Automatic classification of fish germ cells through optimum-path forest

The spermatogenesis is crucial to the species reproduction, and its monitoring may shed light over some important information of such process. Thus, the germ cells quantification can provide useful tools to improve the reproduction cycle. In this paper, we present the first work that address this problem in fishes with machine learning techniques. We show here how to obtain high recognition accuracies in order to identify fish germ cells with several state-of-the-art supervised pattern recognition techniques. © 2011 IEEE.

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.

Cordia verbenacea and secretion of mast cells in different animal species

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Chromosome Mapping of Retrotransposable Elements Rex1 and Rex3 in Three Fish Species in the Subfamily Hypoptopomatinae (Teleostei, Siluriformes, Loricariidae)

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

Evidence supporting the recognition of Cole latent virus as a distinct carlavirus

Some molecular properties are described of Cole latent virus (CoLV), hitherto designated a tentative species of the Carlavirus genus. CoLV genomic RNA (Ribonucleic acid) of 8.3 Kb is polyadenylated. Two unencapsidated polyadenylated subgenomic RNAs (2.6 and 1.3 Kb) and three double-stranded RNAs (dsRNAs) (8.3, 2.6 and 1.3 Kbp), which are twice the size of the genomic and subgenomics ssRNAs, are produced in CoLV-infected plants, two additional dsRNAs (7.2 and 6.3 Kbp) were also detected plant extracts. By using a Carlavirus specific primer and a CoLV cDNA, a-3'-terminus fragment of 116 bp was amplified; it had homology with the carlaviruses Potato virus M (62%)., Hop latent virus (37%) and Blueberry scorch virus (36%) but no significant homology with 11 other carlaviruses. These results support the classification of CoLV as a distinct species of the Carlavirus genus.

Recognition and distribution of Leptodactylus mystaceus (Anura; Leptodactylidae) in the State of São Paulo, Southeastern Brazil

Leptodactylus mystaceus, uma espécie com ampla distribuição geográfica pela América do Sul, é diagnosticada com base em exemplares do Estado de São Paulo, seu limite meridional de distribuição geográfica. Apresentamos aqui o primeiro registro da espécie para o Sudeste do Brasil, ampliando sua distribuição conhecida em cerca de 1.300 km ao sudeste. Também incluímos a descrição da vocalização de anúncio, informações sobre história natural, fotografia em vida e desenhos de caracteres morfológicos que auxiliam na identificação desta espécie.

Phylogenetic relationship of Sirodotia species (Batrachospermales, Rhodophyta) in North and South America

Sequence data from the RUBISCO large subunit (rbcL) plastid gene and nuclear small-subunit ribosomal DNA (SSU rDNA) were examined for five samples of Sirodotia delicatula from southeastern Brazil. Data from six North American samples previously identified as S. huillensis and S. suecica were also included in the analysis. Molecular data supported the continued recognition of these three species as separate entities, although one of the North American collections was misidentified. These results were shown to be congruent with morphology, chromosome number and geographic distribution. S. delicatula is more closely related to S. huillensis, both occurring in tropical-subtropical regions, than either to S. suecica with a temperate-boreal distribution. There was little rbcL variation within S. delicatula from Brazil and Costa Rica (the latter a collection previously identified as S. huillensis), with the six samples sequenced diverging from each other by 0-8 bp (0-0.67%). SSU rDNA data set did not provide sufficient resolution to infer phylogenetic relationships among the species of this group due to the low rates of variation (5 bp). Sirodotia was a well-supported clade (100% bootstrap or 1.00 a posteriori probability) based on rbcL sequences. Thus, the results confirm that Sirodotia is a monophyletic group within the Batrachospermales and we continue to recognize it at the generic level. The species S. delicatula, S. huillensis and S. suecica are morphologically and genetically distinct.

Chemical communication, aggression, and conspecific recognition in the fish Nile tilapia

The chemical modulation of agonistic behavior and conspecific recognition were tested in juveniles of the fish Nile tilapia, Oreochromis niloticus (L.). After a 7-day isolation period, the fish were grouped (four individuals per aquarium) for 7 days. Then fish of alpha and beta ranks (previously matched for similar size) were paired in a neutral territory for analysis of their agonistic interaction. Pairs composed of alpha and beta fish were established with either fish from the same group (familiar) or from two different groups (unfamiliar). The pairs were tested in contiguous compartments, either with water exchange between the compartments or in the absence of water exchange. In each condition the fish were separated by a transparent glass partition. Twelve pairs were tested in each experimental condition. Fish behavior was videotaped and the following variables were analyzed: (a) frequency of and time spent in agonistic patterns, (b) latency to start fighting, and (c) duration of swimming. Water exchange between compartments decreased agonistic interactions. This effect, however, was more pronounced in pairs of fish coming from the same group (in this case, subordinate fish spent less time in confrontations than dominant ones). We conclude that chemical communication decreases aggression in this species by (1) inducing an alarm reaction and (2) increasing conspecific recognition (thus stabilizing the dominance hierarchy). (C) 1997 Elsevier B.V.

Taxonomic status of the genus Sotalia: Species level ranking for tucuxi (Sotalia fluviatilis) and costero (Sotalia guianensis) dolphins

Dolphins of the genus Sotalia are found along the Caribbean and Atlantic coasts of Central and South America and in the Amazon River and most of its tributaries. At present, the taxonomy of these dolphins remains unresolved. Although five species were described in the late 1800s, only one species is recognized currently (Sotalia fluviatilis) with two ecotypes or subspecies, the coastal subspecies (Sotalia fluviatilis guianensis) and the riverine subspecies (Sotalia fluviatilis fluviatilis). Recent morphometric analyses, as well as mitochondrial DNA analysis, suggested recognition of each subspecies as separate species. Here we review the history of the classification of this genus and present new genetic evidence from ten nuclear and three mitochondrial genes supporting the elevation of each subspecies to the species level under the Genealogical/Lineage Concordance Species Concept and the criterion of irreversible divergence. We also review additional evidence for this taxonomic revision from previously published and unpublished genetic, morphological, and ecological studies. We propose the common name costero for the coastal species, Sotalia guianensis (Van Beneden 1864), and accept the previously proposed tucuxi dolphin, Sotalia fluviatilis (Gervais, 1853), for the riverine species.

Pattern recognition theory in nonlinear signal processing

A body of research has developed within the context of nonlinear signal and image processing that deals with the automatic, statistical design of digital window-based filters. Based on pairs of ideal and observed signals, a filter is designed in an effort to minimize the error between the ideal and filtered signals. The goodness of an optimal filter depends on the relation between the ideal and observed signals, but the goodness of a designed filter also depends on the amount of sample data from which it is designed. In order to lessen the design cost, a filter is often chosen from a given class of filters, thereby constraining the optimization and increasing the error of the optimal filter. To a great extent, the problem of filter design concerns striking the correct balance between the degree of constraint and the design cost. From a different perspective and in a different context, the problem of constraint versus sample size has been a major focus of study within the theory of pattern recognition. This paper discusses the design problem for nonlinear signal processing, shows how the issue naturally transitions into pattern recognition, and then provides a review of salient related pattern-recognition theory. In particular, it discusses classification rules, constrained classification, the Vapnik-Chervonenkis theory, and implications of that theory for morphological classifiers and neural networks. The paper closes by discussing some design approaches developed for nonlinear signal processing, and how the nature of these naturally lead to a decomposition of the error of a designed filter into a sum of the following components: the Bayes error of the unconstrained optimal filter, the cost of constraint, the cost of reducing complexity by compressing the original signal distribution, the design cost, and the contribution of prior knowledge to a decrease in the error. The main purpose of the paper is to present fundamental principles of pattern recognition theory within the framework of active research in nonlinear signal processing.

A molecular perspective on the phylogeny of the Hyla pulchella species group (Anura, Hylidae)

A molecular phylogenetic analysis of the Hyla pulchella species group was performed to test its monophyly, explore the interrelationships of its species, and evaluate the validity of the taxa that were considered subspecies of H. pulchella. Approximately 2.8 kb from the mitochondrial genes 12s, tRNA valine, 16s, and Cytochrome b were sequenced. The analysis included 50 terminals representing 10 of the 14-15 species currently recognized in the H. pulchella group, including samples from several localities for some taxa, several outgroups, as well as two species previously suspected to be related with the group (Hyla guentheri and Hyla hischoffi). The results show that the H. pulchella and Hyla circumdata groups are distantly related, and, therefore, should be recognized as separate groups. As currently defined, the H. pulchella group is paraphyletic with respect to the Hyla polytaenia group; therefore, we recognize the Hyla polytaenia clade in the H. pulchella group. Two subspecies of H. pulchella recognized by some authors are considered full species including Hyla pulchella riojana because it is only distantly related to H. pulchella, and Hyla pulchella cordobae because molecular and non-molecular evidence suggests that it is specifically distinct. With the inclusion of the H. polytaenia clade, H. guentheri, and H. bischoffi, and the recognition of the two former subspecies of H. pulchella as distinct species, the H. pulchella group now comprises 25 described species. All representatives of the H. pulchella group with an Andean distribution are monophyletic and nested within a clade from the Atlantic forest from south-southeastern Brazil/northeastern Argentina, and Cerrado gallery forest from central Brazil. (C) 2004 Elsevier B.V. All rights reserved.

Endocytic activity in the thrombocytes of the turtle Phrynopys hilarii (freshwater South American species)

The phagocytic process in cells depends on lysosomal enzymes, high-energy metabolism and cellular recognition. In this paper, we investigated the presence of energy and recognition factors in thrombocytes of turtle Phrynopys hilarii (a freshwater South American species). Turtle thrombocytes (P. hilarii) present glycogen - possibly β particles - dispersed in their cytoplasm and glycoproteins in the cell surface, as well as a large number of enzymes involved in the endocytic process (Pellizzon, 1996). The activity of these enzymes depends on high-energy metabolism and on cellular recognition provided by specific glycoconjugates (Alberts et al., 1994). This metabolic characterization is demonstrated by the large amount of glycogen particles observed in the cytoplasm by Thiéry's method. Glycogen labeling was also observed when concanavalin A-peroxidase was used as a marker for thrombocytes and for endocyted charcoal particles. Our results show that these cells have phagocytic ability, suggesting that their function in blood circulation is not limited to aggregation but may also involve a great potential for phagocytosis.

Cytogenetic study on three species of the genus Triatoma (Heteroptera: Reduviidae) with emphasis on nucleolar organizer regions

The use of banding techniques allows the recognition of chromosomal pairs and karyotypical arrangements. However, its application in Heteroptera holocentric chromosomes is limited. Thus, little is known about their structure, specially their Nucleolar Organizer Regions (NORs). A comparative analysis of the nucleolar characteristics present during spermatogenesis in Triatoma platensis, Triatoma protacta and Triatoma tibiamaculata seems to indicate that in this group of insects nucleolar fragmentation occurs after prophase I. The study of chromosomal structure of these triatomines indicates that NORs are located at some telomeric and interstitial autosome regions and at sexual chromosomes (X/X1X2).

Methodology for automatic selection of passes in surface grinding

The main purpose of this work is the development of computational tools in order to assist the on-line automatic detection of burn in the surface grinding process. Most of the parameters currently employed in the burning recognition (DPO, FKS, DPKS, DIFP, among others) do not incorporate routines for automatic selection of the grinding passes, therefore, requiring the user's interference for the choice of the active region. Several methods were employed in the passes extraction; however, those with the best results are presented in this article. Tests carried out in a surface-grinding machine have shown the success of the algorithms developed for pass extraction. Copyright © 2007 by ABCM.

Automatic segmentation of the secondary austenite-phase island precipitates in a superduplex stainless steel weld metal

Duplex and superduplex stainless steels are class of materials of a high importance for engineering purposes, since they have good mechanical properties combination and also are very resistant to corrosion. It is known as well that the chemical composition of such steels is very important to maintain some desired properties. In the past years, some works have reported that γ 2 precipitation improves the toughness of such steels, and its quantification may reveals some important information about steel quality. Thus, we propose in this work the automatic segmentation of γ 2 precipitation using two pattern recognition techniques: Optimum-Path Forest (OPF) and a Bayesian classifier. To the best of our knowledge, this if the first time that machine learning techniques are applied into this area. The experimental results showed that both techniques achieved similar and good recognition rates. © 2012 Taylor & Francis Group.