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 crucifer cultivars based on the life-history of diamondback moth (Plutella xylostella)

We compared different cultivars and hybrids of crucifers in relation to development and life-history of diamondback moth (Plutella xylostella) to classify the plants according to their resistance to the pest. The plants used were Manteiga da Geórgia kale, Bola de Neve cauliflower, Ramoso Piracicaba Precoce broccoli, Chato-de-quintal cabbage, and the hybrid cabbages Midori, TPC668, TPC308, and TPC681. We evaluated performance daily until the pupal stage. Pupae were assessed individually to determine the pupal weight, performance, and pupal period. We determined the sex ratio, fecundity, fertility, and longevity of the emerged adults and calculated their reproductive potential. Cabbage hybrids TPC668, TPC308, and TPC681 do not support the development and reproduction of the diamondback moth. These hybrids show a level of resistance that is similar to that found the commercially available hybrid Midori and cultivar Chato de Quintal, which are known to be resistant to the diamondback moth. This finding implies that the capitata (cabbage) cultivars are the most suitable for planting because they are more resistant to pest than the cultivar's moth, acephala (kale). © 2013 Copyright Taylor and Francis Group, LLC.

Automatic segmentation and classification of human intestinal parasites from microscopy images

Human intestinal parasites constitute a problem in most tropical countries, causing death or physical and mental disorders. Their diagnosis usually relies on the visual analysis of microscopy images, with error rates that may range from moderate to high. The problem has been addressed via computational image analysis, but only for a few species and images free of fecal impurities. In routine, fecal impurities are a real challenge for automatic image analysis. We have circumvented this problem by a method that can segment and classify, from bright field microscopy images with fecal impurities, the 15 most common species of protozoan cysts, helminth eggs, and larvae in Brazil. Our approach exploits ellipse matching and image foresting transform for image segmentation, multiple object descriptors and their optimum combination by genetic programming for object representation, and the optimum-path forest classifier for object recognition. The results indicate that our method is a promising approach toward the fully automation of the enteroparasitosis diagnosis. © 2012 IEEE.

Classification of honeys from Pará State (Amazon region, Brazil) produced by three different species of bees

Vinte e sete amostras de mel, produzidas em dez cidades do Estado do Pará (Região Amazônica, norte do Brasil) por três espécies diferentes de abelhas (Apis mellifera, Melipona fasciculata e Melipona flavoneata), foram analisadas em seus teores de elementos minerais (Al, As, Ba, Be, Bi, Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Na, Ni, Sr e Zn) e alguns parâmetros fisicoquímicos (cor, umidade, densidade, pH, sólidos insolúveis e solúveis totais, cinzas, condutividade elétrica, índice de formol, acidez livre, hidroximetilfurfural, açúcares redutores e totais e sacarose). Os teores minerais foram determinados via espectrometria de emissão atômica por plasma acoplado indutivamente (ICP OES) e as análises dos parâmetros físico-químicos seguiram metodologias oficiais. Os resultados das análises físico-químicas apresentaram-se de acordo com a legislação nacional e internacional, bem como com outros trabalhos similares ao redor do mundo. A análise estatística multivariada (análise por agrupamento hierárquico (HCA) e por componentes principais (PCA)) foi aplicada aos resultados dos teores metálicos e aos parâmetros físico-químicos, sendo possível a separação das amostras de mel conforme a espécie produtora.

Effect of calcium on the structural properties of Ba(1-x)Ca (x) TiO3 particles synthesized by complex polymerization method

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Development of a CAD system for automatic classification of microcalcifications based on FPGA

This paper presents a Computer Aided Diagnosis (CAD) system that automatically classifies microcalcifications detected on digital mammograms into one of the five types proposed by Michele Le Gal, a classification scheme that allows radiologists to determine whether a breast tumor is malignant or not without the need for surgeries. The developed system uses a combination of wavelets and Artificial Neural Networks (ANN) and is executed on an Altera DE2-115 Development Kit, a kit containing a Field-Programmable Gate Array (FPGA) that allows the system to be smaller, cheaper and more energy efficient. Results have shown that the system was able to correctly classify 96.67% of test samples, which can be used as a second opinion by radiologists in breast cancer early diagnosis. (C) 2013 The Authors. Published by Elsevier B.V.

Entanglement universality of two-qubit X-states

We demonstrate that for every two-qubit state there is a X-counterpart, i.e., a corresponding two-qubit X-state of same spectrum and entanglement, as measured by concurrence, negativity or relative entropy of entanglement. By parametrizing the set of two-qubit X-states and a family of unitary transformations that preserve the sparse structure of a two-qubit X-state density matrix, we obtain the parametric form of a unitary transformation that converts arbitrary two-qubit states into their X-counterparts. Moreover, we provide a semi-analytic prescription on how to set the parameters of this unitary transformation in order to preserve concurrence or negativity. We also explicitly construct a set of X-state density matrices, parametrized by their purity and concurrence, whose elements are in one-to-one correspondence with the points of the concurrence versus purity (CP) diagram for generic two-qubit states. (C) 2014 Elsevier Inc. All rights reserved.

Beef quality of young Angus x Nellore cattle supplemented with rumen-protected lipids during rearing and fatting periods

This work evaluated the beef quality parameters of 108 bulls randomly administered to three treatments during rearing in pastures and two treatments during fatting in feedlots, including mineral and rumen-protected lipids. Meat and fat color, cooking yield, shear force, sensorial traits and chemical and fatty acid compositions were evaluated. Generally, the beef quality parameters were not affected by the rumen protected lipids; however, supplementation with rumen-protected lipids during the rearing period yielded darker beef and brighter fat and increased beef tenderness in meat aged for 28 days compared to the meat from animals that received only mineral supplementation. In addition, the percent of meat polyunsaturated fatty acids was negatively affected by the inclusion of protected lipids, yielding 5.58 and 3.72% in animals fed with and without rumen-protected lipids, respectively, during the fatting period. (C) 2014 Elsevier Ltd. All rights reserved.

Classification of Eucalyptus urograndis hybrids under different water availability based on biometric traits

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effect of different periods of preconditioning with saliva on adhesion of C. albicans to a denture base resin by crystal violet staining and XTT assay.

Aim: The role of saliva on Candida adhesion to biomaterials has not been clearly defined. The present study investigates whether different periods of preconditioning with saliva would influence the adhesion of Candida albicans to a denture base resin. Methods: Ninety samples of acrylic resin with smooth surfaces were made and then divided into five groups: one control without saliva, and four experimental groups conditioned in saliva for periods of 30 min, 1, 3, or 12 h. Candida adhesion was evaluated by crystal violet staining and 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-5-([phenylamino] carbonyl)-2H-tetrazolium-hydroxide assay. Results: The one-way analysis of variance revealed that there were no significant differences among the mean number of adherent cells or among the mean absorbance for all groups. No significant correlation was found between the two methods used for assessing Candida albicans adhesion. Conclusion: The different periods of preconditioning with saliva had no significant influence on the adhesion of Candida albicans to the denture base acrylic resin.

Repetitive DNA chromosomal organization in the cricket Cycloptiloides americanus: a case of the unusual X(1)X(2)0 sex chromosome system in Orthoptera

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

Classification of intact açai (Euterpe oleracea Mart.) and jucara (Euterpe edulis Mart) fruits based on dry matter content by means of near infrared spectroscopy

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

Integrable deformations of strings on symmetric spaces

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

The influence of "C-factor" and light activation technique on polymerization contraction forces of resin composite

Objectives: This study evaluated the influence of the cavity configuration factor ("C-Factor") and light activation technique on polymerization contraction forces of a Bis-GMA-based composite resin (Charisma, Heraeus Kulzer). Material and Methods: Three different pairs of steel moving bases were connected to a universal testing machine (Emic DL 500): groups A and B - 2x2 mm (CF=0.33), groups C and D - 3x2 mm (CF=0.66), groups E and F - 6x2 mm (CF=1.5). After adjustment of the height between the pair of bases so that the resin had a volume of 12 mm(3) in all groups, the material was inserted and polymerized by two different methods: pulse delay (100 mW/cm(2) for 5 s, 40 s interval, 600 mW/cm(2) for 20 s) and continuous pulse (600 mW/cm(2) for 20 s). Each configuration was light cured with both techniques. Tensions generated during polymerization were recorded by 120 s. The values were expressed in curves (Force(N) x Time(s)) and averages compared by statistical analysis (ANOVA and Tukey's test, p<0.05). Results: For the 2x2 and 3x2 bases, with a reduced C-Factor, significant differences were found between the light curing methods. For 6x2 base, with high C-Factor, the light curing method did not influence the contraction forces of the composite resin. Conclusions: Pulse delay technique can determine less stress on tooth/restoration interface of adhesive restorations only when a reduced C-Factor is present.