Survival analysis and iniquities in older Brazilians: a six year follow up survey in São Paulo, Brazil

Maria Lucia Lebrão is the Coordinator of the SABE study. Jair LF Santos and Yeda AO Duarte receive support from National Council of Research (CNPq). The SABE study is supported by The São Paulo Research Foundation (FAPESP).

Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations

Abstract Background Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC Methods Microarray experiments were performed with custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. Samples from 18 primary RCC tumors and 11 nontumor adjacent matched tissues were analyzed. Meta-analyses were performed with microarray expression data from three additional human tissues (normal liver, prostate tumor and kidney nontumor samples), and with large-scale public data for epigenetic regulatory marks and for evolutionarily conserved sequences. Results A signature of 29 intronic lncRNAs differentially expressed between RCC and nontumor samples was obtained (false discovery rate (FDR) <5%). A signature of 26 intronic lncRNAs significantly correlated with the RCC five-year patient survival outcome was identified (FDR <5%, p-value ≤0.01). We identified 4303 intronic antisense lncRNAs expressed in RCC, of which 22% were significantly (p <0.05) cis correlated with the expression of the mRNA in the same locus across RCC and three other human tissues. Gene Ontology (GO) analysis of those loci pointed to 'regulation of biological processes’ as the main enriched category. A module map analysis of the protein-coding genes significantly (p <0.05) trans correlated with the 20% most abundant lncRNAs, identified 51 enriched GO terms (p <0.05). We determined that 60% of the expressed lncRNAs are evolutionarily conserved. At the genomic loci containing the intronic RCC-expressed lncRNAs, a strong association (p <0.001) was found between their transcription start sites and genomic marks such as CpG islands, RNA Pol II binding and histones methylation and acetylation. Conclusion Intronic antisense lncRNAs are widely expressed in RCC tumors. Some of them are significantly altered in RCC in comparison with nontumor samples. The majority of these lncRNAs is evolutionarily conserved and possibly modulated by epigenetic modifications. Our data suggest that these RCC lncRNAs may contribute to the complex network of regulatory RNAs playing a role in renal cell malignant transformation.

Tokamak TCABR: Acquisition system, data analysis, and remote participation using MDSplus

Each plasma physics laboratory has a proprietary scheme to control and data acquisition system. Usually, it is different from one laboratory to another. It means that each laboratory has its own way to control the experiment and retrieving data from the database. Fusion research relies to a great extent on international collaboration and this private system makes it difficult to follow the work remotely. The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The choice of MDSplus (Model Driven System plus) is proved by the fact that it is widely utilized, and the scientists from different institutions may use the same system in different experiments in different tokamaks without the need to know how each system treats its acquisition system and data analysis. Another important point is the fact that the MDSplus has a library system that allows communication between different types of language (JAVA, Fortran, C, C++, Python) and programs such as MATLAB, IDL, OCTAVE. In the case of tokamak TCABR interfaces (object of this paper) between the system already in use and MDSplus were developed, instead of using the MDSplus at all stages, from the control, and data acquisition to the data analysis. This was done in the way to preserve a complex system already in operation and otherwise it would take a long time to migrate. This implementation also allows add new components using the MDSplus fully at all stages. (c) 2012 Elsevier B.V. All rights reserved.

A comparative study between crack analysis and a mechanical test for assessing the polymerization stress of restorative composites

Objectives. To verify the hypothesis that crack analysis and a mechanical test would rank a series of composites in a similar order with respect to polymerization stress. Also, both tests would show similar relationships between stress and composite elastic modulus and/or shrinkage. Methods. Soda-lime glass discs (2-mm thick) with a central perforation (3.5-mm diameter) received four Vickers indentations 500 mu m from the cavity margin. The indent cracks were measured (500x) prior and 10 min after the cavity was restored with one of six materials (Kalore/KL, Gradia/GR, Ice/IC, Wave/WV, Majesty Flow/MF, and Majesty Posterior/MP). Stresses at the indent site were calculated based on glass fracture toughness and increase in crack length. Stress at the bonded interface was calculated using the equation for an internally pressurized cylinder. The mechanical test used a universal testing machine and glass rods (5-mm diameter) as substrate. An extensometer monitored specimen height (2 mm). Nominal stress was calculated dividing the maximum shrinkage force by the specimen cross-sectional area. Composite elastic modulus was determined by nanoindentation and post-gel shrinkage was measured using strain gages. Data were subjected to one-way ANOVA/Tukey or Kruskal-Wallis/Mann-Whitney tests (alpha: 5%). Results. Both tests grouped the composites in three statistical subsets, with small differences in overlapping between the intermediate subset (MF, WV) and the highest (MP, IC) or the lowest stress materials (KL, GR). Higher stresses were developed by composites with high modulus and/or high shrinkage. Significance. Crack analysis demonstrated to be as effective as the mechanical test to rank composites regarding polymerization stress. (c) 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Quantitative proteomic analysis and functional studies reveal that nucleophosmin is involved in cell death in glioblastoma cell line transfected with siRNA

Previously, we reported that nucleophosmin (NPM) was increased in glioblastoma multiforme (GBM). NPM is a phosphoprotein related to apoptosis, ribosome biogenesis, mitosis, and DNA repair, but details about its function remain unclear. We treated U87MG and A172 cells with small interference RNA (siRNA) and obtained a reduction of 80% in NPM1 expression. Knockdown at the protein level was evident after the 4th day and was maintained until the 7th day of transfection that was investigated by quantitative proteomic analysis using isobaric tags. The comparison of proteomic analysis of NPM1-siRNA against controls allowed the identification of 14 proteins, two proteins showed increase and 12 presented a reduction of expression levels. Gene ontology assigned most of the hypoexpressed proteins to apoptosis regulation, including GRP78. NPM1 silencing did not impair cell proliferation until the 7th day after transfection, but sensitized U87MG cells to temozolomide (TMZ), culminating with an increase in cell death and provoking at a later period a reduction of colony formation. In a large data set of GBM patients, both GRP78 and NPM1 genes were upregulated and presented a tendency to shorter overall survival time. In conclusion, NPM proved to participate in the apoptotic process, sensitizing TMZ-treated U87MG and A172 cells to cell death, and in association with upregulation of GRP78 may be helpful as a predictive factor of poor prognosis in GBM patients.

Postispinatus youngi n. gen., n. sp (Apseudomorpha; Tanaidacea; Crustacea): phylogenetic analysis and taxonomic remarks about kalliapseudids

The presence of setae or a sensorial structure on the dactylus of pereopod 1 as one of the defining features of the family Kalliapseudidae is re-evaluated. A new genus, Postispinatus, including the new species P. youngi n. gen., n. sp., is described and thought to belong to the Kalliapseudidae based on phylogenetic analysis. The diagnostic features of new genus-and species by monotypy -are: basal article of uropod with two curved spiniform processes; exopods on the fourth and fifth pereopods of the manca stage; absence of a maxillule palp.

In Silico Analysis and Immunohistochemical Characterization of NaPi2b Protein Expression in Ovarian Carcinoma With Monoclonal Antibody Mx35

Introduction: Ovarian adenocarcinoma is frequently detected at the late stage, when therapy efficacy is limited and death occurs in up to 50% of the cases. A potential novel treatment for this disease is a monoclonal antibody that recognizes phosphate transporter sodium-dependent phosphate transporter protein 2b (NaPi2b). Materials and Methods: To better understand the expression of this protein in different histologic types of ovarian carcinomas, we immunostained 50 tumor samples with anti-NaPi2b monoclonal antibody MX35 and, in parallel, we assessed the expression of the gene encoding NaPi2b (SCL34A2) by in silico analysis of microarray data. Results: Both approaches detected higher expression of NaPi2b (SCL34A2) in ovarian carcinoma than in normal tissue. Moreover, a comprehensive analysis indicates that SCL34A2 is the only gene of the several phosphate transporters genes whose expression differentiates normal from carcinoma samples, suggesting it might exert a major role in ovarian carcinomas. Immunohistochemical and mRNA expression data have also shown that 2 histologic subtypes of ovarian carcinoma express particularly high levels of NaPi2b: serous and clear cell adenocarcinomas. Serous adenocarcinomas are the most frequent, contrasting with clear cell carcinomas, rare, and with worse prognosis. Conclusion: This identification of subgroups of patients expressing NaPi2b may be important in selecting cohorts who most likely should be included in future clinical trials, as a recently generated humanized version of MX35 has been developed.

Bioelectrical Impedance Analysis and Skinfold Thickness Sum in Assessing Body Fat Mass of Renal Dialysis Patients

Objective: In chronic renal failure patients under hemodialysis (HD) treatment, the availability of simple, safe, and effective tools to assess body composition enables evaluation of body composition accurately, in spite of changes in body fluids that occur in dialysis therapy, thus contributing to planning and monitoring of nutritional treatment. We evaluated the performance of bioelectrical impedance analysis (BIA) and the skinfold thickness sum (SKF) to assess fat mass (FM) in chronic renal failure patients before (BHD) and after (AHD) HD, using air displacement plethysmography (ADP) as the standard method. Design: This single-center cross-sectional trial involved comparing the FM of 60 HD patients estimated BHD and AHD by BIA (multifrequential; 29 women, 31 men) and by SKF with those estimated by the reference method, ADP. Body fat-free mass (FFM) was also obtained by subtracting the total body fat from the individual total weight. Results: Mean estimated FM (kg [%]) observed by ADP BHD was 17.95 +/- 0.99 kg (30.11% +/- 1.30%), with a 95% confidence interval (CI) of 16.00 to 19.90 (27.56 to 32.66); mean estimated FM observed AHD was 17.92 +/- 1.11 kg (30.04% +/- 1.40%), with a 95% CI of 15.74 to 20.10 (27.28 to 32.79). Neither study period showed a difference in FM and FFM (for both kg and %) estimates by the SKF method when compared with ADP; however, the BIA underestimated the FM and overestimated the FFM (for both kg and %) when compared with ADP. Conclusion: The SKF, but not the BIA, method showed results similar to ADP and can be considered adequate for FM evaluation in HD patients. (C) 2012 by the National Kidney Foundation, Inc. All rights reserved.

The Environmental Theme in Representations and Practices of Family Health Professionals in the Municipality of Manaus - State of Amazonas/Brazil

There are abundant scientific evidences showing that the increased risk of exposure to diseases is a consequence of anthropogenic environmental changes. In the Family Health Strategy, tasks with a clear environmental focus are prescribed, indicating to the professional teams that they should consider these aspects in their health practices. The objective of this research was to study representations and practices of Family Health Professionals of Manaus - State of Amazonas, Northern Brazil - about environmental issues and their interface with public health. Data were collected by means of participant observation and semi-structured interviews, and the qualitative analysis was carried out through Content Analysis and Methodological Triangulation. The results showed that most professionals do not understand the environment in a systemic way, even though they recognize the great impact that environmental factors have on human health; as interventions, the educational practices follow traditional methodologies and focus on blaming the individual and on the simple transmission of knowledge; the professionals' relationship with the community is limited to personal and/or collective care. It is concluded that in order to the Family Health Strategy to contribute to restructure the system, it is essential to redirect this new health policy model so that it becomes effective as a social and environmental practice.

Bioelectrical impedance analysis and anthropometry for the determination of body composition in rats: effects of high-fat and high-sucrose diets

Objective The aim of the present study was to determine the impedance of Wistar rats treated with high-fat and high-sucrose diets and correlate their biochemical and anthropometric parameters with chemical analysis of the carcass. Methods Twenty-four male Wistar rats were fed a standard (AIN-93), high-fat (50% fat) or high-sucrose (59% of sucrose) diet for 4 weeks. Abdominal and thoracic circumference and body length were measured. Bioelectrical impedance analysis was used to determine resistance and reactance. Final body composition was determined by chemical analysis. Results Higher fat intake led to a high percentage of liver fat and cholesterol and low total body water in the High-Fat group, but these changes in the biochemical profile were not reflected by the anthropometric measurements or bioelectrical impedance analysis variables. Anthropometric and bioelectrical impedance analysis changes were not observed in the High-Sucrose group. However, a positive association was found between body fat and three anthropometric variables: body mass index, Lee index and abdominal circumference. Conclusion Bioelectrical impedance analysis did not prove to be sensitive for detecting changes in body composition, but body mass index, Lee index and abdominal circumference can be used for estimating the body composition of rats.

Thermal Analysis and Raman Spectra of Different Phases of the Ionic Liquid Butyltrimethylammonium Bis(trifluoromethylsulfonyl)imide

The ionic liquid butyltrimethylammonium bis(trifluoromethylsulfonyl)imide, [C4C1C1C1N][Tf2N], is a glass-forming liquid that exhibits partial crystallization depending on the cooling rate. Differential scanning calorimetry (DSC) indicates crystallization at T-c = 227 K, melting at T-m = 258 K, glass transition at T-g similar to 191 K, and also cold crystallization at T-cc similar to 219 K. Raman spectroscopy shows that the crystalline structure obtained by slow cooling is formed with [Tf2N](-) in cisoid conformation, whereas [Tf2N](-) in transoid conformation results from fast cooling. No preferred conformation of the butyl chain of the [C4C1C1C1N](+) cation is favored by slow or fast cooling of [C4C1C1C1N][Tf2N]. Low-frequency Raman spectroscopy shows that crystalline domains developing in the supercooled liquid result in a glacial state made of a mixture of crystallites and amorphous phase. However, these crystalline structures obtained by slow cooling or cold crystallization are not the same because anion-cation interactions promote local structures with distinct conformations of the [Tf2N](-) anion.

Preparation and characterization of chloroaluminum phthalocyanine-loaded solid lipid nanoparticles by thermal analysis and powder X-ray diffraction techniques

Solid lipid nanoparticles (SLN) without drug and SLN loaded with chloroaluminum phthalocyanine (AlClPc) were prepared by solvent diffusion method in aqueous system and characterized by thermal analyses and X-ray diffraction (XRD) in this study. Determination of particle size, zeta potential (ZP), and encapsulation efficiency were also evaluated. SLN containing AlClPc of nanometer size with high encapsulation efficiency and ZP were obtained. The results indicated that the size of SLN loaded with AlClPc is larger than that of the inert particle, but ZP is not changed significantly with incorporation of the drug. In differential scanning calorimetry (DSC) curves, it was observed that the melting point of stearic acid (SA) isolated and in SLN occurred at 55 and 64 degrees C, respectively, suggesting the presence of different polymorphs. DSC also shows that the crystallinity state of SLN was much less than that of SA isolated. The incorporation of drug in SLN may have been favored by this lower crystallinity degree of the samples. XRD techniques corroborated with the thermal analytic techniques, suggesting the polymorphic modifications of stearic acid.

Behavioral and EEG effects of GABAergic manipulation of the nigro-tectal pathway in the Wistar audiogenic rat (WAR) strain II: An EEG wavelet analysis and retrograde neuronal tracer approach

The role of the substantia nigra pars reticulata (SNPr) and superior colliculus (SC) network in rat strains susceptible to audiogenic seizures still remain underexplored in epileptology. In a previous study from our laboratory, the GABAergic drugs bicuculline (BIC) and muscimol (MUS) were microinjected into the deep layers of either the anterior SC (aSC) or the posterior SC (pSC) in animals of the Wistar audiogenic rat (WAR) strain submitted to acoustic stimulation, in which simultaneous electroencephalographic (EEG) recording of the aSC, pSC, SNPr and striatum was performed. Only MUS microinjected into the pSC blocked audiogenic seizures. In the present study, we expanded upon these previous results using the retrograde tracer Fluorogold (FG) microinjected into the aSC and pSC in conjunction with quantitative EEG analysis (wavelet transform), in the search for mechanisms associated with the susceptibility of this inbred strain to acoustic stimulation. Our hypothesis was that the WAR strain would have different connectivity between specific subareas of the superior colliculus and the SNPr when compared with resistant Wistar animals and that these connections would lead to altered behavior of this network during audiogenic seizures. Wavelet analysis showed that the only treatment with an anticonvulsant effect was MUS microinjected into the pSC region, and this treatment induced a sustained oscillation in the theta band only in the SNPr and in the pSC. These data suggest that in WAR animals, there are at least two subcortical loops and that the one involved in audiogenic seizure susceptibility appears to be the pSC-SNPr circuit. We also found that WARs presented an increase in the number of FG + projections from the posterior SNPr to both the aSC and pSC (primarily to the pSC), with both acting as proconvulsant nuclei when compared with Wistar rats. We concluded that these two different subcortical loops within the basal ganglia are probably a consequence of the WAR genetic background. (C) 2012 Elsevier Inc. All rights reserved.

Pedigree analysis and inbreeding depression on growth traits in Brazilian Marchigiana and Bonsmara breeds

The study of population structure by pedigree analysis is useful to identify important circumstances that affect the genetic history of populations. The intensive use of a small number of superior individuals may reduce the genetic diversity of populations. This situation is very common for the beef cattle breeds. Therefore, the objectives of the present study were to analyze the pedigree and possible inbreeding depression on traits of economic interest in the Marchigiana and Bonsmara breeds and to test the inclusion of the individual inbreeding coefficient (F-i) or individual increases in inbreeding coefficient (Delta F-i) in the genetic evaluation model for the quantification of inbreeding depression. The complete pedigree file of the Marchigiana breed included 29,411 animals born between 1950 and 2003. For the Bonsmara breed, the pedigree file included 18,695 animals born between 1988 and 2006. Only animals with at least 2 equivalent generations of known pedigree were kept in the analyses of inbreeding effect on birth weight, weaning weight measured at about 205 d, and BW at 14 mo in the Marchigiana breed, and on birth weight, weaning weight, and scro-tal circumference measured at 12 mo in the Bonsmara breed. The degree of pedigree knowledge was greater for Marchigiana than for Bonsmara animals. The average generation interval was 7.02 and 3.19 for the Marchigiana and Bonsmara breed, respectively. The average inbreeding coefficient was 1.33% for Marchigiana and 0.26% for Bonsmara. The number of ancestors explaining 50% of the gene pool and effective population size computed via individual increase in coancestry were 13 and 97.79 for Marchigiana and 41 and 54.57 for Bonsmara, respectively. These estimates indicate reduction in genetic variability in both breeds. Inbreeding depression was observed for most of the growth traits. The model including Delta F-i can be considered more adequate to quantify inbreeding depression. The inclusion of F-i or Delta F-i in the genetic evaluation model may not result in better fit to the data. A genetic evaluation with simultaneous estimation of inbreeding depression can be performed in Marchigiana and Bonsmara breeds, providing additional information to producers and breeders.

Effects of discontinuous Percoll gradient centrifugation on the quality of bovine spermatozoa evaluated with computer-assisted semen analysis and fluorescent probes association

The objective of this study was to evaluate the quality of bovine frozen-thawed sperm cells after Percoll gradient centrifugation. Frozen semen doses were obtained from six bulls of different breeds, including three taurine and three Zebu animals. Four ejaculates per bull were evaluated before and after discontinuous Percoll gradient centrifugation. Sperm motility was assessed by computer-assisted semen analysis and the integrity of the plasma and acrosomal membranes, as well as mitochondrial function, were evaluated using a combination of fluorescent probes propidium iodide, fluorescein isothiocyanate-conjugated Pisum sativum agglutinin and 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolcarbocyanine iodide. The procedure of Percoll gradient centrifugation increased the percentage of total and progressive sperm motility, beat frequency, rectilinear motility, linearity and rapidly moving cells. In addition, the percentage of cells with intact plasma membrane and mitochondrial membrane potential was increased in post-centrifugation samples. However, the percentage of sperm cells with intact acrosomal membrane was markedly reduced. The method used selected the motile cells with intact plasma membrane and higher mitochondrial functionality in frozen-thawed bull semen, but processing, centrifugation and/or the Percoll medium caused damage to the acrosomal membrane.