An automatic method for segmentation of fission tracks in epidote crystal photomicrographs

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

Biological and molecular characterisation of Bidens mosaic virus supports its assignment as a member of a distinct species in the genus Potyvirus

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

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.

Automatic visual dictionary generation through optimum-path forest clusteringautomatic visual dictionary generation through optimum-path forest clustering

Image categorization by means of bag of visual words has received increasing attention by the image processing and vision communities in the last years. In these approaches, each image is represented by invariant points of interest which are mapped to a Hilbert Space representing a visual dictionary which aims at comprising the most discriminative features in a set of images. Notwithstanding, the main problem of such approaches is to find a compact and representative dictionary. Finding such representative dictionary automatically with no user intervention is an even more difficult task. In this paper, we propose a method to automatically find such dictionary by employing a recent developed graph-based clustering algorithm called Optimum-Path Forest, which does not make any assumption about the visual dictionary's size and is more efficient and effective than the state-of-the-art techniques used for dictionary generation.

The Automatic Mapping of Princeton WordNet Lexical-Conceptual Relations onto the Brazilian Portuguese WordNet Database

Princeton WordNet (WN.Pr) lexical database has motivated efficient compilations of bulky relational lexicons since its inception in the 1980's. The EuroWordNet project, the first multilingual initiative built upon WN.Pr, opened up ways of building individual wordnets, and interrelating them by means of the so-called Inter-Lingual-Index, an unstructured list of the WN.Pr synsets. Other important initiative, relying on a slightly different method of building multilingual wordnets, is the MultiWordNet project, where the key strategy is building language specific wordnets keeping as much as possible of the semantic relations available in the WN.Pr. This paper, in particular, stresses that the additional advantage of using WN.Pr lexical database as a resource for building wordnets for other languages is to explore possibilities of implementing an automatic procedure to map the WN.Pr conceptual relations as hyponymy, co-hyponymy, troponymy, meronymy, cause, and entailment onto the lexical database of the wordnet under construction, a viable possibility, for those are language-independent relations that hold between lexicalized concepts, not between lexical units. Accordingly, combining methods from both initiatives, this paper presents the ongoing implementation of the WN.Br lexical database and the aforementioned automation procedure illustrated with a sample of the automatic encoding of the hyponymy and co-hyponymy relations.

Automatic Indexing and Information Visualization: A Study Based on Paraconsistent Logic

This paper reports a research to evaluate the potential and the effects of use of annotated Paraconsistent logic in automatic indexing. This logic attempts to deal with contradictions, concerned with studying and developing inconsistency-tolerant systems of logic. This logic, being flexible and containing logical states that go beyond the dichotomies yes and no, permits to advance the hypothesis that the results of indexing could be better than those obtained by traditional methods. Interactions between different disciplines, as information retrieval, automatic indexing, information visualization, and nonclassical logics were considered in this research. From the methodological point of view, an algorithm for treatment of uncertainty and imprecision, developed under the Paraconsistent logic, was used to modify the values of the weights assigned to indexing terms of the text collections. The tests were performed on an information visualization system named Projection Explorer (PEx), created at Institute of Mathematics and Computer Science (ICMC - USP Sao Carlos), with available source code. PEx uses traditional vector space model to represent documents of a collection. The results were evaluated by criteria built in the information visualization system itself, and demonstrated measurable gains in the quality of the displays, confirming the hypothesis that the use of the para-analyser under the conditions of the experiment has the ability to generate more effective clusters of similar documents. This is a point that draws attention, since the constitution of more significant clusters can be used to enhance information indexing and retrieval. It can be argued that the adoption of non-dichotomous (non-exclusive) parameters provides new possibilities to relate similar information.

Algorithms for automatic segmentation of bovine embryos produced

In vitro production has been employed in bovine embryos and quantification of lipids is fundamental to understand the metabolism of these embryos. This paper presents a unsupervised segmentation method for histological images of bovine embryos. In this method, the anisotropic filter was used in the differents RGB components. After pre-processing step, the thresholding technique based on maximum entropy was applied to separate lipid droplets in the histological slides in different stages: early cleavage, morula and blastocyst. In the postprocessing step, false positives are removed using the connected components technique that identify regions with excess of dye near pellucid zone. The proposed segmentation method was applied in 30 histological images of bovine embryos. Experiments were performed with the images and statistical measures of sensitivity, specificity and accuracy were calculated based on reference images (gold standard). The value of accuracy of the proposed method was 96% with standard deviation of 3%.

Automatic classification of prostate stromal tissue in histological images using Haralick descriptors and Local Binary Patterns

In this paper we presente a classification system that uses a combination of texture features from stromal regions: Haralick features and Local Binary Patterns (LBP) in wavelet domain. The system has five steps for classification of the tissues. First, the stromal regions were detected and extracted using segmentation techniques based on thresholding and RGB colour space. Second, the Wavelet decomposition was applied in the extracted regions to obtain the Wavelet coefficients. Third, the Haralick and LBP features were extracted from the coefficients. Fourth, relevant features were selected using the ANOVA statistical method. The classication (fifth step) was performed with Radial Basis Function (RBF) networks. The system was tested in 105 prostate images, which were divided into three groups of 35 images: normal, hyperplastic and cancerous. The system performance was evaluated using the area under the ROC curve and resulted in 0.98 for normal versus cancer, 0.95 for hyperplasia versus cancer and 0.96 for normal versus hyperplasia. Our results suggest that texture features can be used as discriminators for stromal tissues prostate images. Furthermore, the system was effective to classify prostate images, specially the hyperplastic class which is the most difficult type in diagnosis and prognosis.

Diploid chromosome set of kissing bug Triatoma baratai (Hemiptera, Triatominae)

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

Automatic method to classify images based on multiscale fractal descriptors and paraconsistent logic

In this study is presented an automatic method to classify images from fractal descriptors as decision rules, such as multiscale fractal dimension and lacunarity. The proposed methodology was divided in three steps: quantification of the regions of interest with fractal dimension and lacunarity, techniques under a multiscale approach; definition of reference patterns, which are the limits of each studied group; and, classification of each group, considering the combination of the reference patterns with signals maximization (an approach commonly considered in paraconsistent logic). The proposed method was used to classify histological prostatic images, aiming the diagnostic of prostate cancer. The accuracy levels were important, overcoming those obtained with Support Vector Machine (SVM) and Bestfirst Decicion Tree (BFTree) classifiers. The proposed approach allows recognize and classify patterns, offering the advantage of giving comprehensive results to the specialists.

De novo transcriptome assembly for a non-model species, the blood-sucking bug Triatoma brasiliensis, a vector of Chagas disease

High throughput sequencing (HTS) provides new research opportunities for work on non-model organisms, such as differential expression studies between populations exposed to different environmental conditions. However, such transcriptomic studies first require the production of a reference assembly. The choice of sampling procedure, sequencing strategy and assembly workflow is crucial. To develop a reliable reference transcriptome for Triatoma brasiliensis, the major Chagas disease vector in Northeastern Brazil, different de novo assembly protocols were generated using various datasets and software. Both 454 and Illumina sequencing technologies were applied on RNA extracted from antennae and mouthparts from single or pooled individuals. The 454 library yielded 278 Mb. Fifteen Illumina libraries were constructed and yielded nearly 360 million RNA-seq single reads and 46 million RNA-seq paired-end reads for nearly 45 Gb. For the 454 reads, we used three assemblers, Newbler, CAP3 and/or MIRA and for the Illumina reads, the Trinity assembler. Ten assembly workflows were compared using these programs separately or in combination. To compare the assemblies obtained, quantitative and qualitative criteria were used, including contig length, N50, contig number and the percentage of chimeric contigs. Completeness of the assemblies was estimated using the CEGMA pipeline. The best assembly (57,657 contigs, completeness of 80 %, < 1 % chimeric contigs) was a hybrid assembly leading to recommend the use of (1) a single individual with large representation of biological tissues, (2) merging both long reads and short paired-end Illumina reads, (3) several assemblers in order to combine the specific advantages of each.

Interactions of Bacillus thuringiensis bioinsecticides and the predatory stink bug Podisus nigrispinus to control Plutella xylostella

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Synthesis and total 1H- and 13C-NMR assignment of cephem derivatives for use in ADEPT approaches

We report the synthesis and total NMR characterization of 5-thia-1-azabicyclo-[4.2.0]oct-2-ene-2-carboxylic acid-3-[[[(4″- nitrophenoxy)carbonyl]oxy]-methyl]-8-oxo-7-[(2-thienyloxoacetyl)amino] -diphenylmethyl ester-5-dioxide (5), a new cephalosporin derivative. This compound can be used as the carrier of a wide range of drugs containing an amino group. The preparation of the intermediate product, 5-thia-1-azabicyclo[4.2.0] oct-2-ene-2-carboxylic acid-3-[methyl 4-(6-methoxyquinolin-8-ylamino) pentylcarbamate]-8-oxo-7-[(2-thienyloxoacetyl)amino]-diphenylmethyl ester-5-dioxide (6), as well as the synthesis of the antimalarial primaquine prodrug 5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid-3-[methyl 4-(6-methoxyquinolin-8-ylamino)pentylcarbamate]-8-oxo-7-[(2-thienyloxoacetyl) amino]- 5-dioxide (7) are also described, together with their total 1H- and 13C-NMR assignments. © 2008 by MDPI.

Towards biological control strategies for the bronze bug, Thaumastocoris peregrinus, on eucalyptus plantations in South America

The bronze bug is an invasive Australian pest that has reached eucalypt production areas worldwide in <10 years. The fi rst record in South America was in 2005 in Argentina. Collaboration in the region towards a unifi ed strategy for the management of the bronze bug started soon after the dispersal of the pest into Brazil and Uruguay was confi rmed. Here, we present the main achievements of this collaboration in four main topics: 1) biology of the pest, 2) monitoring, 3) biological control, and 4) cooperative networks. Two mass rearing procedures have been implemented in the region with relative success, allowing basic biological studies on the pest. Continuous monitoring in the region for >5 years has provided a reasonable knowledge on seasonal patterns of T. peregrinus. Biological control strategies developed include the use of local natural enemies of T. peregrinus, the development of biopesticides, and the introduction of Cleruchoides noackae, an egg parasitoid of T. peregrinus from Australia. We review the main achievements in each country. Finally, a regional network of institutions, researchers, and students has strengthened in the region, providing a solid background for future collaboration.