A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data

Background: The genome-wide identification of both morbid genes, i.e., those genes whose mutations cause hereditary human diseases, and druggable genes, i.e., genes coding for proteins whose modulation by small molecules elicits phenotypic effects, requires experimental approaches that are time-consuming and laborious. Thus, a computational approach which could accurately predict such genes on a genome-wide scale would be invaluable for accelerating the pace of discovery of causal relationships between genes and diseases as well as the determination of druggability of gene products.Results: In this paper we propose a machine learning-based computational approach to predict morbid and druggable genes on a genome-wide scale. For this purpose, we constructed a decision tree-based meta-classifier and trained it on datasets containing, for each morbid and druggable gene, network topological features, tissue expression profile and subcellular localization data as learning attributes. This meta-classifier correctly recovered 65% of known morbid genes with a precision of 66% and correctly recovered 78% of known druggable genes with a precision of 75%. It was than used to assign morbidity and druggability scores to genes not known to be morbid and druggable and we showed a good match between these scores and literature data. Finally, we generated decision trees by training the J48 algorithm on the morbidity and druggability datasets to discover cellular rules for morbidity and druggability and, among the rules, we found that the number of regulating transcription factors and plasma membrane localization are the most important factors to morbidity and druggability, respectively.Conclusions: We were able to demonstrate that network topological features along with tissue expression profile and subcellular localization can reliably predict human morbid and druggable genes on a genome-wide scale. Moreover, by constructing decision trees based on these data, we could discover cellular rules governing morbidity and druggability.

Performance of the constructed wetland system for the treatment of water from the corumbataí river

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

A and B mode ultrasonography in preoperative evaluation of lens and posterior segment of dogs eyes with cataract

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

B-chromosomes in two Brazilian populations of Dendropsophus nanus (Anura, Hylidae)

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

THE B-FORM TO Z-FORM TRANSITION OF POLY(DG-M(5)DC) IS SENSITIVE TO NEUTRAL SOLUTES THROUGH AN OSMOTIC-STRESS

Several neutral solutes, ranging in size from methanol to a tetrasaccharide, stachyose, are shown to stabilize the left-handed Z form of the methylated polynucleotide poly(dG-m(5)dC). The action of these solutes is consistent with an osmotic stress, that is, with their effect on water chemical potentials coupled to a difference in the number of-associated water molecules between the B and Z conformations. The apparent difference in hydration between the two forms is, however, dependent on the particular solute used to probe the reaction. The effect of solutes is not consistent either with a direct binding of solute or with an indirect effect on electrostatics or ion binding through changes in the solution dielectric constant. The interplay of NaCl and neutral solute in modulating the B-Z transition suggests that salt also could be stabilizing the Z form through an osmotic stress.

LIFE QUALITY of PEOPLE INFECTED BY HIV WITH OR WITHOUT ANTIRETROVIRAL TREATMENT

The "HIV/Aids-Quality of Life" (HAT-Qol) is a specific multifunctional instrument used to measure the life quality of HIV infected persons. It is divided into nine domains: general activity, sexual activity, secrecy about HIV seropositivity, concern about health, financial concern, awareness about HIV, satisfaction with life, issues about medications and belief in the doctor. The current study analyzed the life quality of HIV infected individuals-who attended the DST/Aids Program in Maringa city, Parana state-regarding the use or not of antiretroviral therapy (TARV) and their demographic, epidemiological and clinical characteristics. Data were collected by retrospective analysis from 1,200 medical charts of patients registered in the program. The HAT-Qol instrument was applied before routine medical consultation. One hundred and sixty-nine patients, who had HIV infection confirmed, were divided into two groups, G1 with 118 individuals receiving antiretroviral therapy and G2 with 51 individuals who were not under this therapy.Result analysis, regarding social and demographic characteristics, revealed no difference among responses related to gender, educational degree and sexual option. Age influenced satisfaction with sexual activity and marital status. Regarding HIV awareness, the lowest response index or worst quality of life came from, respectively, men between 50 and 69 years old and patients who did not have regular partners compared with the ones who did. Additionally, it was observed that the time of diagnosis influenced general activities, HIV awareness, concern about health and financial issues, satisfaction with life and topics about medications. The variables were compared in both groups. There was no influence on the use or not of antiretroviral therapy regarding age, sexual activity, HIV diagnosis time and the domains that evaluated general activities, financial concern, awareness of HIV and satisfaction with life. In relation to time of diagnosis, there was an influence only in persons who had been diagnosed two or three years before, in which a lower quality of life was observed among individuals who were not under antiretroviral therapy. It was not possible to compare variables about medication use, HIV plasmatic viral rate ant time of diagnosis, because G2 individuals were not receiving the antiretroviral therapy. Furthermore, no comparison was made regarding marital status and HIV awareness, because there were no married individuals in G2. Thus, the analysis of the results showed that the use of antiretroviral treatment did not influence the life quality of HIV patients studied by the HAT-Qol scale.

Interaction between areas of the central nervous system in the control of water intake and arterial pressure in rats

1. Water intake induced by injection of 0.2 M-NaCl into the lateral preoptic area was increased by the injection of angiotensin II into the subfornical organ of rats. The injection of hypertonic saline solution into the subfornical organ increased water intake. However, the increase was lower than when the solution was injected into the lateral preoptic area. The injection of 4 μg angiotensin II into the lateral preoptic area further augmented this effect. 2. Injection of angiotensin II into the subfornical organ caused a rise in blood pressure which preceded the thirst-inducing effect. The injection of 0.2 M NaCl into the subfornical organ caused no changes in blood pressure, whereas the injection of angiotensin II into the lateral preoptic area caused some increase. 3. Dehydration of the lateral preoptic area by means of 0.2 M NaCl in combination with intravenous infusion of angiotensin II caused a summation of effects in terms of the water intake, without changing cardiovascular alterations induced by the infusion of angiotensin II. A summation of effects in the water intake, but not in blood pressure, was also observed when 0.5 M NaCl was infused intravenously in combination with the injection of angiotensin II into the subfornical organ and into the lateral preoptic area. 4. The results indicate that there are interactions between the subfornical organ and lateral preoptic area in the regulation of cardiovascular and thirst mechanisms.

Shelf life extension of individually film-wrapped mangoes

Mangoes cv. Keitt were individually sealed in a heat-shrinkable polyolefin film (D-955) and a low-density polyethylene film (LDPE), stored for 0-5 weeks at 12°C and 17°C, and then ripened unwrapped at 22°C. Weight loss of packaged mangoes was significantly lower than that of the non-wrapped control. A sensory panel ranked the mangoes for overall eating quality and appearance. D-955 and LDPE film-sealed mangoes and control had shelf lives of 33, 15 and 7 days at 12°C and 17,10 and 7 days at 17°C, respectively.

Association between polyclonal B cell activation and the presence of autoantibodies in mice infected with Yersinia enterocolitica O:3

Eight-week old conventional female Swiss mice were inoculated intravenously with Yersinia enterocolitica O:3. A second group of normal mice was used as control. Five mice from each group were bled by heart puncture and their spleens were removed for spleen cell collection on the 3rd, 5th, 7th, 10th, 14th and 21st day after infection. Immunoglobulin-secreting spleen cells were detected by the isotype-specific protein A plaque assay. Total immunoglobulin levels were determined in mouse serum by single radial immunodiffusion and the presence of autoantibodies was determined by ELISA. We observed a marked increase in the total number of cells secreting immunoglobulins of all isotypes as early as on the 3rd day post-infection and the peak of secretion occurred on the 7th day. At the peak of the immunoglobulin response, the total number of secreting cells was 19 times higher than that of control mice and most immunoglobulin-secreting cells were of the IgG2a isotype. On the 10th day post-infection, total serum immunoglobul in values were 2 times higher in infected animals when compared to the control group, and continued at this level up to the 21st day post-infection. Serum absorption with viable Y. enterocolitica cells had little effect on antibody levels detected by single radial immunodiffusion. Analysis of serum autoantibody levels revealed that Y. enterocolitica infection induced an increase of anti-myosin and anti-myelin immunoglobulins. The sera did not react with collagen. The present study demonstrates that Y. enterocolitica O:3 infection induces polyclonal activation of murine B cells which is correlated with the activation of some autoreactive lymphocyte clones.

Functional feeding habits of Chironomidae larvae (Insecta, Diptera) in a lotic system from Midwestern region of São Paulo State, Brazil

Functional feeding habits of Chironomidae larvae (Insecta, Diptera) in a lotic system from Mid-western region of São Paulo State, Brazil were analyzed. Collectors were the dominant organisms, repre-sented by genera Chironomus, Fissimentum and Cryptochironomus, following by shredders and predators.

Impact of the Caribbean Information System on the activities of the Caribbean Community Secretariat: with special reference to CARISPLAN abstracts

Includes bibliography

Classification of crucifer cultivars based on the life-history of diamondback moth (Plutella xylostella)

We compared different cultivars and hybrids of crucifers in relation to development and life-history of diamondback moth (Plutella xylostella) to classify the plants according to their resistance to the pest. The plants used were Manteiga da Geórgia kale, Bola de Neve cauliflower, Ramoso Piracicaba Precoce broccoli, Chato-de-quintal cabbage, and the hybrid cabbages Midori, TPC668, TPC308, and TPC681. We evaluated performance daily until the pupal stage. Pupae were assessed individually to determine the pupal weight, performance, and pupal period. We determined the sex ratio, fecundity, fertility, and longevity of the emerged adults and calculated their reproductive potential. Cabbage hybrids TPC668, TPC308, and TPC681 do not support the development and reproduction of the diamondback moth. These hybrids show a level of resistance that is similar to that found the commercially available hybrid Midori and cultivar Chato de Quintal, which are known to be resistant to the diamondback moth. This finding implies that the capitata (cabbage) cultivars are the most suitable for planting because they are more resistant to pest than the cultivar's moth, acephala (kale). © 2013 Copyright Taylor and Francis Group, LLC.