Phytophthora parasitica transcriptome, a new concept in the understanding of the citrus gummosis

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

A SYSTEMIC CONCEPT OF THE GENE

The univocal correspondence between one gene and one polypeptide has been challenged by many examples of ambiguities. A rapidly expanding list of one-to-many or many-to-one correspondences includes: genomic rearrangements, alternative processing of transcripts, overlapping translation frames, RNA editing, alternative translation modes, and polyprotein cleavage.The genomic message requires interpretation through decoding by a sophisticated information retrieval system which should also carry some kind of information. The full meaning of the whole cell, as a unit, is emphasized.The gene is a combination of (one or more) nucleic acid (DNA or RNA) sequences, defined by the system (the whole cell, interacting with the environment, or the environment alone, in subcellular or pre-cellular systems), that gives origin to a product (RNA or polypeptide).

Integrated assessment of multilevel biomarker responses and chemical analysis in Mussels from Sao Sebastiao, São Paulo, Brazil

The aim of the present study was to investigate the presence of contaminants in the mussel Perna perna from Sao Sebastiao Channel, São Paulo, Brazil, and to evaluate the effects of these contaminants on these organisms at biochemical (catalase [CAT], glutathione-S-transferase [GST], and cholinesterase [ChE]), cellular (neutral red retention time [NRRT] assay), and physiological (cardiac monitoring) levels. Two sampling surveys were performed (winter of 2001 and summer of 2002) at six stations along the channel: Cigarras, station 1; late Clube de Ilhabela, station 2; Oil Terminal, station 3; Toque Toque, station 4; Ponta da Sela, station 5 (reference station); and Taubate, station 6. Differences in CAT activity were observed between mussels from stations 3 and 5 during the winter, but no differences were detected in the summer. No differences in GST activity were found among stations during the winter, although animals from station 3 showed higher activity during the summer. The ChE activity was significantly higher in the mussels from stations I and 2 during the winter and from stations I and 3 during the summer. Organisms from stations I through 4 showed statistically lower NRRT in both seasons. Similar heart rates were observed in the mussels from all stations. Hydrocarbons were detected in organisms from all the stations in both seasons. During the winter, higher polycyclic aromatic hydrocarbon (PAH) levels were observed in organisms from station 3, whereas during the summer, higher levels of metals were found in organisms from stations 1, 3, and 4. The multivariate analyses showed a strong influence of PAHs on the winter biological results, but metals showed higher influence on these responses in the summer, indicating multiple contaminant sources.

Preliminary study of a methodology based on the degree-days concept for predicting the phenological phases of crops

This work develops a methodology (using the degree-days concept and linear regression), to forecast the duration of phenological phases in crops. An experiment was conducted in the greenhouse with three cultivars of cowpea (Vigna unguiculata (C.) Walp.), cv. California-781, Tvx 5058-09C and IT 81D-1032. The methodology was based on the relative thermal efficiency rate, determined for each species or cv. The results show that the proposed methodology may be a good alternative in works involving crops, especially because it does not require the repetition of the experiments.

Insights into the concept of fish welfare

Fish welfare issues are predicated on understanding whether fish are sentient beings. Therefore, we analyzed the logic of the methodologies used for studying this attribute. We conclude that empirical science is unable to prove or to disprove that fish are sentient beings. Thus, we propose a combined ethical-scientific approach for considering fish as sentient beings. The most difficult ongoing question is to determine which conditions fish prefer. Approaches to assess fish preferences should be rigorously and cautiously employed. In light of these considerations, attempts to establish physiological standards for fish welfare are discouraged, and a preference-based definition of fish welfare is proposed.

Use of ideal protein concept for precision formulation of amino acid levels in fish-meal-free diets for juvenile Nile tilapia (Oreochromis niloticus L.)

This study was undertaken in a closed system with Nile tilapia (Oreochromis niloticus) to examine the effects of total replacement of fish meal (FM) by soybean meal. Nile tilapia fingerlings with an average weight of 5.34+/-0.08 g were hand-fed one of the five isoenergetic (approximate to13.5 MJ digestible energy kg(-1)) and isoproteic (approximate to31% of digestible protein) experimental diets to satiation, six times a day during 85 days in eight replicate fibreglass tanks (six fish per tank). The control diet containing FM was substituted by soybean meal, with and without essential amino acids (lysine, methionine and threonine) or dicalcium phosphate supplementation. The supplemental amino acids were added at levels to simulate the reference amino acid profile of Nile tilapia carcass protein, based on the ideal protein concept. The results showed that soybean meal diet supplemented only with dicalcium phosphate was inferior to the control diet with FM and soybean meal diets supplemented with dicalcium phosphate and essential amino acids. Multiple essential amino acids and dicalcium phosphate incorporation in soybean meal diets was associated with performance, whole-body composition and carcass yield equal to that of the fish fed with the control diet containing FM. These data suggest that a diet with all plant protein source, supplemented with essential amino acids, based on tissue amino acid profile, can totally replace FM in a diet for Nile tilapia, without adverse effects on the growth performance, carcass yield and composition.

All-on-four concept and immediate loading for simultaneous rehabilitation of the atrophic maxilla and mandible with conventional and zygomatic implants

We report the simultaneous rehabilitation of an edentulous patient with a hybrid (zygomatic and conventional implants) all-on-four implant-supported prosthesis for the maxilla and a standard (conventional implants) all-on-four implant-supported prosthesis for the mandible. The transfer impression was made with a multifunctional guide and the upper and lower prostheses were placed 24 h postoperatively. Clinical and radiographic examinations showed no infection or bony resorption 2 years later. Simultaneous maxillary and mandibular rehabilitation with all-on-four immediate loading is a viable, fast and effective option for edentulous patients. (C) 2009 Published by Elsevier Ltd on behalf of The British Association of Oral and Maxillofacial Surgeons.

Particle Competition and Cooperation in Networks for Semi-Supervised Learning with Concept Drift

Concept drift is a problem of increasing importance in machine learning and data mining. Data sets under analysis are no longer only static databases, but also data streams in which concepts and data distributions may not be stable over time. However, most learning algorithms produced so far are based on the assumption that data comes from a fixed distribution, so they are not suitable to handle concept drifts. Moreover, some concept drifts applications requires fast response, which means an algorithm must always be (re) trained with the latest available data. But the process of labeling data is usually expensive and/or time consuming when compared to unlabeled data acquisition, thus only a small fraction of the incoming data may be effectively labeled. Semi-supervised learning methods may help in this scenario, as they use both labeled and unlabeled data in the training process. However, most of them are also based on the assumption that the data is static. Therefore, semi-supervised learning with concept drifts is still an open challenge in machine learning. Recently, a particle competition and cooperation approach was used to realize graph-based semi-supervised learning from static data. In this paper, we extend that approach to handle data streams and concept drift. The result is a passive algorithm using a single classifier, which naturally adapts to concept changes, without any explicit drift detection mechanism. Its built-in mechanisms provide a natural way of learning from new data, gradually forgetting older knowledge as older labeled data items became less influent on the classification of newer data items. Some computer simulation are presented, showing the effectiveness of the proposed method.

Knowledge Representation and Orthophemism: A Reflection Aiming to a Concept

Characteristics of speech, especially figures of speech, are used by specific communities or domains, and, in this way, reflect their identities through their choice of vocabulary. This topic should be an object of study in the context of knowledge representation once it deals with different contexts of production of documents. This study aims to explore the dimensions of the concepts of euphemism, dysphemism, and orthophemism, focusing on the latter with the goal of extracting a concept which can be included in discussions about subject analysis and indexing. Euphemism is used as an alternative to a non-preferred expression or as an alternative to an offensive attribution-to avoid potential offense taken by the listener or by other persons, for instance, pass away. Dysphemism, on the other hand, is used by speakers to talk about people and things that frustrate and annoy them-their choice of language indicates disapproval and the topic is therefore denigrated, humiliated, or degraded, for instance, kick the bucket. While euphemism tries to make something sound better, dysphemism tries to make something sound worse. Orthophemism (Allan and Burridge 2006) is also used as an alternative to expressions, but it is a preferred, formal, and direct language of expression when representing an object or a situation, for instance, die. This paper suggests that the comprehension and use of such concepts could support the following issues: possible contributions from linguistics and terminology to subject analysis as demonstrated by Talamo et al. (1992); decrease of polysemy and ambiguity of terms used to represent certain topics of documents; and construction and evaluation of indexing languages. The concept of orthophemism can also serves to support associative relationships in the context of subject analysis, indexing, and even information retrieval related to more specific requests.

Integrated biomarker responses as environmental status descriptors of a coastal zone (São Paulo, Brazil)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Establishment of the epithelial attachment and connective tissue adaptation to implants installed under the concept of "platform switching": a histologic study in minipigs

Aim: To validate the platform switching concept at oral implants with respect to the preservation of the alveolar crestal bone levels in an animal model. Material & methods: Five minipigs received three implants each with a 0.25mm implant/ abutment mismatch and were placed flush (T(0)), 1 mm below (T(1)) and 1 mm above (T(+1)) the alveolar bony crest, and as a control, one conventionally restored implant placed at the bone level. The implants were randomly inserted flapless into the mandible. Four months after implant insertion, the animals were sacrificed, and undecalcified block sections were obtained and used for histological analyses. Results: The mean values for peri- implant bone resorption were 1.09 +/- 0.59mm (Control), 0.51 (+/- 0.27 mm, T(0)), 0.50 (+/- 0.46 mm, T(1)) and 1.30 (+/- 0.21 mm, T (+1)), respectively. Statistically significant differences (P< 0.05) were found among the test (T(0), T(-1)) and the control sites. Control implants presented an average biologic width length of 3.20mm (+/- 0.33), with a connective tissue adaptation compartment of 1.29mm (+/- 0.53) and an epithelial attachment of 1.91 mm (+/- 0.71). T(0), T(1) and T(+1) implants presented with a mean biologic width of 1.97mm (+/- 1.20), 2.70 mm (+/- 1.36) and 2.84mm (+/- 0.90), respectively, with a connective tissue adaptation compartment of 1.21mm (+/- 0.97), 1.21 mm (+/- 0.65) and 1.50 mm (+/- 0.70) and an epithelial attachment of 0.84 mm (+/- 0.93), 1.66 mm (+/- 0.88) and 1.35 mm (+/- 0.44), respectively. Differences between the configurations were mainly associated with the length of the epithelial attachment. The epithelial attachment was significantly longer in the C sites than in T(0) (P = 0.014). However, no other differences between configurations were detected. Conclusion: If the implants are positioned at the level of the alveolar bony crest, the platform switching concept may have a minor impact on the length of the epithelial attachment (0.84 vs. 1.91 mm), while the connective tissue adaptation compartment remains relatively unaffected. Moreover, platform switching resulted in less resorption of the alveolar crest (0.58 mm).

Concept of Matching Parallelepiped and its use in the correspondence problem

In this paper, the concept of Matching Parallelepiped (MP) is presented. It is shown that the volume of the MP can be used as an additional measure of `distance' between a pair of candidate points in a matching algorithm by Relaxation Labeling (RL). The volume of the MP is related with the Epipolar Geometry and the use of this measure works as an epipolar constraint in a RL process, decreasing the efforts in the matching algorithm since it is not necessary to explicitly determine the equations of the epipolar lines and to compute the distance of a candidate point to each epipolar line. As at the beginning of the process the Relative Orientation (RO) parameters are unknown, a initial matching based on gradient, intensities and correlation is obtained. Based on this set of labeled points the RO is determined and the epipolar constraint included in the algorithm. The obtained results shown that the proposed approach is suitable to determine feature-point matching with simultaneous estimation of camera orientation parameters even for the cases where the pair of optical axes are not parallel.

Two new species of Zetzellia Oudemans (Acari: Stigmaeidae) that threaten the concept of genera: Disgeneric marriage?

Two new species of Zetzellia Oudemans, Z. agistzellia sp. n. and Z. quasagistemas sp. n., are described from rubber trees of northwestern São Paulo State, Brazil. Females have clear features of Zetzellia, whereas males resemble Agistemus in some characters. Immatures are also described. The discovery of these species raises some problems concerning generic concepts in Stigmaeidae. Since features of different genera are present in the same species, the authors suggest that the scope of those genera should be reviewed. Copyright © 2005 Magnolia Press.