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.

What is Consciousness? Towards a Preliminary Definition

There is little or no general agreement about what researchers should focus on when studying consciousness. The most active scientific studies often use the methods of Cognitive Neuroscience and focus mainly on vision. Other aspects and contents of consciousness, namely thoughts and emotions, are much less studied, possibly leading to a biased view of what consciousness is and how it works. In this essay we describe what we call a referential nucleus, implicit in much of consciousness research. In this context, 'consciousness' refers to (partially) reportable content experienced by living individuals. We then discuss the philosophical concept of a phenomenal world and another contemporary view that conscious experience involves, besides integration of information in the brain, participation in action-perception cycles in a natural, social and cultural environment. These views imply a need to reconceptualize 'qualia' as the conscious aspect of subjective experiences, thus stating properties of consciousness that pose serious challenges to an exclusive approach via Cognitive Neuroscience, because experimental settings oversimplify conscious experiences, narrowing them to fragments correlated with measured brain activity and behaviour In conclusion we argue that a science of consciousness requires a broad interdisciplinary range of research, including qualitative methods from the Human Sciences.

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.

Yolks color definition by supplementing yellow and red xanthophylls to hen's diets

Egg yolk color may be controlled both by the concentration and the type of xanthophylls added to diets, with the aim of meeting consumers demand. The objectives of this work were to study how yellow and red xanthophylls present in laying hens` diets influence yolks colors and find the concentrations of these ingredients that meet the regional consumer desire. A factorial design 5 x 3 with 5 concentrations of yellow xanthophylls (lutein + zeaxantin 40%; 1.0, 1.25, 1.5, 1.75 and 2.0 mg/hen/d) and 3 concentrations of red xanthophylls (canthaxantin 10%; 0, 0.35, 0.7 mg/hen/d) was used. After a 30 d period receiving corn basal diets and water ad libitum, 60 White Dekalbe hens were distributed to receive the 15 dietary treatments in 4 replicates. Diets were provided daily at 110 g, during 21 d under 16 h light/8 h dark. Yolks colors were evaluated daily using the CIE L, a, b color space and the Roche color index. After the color stabilization, data were analyzed by ANOVA, regression analysis and Response Surface Methodology (MRS). Global acceptance for the Roche colors was evaluated with a 5 points hedonic scale and data were analyzed by Friedman and Dunn tests. Significance was established at 95% (P < 0.05). Regression analysis showed that the red xanthophylls content was the most important factor that defined L, a and b values for yolk color (P < 0.0001; square function), although its effect was significantly affected by the yellow xanthophylls contents (P = 0.0277; P < 0.0001; P = 0.0002 for L, a, b, respectively), providing evidence for a synergistic effect and not for a saturation effect. MRS showed that the highest redness of yolks was reached with 1.5 mg/hen/d of yellow and 0.5 mg/hen/d of red xanthophylls. So, higher supplementations aiming at increasing yolk color would bring an unnecessary cost to the ration. The most accepted yolk color scored 9, which corresponded to mean color attributes L = 65; a = 16; and b = 64. MRS showed that these values could be reached with combinations of yellow:red xanthophylls like 1.0:0.15 or 1.5:0.1 mg/ hen/d or simply with the yellow xanthophylls at 2.0 mg/hen/d. So, it was concluded that both yellow and red xanthophylls are important to define yolks color; that high amounts of xanthophylls are unnecessary to bring changes to color; and that Brazilian consumer requires yolks color attainable with few amounts of red xanthophylls or only with the yellow ones.

Design of static var compensators using a general reactive energy definition

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