The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome

open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription-PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning.

The definition of potential infiltration areas in Guaratingueta watershed, Paraiba do Sul Basin, Southeastern Brazil: an integrated approach using physical and land-use elements

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

Definition of a diagnostic routine in individuals with inconclusive serology for chagas disease

Despite the existence of highly sensitive tests, inconclusive serological results are frequent in chronic chagasic infection. This study aimed to define a diagnostic conduct for 30 individuals with inconclusive serology (G3) for chagasic infection assisted at the Outpatient Unit for Infectious and Parasitic Diseases of the Botucatu School of Medicine. Twenty-one individuals with negative serology (G1) and 33 with positive serology (G2) were also studied. Serological methods ELISA, HAI, IFI and immunoblotting TESA-cruzi were used for G1, G2 and G3, and parasitological methods xenodiagnosis, hemoculture and PCR-LIT were used for G2 and G3 individuals. ELISA, HAI and IFI were performed in 5 different blood samples in G2 and G3. TESA-cruzi was carried out only once in G1, G2 and G3 and, since it is the most sensitive, it was utilized as standard. In G3, positivity for ELISA reached 86% in the fifth blood sample; the ELISA+HAI+IFI combination showed a maximum of 44.8% in the second sample; and TESA-cruzi, 76% in one single sample. Xenodiagnosis positivity was 9.4%; hemoculture showed 15.2%; and PCR-LIT exhibited 22% positivity in G2. Nevertheless, in G3, positivity percentage was 3.4% for xenodiagnosis, 6.7% for PCR-LIT, and no positive result was found for hemoculture. In G3, PCR-LIT resolved one case which was still inconclusive according to serology tests. In order to define inconclusive diagnoses, the results suggest the combined use of ELISA+HAI+IFI in 2 blood samples, decreasing the occurrence of false positive/negative results. If results remain inconclusive, the performance of TESA-cruzi and PCR-LIT, if necessary, is recommended.

Are affects important for the definition of depression?

Many of the nosological features, subtypes, biochemical, neurophysiological mechanisms, and therapeutic proposals are controversial in depression. Methods: We review theories and discuss affects and mood as criteria For depression or mania diagnosis. Results: Our work was to show that mood and affections are poorly conceived. Conclusions: Mood and affection do not serve as a basis for the diagnosis of depression or mania.

The Pediatric Rheumatology International Trials Organization American-College-of-Rheumatology provisional criteria for the evaluation of response to therapy in juvenile systemic lupus erythematosus: Prospective validation of the definition of improvement

Objective. To use the Pediatric Rheumatology International Trials Organization (PRINTO) core set of outcome measures to develop a validated definition of improvement for the evaluation of response to therapy in juvenile systemic lupus erythematosus (SLE).Methods. Thirty-seven experienced pediatric rheumatologists from 27 countries, each of whom had specific experience in the assessment of juvenile SLE patients, achieved consensus on 128 patient profiles as being clinically improved or not improved. Using the physicians' consensus ratings as the gold standard measure, the chi-square, sensitivity, specificity, false-positive and false-negative rates, area under the receiver operating characteristic curve, and kappa level of agreement for 597 candidate definitions of improvement were calculated. Only definitions with a kappa value greater than 0.7 were retained. The top definitions were selected based on the product of the content validity score multiplied by its kappa statistic.Results. The definition of improvement with the highest final score was at least 50% improvement from baseline in any 2 of the 5 core set measures, with no more than 1 of the remaining worsening by more than 30%.Conclusion. PRINTO proposes a valid and reproducible definition of improvement that reflects well the consensus rating of experienced clinicians and that incorporates clinically meaningful change in core set measures in a composite end point for the evaluation of global response to therapy in patients with juvenile SLE. The definition is now proposed for use in juvenile SLE clinical trials and may help physicians to decide whether a child with SLE responded adequately to therapy.

The endangered species Brycon orbignyanus: genetic analysis and definition of priority areas for conservation

Currently, biodiversity is threatened by several factors often associated with human population growth and the extension of areas occupied by human activity. In particular, freshwater fish fauna is affected by overfishing, deforestation, water pollution, introduction of exotic species and habitat fragmentation promoted by hydroelectric dams, among other environmental impact factors. Several action plans to preserve ichthyofauna biodiversity have been adopted; however, these plans frequently cover only a small number of species, and decisions are often made without strong scientific support. This study aimed to evaluate the genetic aspects of wild groups of Brycon orbignyanus, an endangered fish species, using microsatellites and D-loop regions to identify the genetic structure of the samples and to establish priority areas for conservation based on the genetic patterns of this species. The results indicated that the samples showed levels of genetic variability compatible with others studies with Neotropical fishes. However, the results obtained in the analysis of molecular variance (AMOVA) for microsatellites (F (ST) = 0.258) and D-loop (F (ST) = 0.234) and the interpopulation fixation index revealed that B. orbignyanus was structured in different subpopulations in the La Plata River basin; the areas with better environmental conditions also showed subgroups with higher rates of genetic variability. Future conservation actions addressing these sites should consider two different management units: the complex formed by the Ivinhema River, Upper Parana, Camargo Port and Ilha Grande groups; and the complex formed by the Verde River and Sucuriu River groups.

Description of three new species of Moenkhausia (Teleostei, Characiformes, Characidae) with the definition of the Moenkhausia jamesi species complex

From the examination of extensive comparative material currently identified as M. jamesi we verified that there are, at least, three new species under this name. These, along with M. jamesi and M. justae, form what we herein called the M. jamesi species complex, by sharing the following group of characters: a short maxilla, with its distal margin not exceeding anterior third of the second infraorbital; first through third teeth of the inner row of premaxilla and first and second dentary teeth with cusps arranged in a pronounced arch, humeral spot positioned between the fourth and seventh scales of the lateral line and extending up to four scale rows above the lateral line and one scale row below the lateral line, and a vertically oval to round spot at the base of the caudal fin rays. Moenkhausia ischyognatha sp. n., from Rio Xingu basin, differs from the other species of the complex by its lower head depth. Moenkhausia alesis sp. n., from the river system Tocantins-Araguaia, differs from M. jamesi, M. ischyognatha, and M. sthenosthoma by the number of scale rows above the lateral line. Moenkhausia sthenosthoma sp. n., from the Rio Madeira basin, differs from M. jamesi by the number of scale rows between the lateral line and the midventral scale series. Moenkhausia justae can be diagnosed from the other species of the complex by having a tri to pentacuspidate tooth on the maxilla.

Space dependency of chemical attributes in an area with sugarcane plantation in Pereira Barreto, SP

The behavior of the chemical attributes is directly influenced by superficial flow and water movement inside the soil. This work aimed to study the space dependency of chemical attributes in an area with sugarcane plantation in Pereira Barreto, SP. An area of 530.67 hectares was mapped using an equipment of Global Positioning System and obtaining a Digital Elevation Model. A set of 134 soil samples were collected every seven hectares in the depths of 0-0.25 m and 0.80-1.00 m. The pH, organic matter (OM), Ca, Mg, K, BS, CEC and base saturation (BS) were analyzed. All the chemical attributes presented similar behavior in the superficial and subsuperficial layer of the soil, which provided better visualization and definition of the homogeneous tillage zones.

Electrical conductivity of the seed soaking solution and soybean seedling emergence

Vigor of soybean [Glycine max (L.) Merrill] seeds can be evaluated by measuring the electrical conductivity (EC) of the seed soaking solution, which has shown a satisfactory relationship with field seedling emergence, but has not had aproper definition of range yet. This work studies the relationship between EC and soybean seedling emergence both in the field and laboratory conditions, using twenty two seed lots. Seed water content, standard germination and vigor (EC, accelerated aging and cold tests) were evaluated under laboratory conditions using -0.03; -0.20; -0.40 and -0.60 MPa matric potentials, and field seedling emergence was also observed. There was direct relationship between EC and field seedling emergence (FE). Under laboratory conditions, a decreasing relationship was found between EC and FE as water content in the substrate decreased, Relationships between these two parameters were also found when -0.03; -0.20 and -0.40 MPa matric potentials were used. EC tests can be used successfully to evaluate soybean seed vigor and identify lots with higher or lower field emergence potential.

Estimation of genetic parameters for body weights, scrotal circumference, and testicular volume measured at different ages in Nellore cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic analysis of visual scores and their relationships to mature female weight in Nellore breed

Dados de 79.884 animais da raça Nelore foram utilizados para estimar parâmetros genéticos e avaliar as relações entre os escores de conformação, precocidade e musculatura obtidos à desmama e ao sobreano e o peso das fêmeas à idade adulta. Utilizou-se o método da máxima verossimilhança restrita, em análise multicaracterísticas, com modelo que incluiu os efeitos genéticos aditivos direto e residual, como aleatórios, e os efeitos fixos de grupo de contemporâneos e, como covariáveis, a idade do animal à pesagem e a idade da mãe ao parto (exceto para o peso das fêmeas à idade adulta). Os grupos contemporâneos à desmama foram definidos pelas variáveis: sexo, rebanho, ano e mês de nascimento, grupo de manejo ao nascimento e à desmama. Na definição de grupo contemporâneo ao sobreano também foi incluída a variável grupo de manejo ao sobreano. Para o peso das fêmeas à idade adulta, o grupo de contemporâneos foi composto por rebanho, ano de nascimento, grupo de manejo ao sobreano, ano e estação da pesagem. Os efeitos genético materno e de ambiente permanente materno também foram incluídos no modelo para análise dos escores de conformação, precocidade e musculatura à desmama. As estimativas de herdabilidade direta obtidas foram 0,18 ± 0,02 para o escore de conformação; 0,21 ± 0,01 para o escore de precocidade; 0,22 ± 0,01 para o escore de musculatura à desmama e 0,24 ± 0,01 para o escore de conformação; 0,27 ± 0,01 para o escore de precocidade; e 0,26 ± 0,01 para o escore de musculatura ao sobreano e 0,42 ± 0,02 para o peso das fêmeas à idade adulta. As correlações genéticas estimadas entre os escores visuais medidos à desmama e ao sobreano foram positivas, variando de média a alta magnitude (0,56 ± 0,03 a 0,85 ± 0,01). Por outro lado, as correlações genéticas estimadas entre os escores visuais e o peso das fêmeas à idade adulta foram positivas e moderadas, variando de 0,21 ± 0,03 a 0,35 ± 0,03. Os resultados obtidos indicam que a seleção de animais com maiores escores visuais, principalmente ao sobreano, deve promover aumento do peso das fêmeas à idade adulta.

Molecular and biological characterization of Lettuce mosaic virus (LMV) isolates reveals a distinct and widespread type of resistance-breaking isolate: LMV-Most

Lettuce mosaic virus (LMV) causes an economically important seedborne and aphid-transmitted disease of lettuce and ornamental crops worldwide. The genetic diversity among 73 LMV isolates was examined based on a 216-nucleotide sequence at the variable region encoding the NIb-coat protein junction, Three clusters of LMV isolates were distinguished: LMV-Yar, LMV-Greck, and LMV-RoW. In the latter cluster, two subgroups of isolates, LMV-Common and LMV-Most, accounted for a large proportion of the LMV isolates analyzed. These two subgroups included the seedborne isolates, consistent with this property contributing a selective advantage and resulting in widespread distribution. In addition to being seedborne, LMV-Most isolates overcome the two resistance genes commonly used in lettuce, mol(1) and mol(2), and thus represent a potential threat to lettuce cultivation. The complete sequence of an LMV-Most isolate (LMV-AF199) was determined, allowing a better definition of the genetic relationships among LMV-Most, LMV-Common, and an additional isolate of the LMV-RoW cluster.

Framework for analysis and representation of external systems for online reactive-optimisation studies

The paper proposes a framework for the analysis and representation of external systems for online optimisation studies. The basis for this framework is the equivalent OPF (EOPF), an optimisation model obtained by partitioning of the OPF model. The EOPF is mathematically redefined in the paper to accommodate the concept of a buffer zone. The resulting model is more useful for online optimisation, since external information obtained through intercontrol-centre exchange contracts can be used to improve internal control calculation. Numerical results obtained with original studies involving the boundary-matching procedure have provided a conceptual basis for the definition of a buffer zone for optimisation studies with the EOPF. In the proposed framework, the accuracy of the external representation in optimisation studies is evaluated by comparing the controls obtained by an EOPF procedure with those obtained by the reference-optimisation procedure defined in this paper. The framework is then used to evaluate the accuracy of equivalent optimisation studies involving the IEEE 118-bus test system and the Brazilian South Southeast 810-bus system. The results show that the incorporation of a buffer zone improves the external system representation for all optimisation studies performed.

Boundary identification criteria and geometry analysis of Al 7050 stretch zone from elevation profiles

This article describes the development of a method for analysis of the shape of the stretch zone surface based on parallax measurement theory and using digital image processing techniques. Accurate criteria for the definition of the boundaries of the stretch zone are established from profiles of fracture surfaces obtained from crack tip opening displacement tests on Al-7050 alloy samples. The elevation profiles behavior analysis is based on stretch zone width and height parameters. It is concluded that the geometry of the stretch zone profiles under plane strain conditions can be described by a semi-parabolic relationship. (C) Elsevier B.V., 1999. All rights reserved.