coriônica e o saco vitelino foram encontrados no início da gestação e apresentaram grande quantidade de NORs, sugerindo função de síntese e proliferação no inicio da gestação, visto que suas funções é manutenção do embrião até a formação completa da placenta verdadeira (cório-alantoide). Concluímos que as membranas que se desenvolvem de maneira progressiva de acordo com o crescimento embrionário/fetal (cório, alantoide e âmnio) têm aumento no número de NORs e as membranas que involuem após a formação do embrião/feto (saco vitelino e cinta coriônica) têm um decréscimo neste número, sugerindo a diminuição da atividade proliferativa nestas membranas

Antiproliferative and anti-inflammatory activity from aerial parts of Psychotria cupularis (Rubiaceae) / Atividade antiproliferativa e anti-inflamatória das partes aéreas de Psychotria cupularis (Rubiaceae)

The crude extract and fractions of aerial parts from Psychotria cupularis, collected at Camacan (Brazil), were tested for anti-inflammatory and antiproliferative activity. A phytochemical screening indicated the presence of tannins, anthraquinones, triterpenes, steroids and flavonoids. The crude extract and fractions inhibited the ear oedema in mice between 50.2 to 87.2% and the myeloperoxidase enzyme activity between 51.6 to 97.1%. The butanolic and ethyl acetate fractions was active against glioma, breast, ovary, kidney, colon and leukaemia cell line (IG50 = 4.3 to 16.9 ?g/mL).