A Bayesian Approach for Decision Making on the Identification of Genes with Different Expression Levels: An Application to Escherichia coli Bacterium Data

A common interest in gene expression data analysis is to identify from a large pool of candidate genes the genes that present significant changes in expression levels between a treatment and a control biological condition. Usually, it is done using a statistic value and a cutoff value that are used to separate the genes differentially and nondifferentially expressed. In this paper, we propose a Bayesian approach to identify genes differentially expressed calculating sequentially credibility intervals from predictive densities which are constructed using the sampled mean treatment effect from all genes in study excluding the treatment effect of genes previously identified with statistical evidence for difference. We compare our Bayesian approach with the standard ones based on the use of the t-test and modified t-tests via a simulation study, using small sample sizes which are common in gene expression data analysis. Results obtained report evidence that the proposed approach performs better than standard ones, especially for cases with mean differences and increases in treatment variance in relation to control variance. We also apply the methodologies to a well-known publicly available data set on Escherichia coli bacterium.

Morse taper implants at different bone levels: a finite element analysis of stress distribution

AIM: To explore the biomechanical effects of the different implantation bone levels of Morse taper implants, employing a finite element analysis (FEA). METHODS: Dental implants (TitamaxCM) with 4x13 mm and 4x11 mm, and their respective abutments with 3.5 mm height, simulating a screwed premolar metal-ceramic crown, had their design performed using the software AnsysWorkbench 10.0. They were positioned in bone blocks, covered by 2.5 mm thickness of mucosa. The cortical bone was designed with 1.5 mm thickness and the trabecular bone completed the bone block. Four groups were formed: group 11CBL (11 mm implant length on cortical bone level), group 11TBL (11 mm implant length on trabecular bone level), group 13CBL (13mm implant length on cortical bone level) and group 13TBL (13 mm implant length on trabecular bone level). Oblique 200 N loads were applied. Von Mises equivalent stresses in cortical and trabecular bones were evaluated with the same design program. RESULTS: The results were shown qualitatively and quantitatively by standard scales for each type of bone. By the results obtained, it can be suggested that positioning the implant completely in trabecular bone brings harm with respect to the generated stresses. Its implantation in the cortical bone has advantages with respect to better anchoring and locking, reflecting a better dissipation of the stresses along the implant/bone interfaces. In addition, the search for anchoring the implant in its apical region in cortical bone is of great value to improve stabilization and consequently better stress distribution. CONCLUSIONS: The implant position slightly below the bone in relation to the bone crest brings advantages as the best long-term predictability with respect to the expected neck bone loss.

Intraspecific competition in Zabrotes subfasciatus: Physiological and behavioral adaptations to different amounts of host

The effects of competition on populations of the bean weevil Zabrotes subfasciatus were analyzed during 41 generations under different competition levels. Three competition environments were established by maintaining the number of couples (6) and varying the amount of available host seeds: HC, high (limited availability of host: 1.35 g); IC, intermediate (intermediate availability of host: 6 g); and LC, low competition (abundance of host: 36 g). It was found that the distribution of the eggs laid on grains was different among treatments: in LC, for example, although females showed high fecundity (35.4 +/- 5.6 eggs/female) the number of eggs laid on each grain was small (1.2 +/- 0.4 eggs on each seed), thus avoiding larval competition of their offspring; whereas in HC treatment, females showed low fecundity (27.04 +/- 4.5 eggs/female) but laid many eggs on each grain (15.03 +/- 4.3 eggs). There were no changes in the ability to respond to different amounts of host via oviposition behavior (egg distribution) during 41 generations. However, HC females had more offspring than LC females under HC conditions. This suggests that HC insects evolved toward higher fitness in crowded conditions. In addition, after inverting the competition level, insects behaved independently of the treatment conditions they experienced through generations, thus showing that oviposition behavior is flexible. Taken together, our results show that Z. subfasciatus presents a broad range of behavioral and physiological responses which allows for quick and reversible adjustments to sudden changes in the amount of resources.

Poly(2,5-bibenzimidazole) Membranes: Physico-Chemical Characterization Focused on Fuel Cell Applications

Membranes of Poly(2,5-benzimidazole) (ABPBI), prepared by polycondensation in polyphosphoric acid, were characterized from the fuel cell application point of view: mechanical properties of the membranes for different acid doping levels, thermal stability, permeability for the different gases/vapors susceptible of use in the cell (hydrogen, oxygen, methanol and ethanol), electro-osmotic water drag coefficient, oxidation stability to hydroxyl radicals, phosphoric acid leaching rate and, finally, in-plane membrane conductivity. ABPBI membranes presented an excellent thermal stability, above 500 degrees C in oxygen, suitable mechanical properties for high phosphoric acid doping levels, a low methanol and ethanol limiting permeation currents, and oxygen permeability compared to Nafion membranes, and a low phosphoric acid leaching rate when exposed to water vapor. On the contrary, hydrogen permeation current was higher than that of Nafion, and the chemical stability was very limited. Membrane conductivity achieved 0.07 S cm(-1) after equilibration with a humid environment. Fuel cell tests showed reasonable good performances, with a maximum power peak of 170 mW cm(-2) for H-2/air at 170 degrees C operating under a humidified hydrogen stream, 39.9 mW cm(-2) for CH3OH/O-2 at 200 degrees C for a methanol/water weight ratio of 1: 2, and 31.5 mW cm(-2) for CH3CH2OH/O-2 at the same conditions than for methanol. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.014207jes] All rights reserved.

Mating system parameters at hierarchical levels of fruits, individuals and populations in the Brazilian insect-pollinated tropical tree, Tabebuia roseo-alba (Bignoniaceae)

For many tree species, mating system analyses have indicated potential variations in the selfing rate and paternity correlation among fruits within individuals, among individuals within populations, among populations, and from one flowering event to another. In this study, we used eight microsatellite markers to investigate mating systems at two hierarchical levels (fruits within individuals and individuals within populations) for the insect pollinated Neotropical tree Tabebuia roseo-alba. We found that T. roseo-alba has a mixed mating system with predominantly outcrossed mating. The outcrossing rates at the population level were similar across two T. roseo-alba populations; however, the rates varied considerably among individuals within populations. The correlated paternity results at different hierarchical levels showed that there is a high probability of shared paternal parentage when comparing seeds within fruits and among fruits within plants and full-sibs occur in much higher proportion within fruits than among fruits. Significant levels of fixation index were found in both populations and biparental inbreeding is believed to be the main cause of the observed inbreeding. The number of pollen donors contributing to mating was low. Furthermore, open-pollinated seeds varied according to relatedness, including half-sibs, full-sibs, self-sibs and self- half-sibs. In both populations, the effective population size within a family (seed-tree and its offspring) was lower than expected for panmictic populations. Thus, seeds for ex situ conservation genetics, progeny tests and reforestation must be collected from a large number of seed-trees to guarantee an adequate effective population in the sample.

Shifts in phylogenetic diversity of archaeal communities in mangrove sediments at different sites and depths in southeastern Brazil

This study focused on the structure and composition of archaeal communities in sediments of tropical mangroves in order to obtain sufficient insight into two Brazilian sites from different locations (one pristine and another located in an urban area) and at different depth levels from the surface. Terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene fragments was used to scan the archaeal community structure, and 16S rRNA gene clone libraries were used to determine the community composition. Redundancy analysis of T-RFLP patterns revealed differences in archaeal community structure according to location, depth and soil attributes. Parameters such as pH, organic matter, potassium and magnesium presented significant correlation with general community structure. Furthermore, phylogenetic analysis revealed a community composition distributed differently according to depth where, in shallow samples, 74.3% of sequences were affiliated with Euryarchaeota and 25.7% were shared between Crenarchaeota and Thaumarchaeota, while for the deeper samples, 24.3% of the sequences were affiliated with Euryarchaeota and 75.7% with Crenarchaeota and Thaumarchaeota. Archaeal diversity measurements based on 16S rRNA gene clone libraries decreased with increasing depth and there was a greater difference between depths (<18% of sequences shared) than sites (>25% of sequences shared). Taken together, our findings indicate that mangrove ecosystems support a diverse archaeal community; it might possibly be involved in nutrient cycles and are affected by sediment properties, depth and distinct locations. (C) 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

HEMATOLOGICAL ANALYSIS OF Micropogonias furnieri, DESMAREST, 1823, SCIANIDAE, FROM TWO ESTUARIES OF BAIXADA SANTISTA, SAO PAULO, BRAZIL

Hematological alterations in fish are considered a useful tool to evaluate pathological processes resulting from the exposure to environmental pollutants. The whitemouth croaker Micropogonias furnieri is a common species in estuarine areas and potentially exposed to many contaminants. In the present study, the hematological characteristics of fish collected at two sites in Baixada Santista (Santos Estuarine System - SES, a polluted site; and the Estuary of Itanhaem River - EIR, unpolluted site) del was analysed. The following blood descriptors were analyzed: number of Erythrocytes (Er), Hematocrit (Ht), Hemoglobin (Hb), Mean Corpuscular Volume (MCV) and Mean Corpuscular Hemoglobin concentration (MCHC). Fish from SES exhibited significant lower levels of Ht and increase on MCHC and Hb. Such differences are likely related to the different contamination levels found in these estuaries.

Toward a Clinical Protocol for Assessing Rod, Cone, and Melanopsin Contributions to the Human Pupil Response

PURPOSE. To better understand the relative contributions of rod, cone, and melanopsin to the human pupillary light reflex (PLR) and to determine the optimal conditions for assessing the health of the rod, cone, and melanopsin pathways with a relatively brief clinical protocol. METHODS. PLR was measured with an eye tracker, and stimuli were controlled with a Ganzfeld system. In experiment 1, 2.5 log cd/m(2) red (640 +/- 10 nm) and blue (467 +/- 17 nm) stimuli of various durations were presented after dark adaptation. In experiments 2 and 3, 1-second red and blue stimuli were presented at different intensity levels in the dark (experiment 2) or on a 0.78 log cd/m(2) blue background (experiment 3). Based on the results of experiments 1 to 3, a clinical protocol was designed and tested on healthy control subjects and patients with retinitis pigmentosa and Leber`s congenital amaurosis. RESULTS. The duration for producing the optimal melanopsin-driven sustained pupil response after termination of an intense blue stimulus was 1 second. PLR rod-and melanopsin-driven components are best studied with low-and high-intensity flashes, respectively, presented in the dark (experiment 2). A blue background suppressed rod and melanopsin responses, making it easy to assess the cone contribution with a red flash (experiment 3). With the clinical protocol, robust melanopsin responses could be seen in patients with few or no contributions from the rods and cones. CONCLUSIONS. It is possible to assess the rod, cone, and melanopsin contributions to the PLR with blue flashes at two or three intensity levels in the dark and one red flash on a blue background. (Invest Ophthalmol Vis Sci. 2011; 52: 6624-6635) DOI: 10.1167/iovs.11-7586

Comparison of pattern VEP results acquired using CRT and TFT stimulators in the clinical practice

There are several electrophysiological systems available commercially. Usually, control groups are required to compare their results, due to the differences between display types. Our aim was to examine the differences between CRT and LCD/TFT stimulators used in pattern VEP responses performed according to the ISCEV standards. We also aimed to check different contrast values toward thresholds. In order to obtain more precise results, we intended to measure the intensity and temporal response characteristics of the monitors with photometric methods. To record VEP signals, a Roland RetiPort electrophysiological system was used. The pattern VEP tests were carried out according to ISCEV protocols on a CRT and a TFT monitor consecutively. Achromatic checkerboard pattern was used at three different contrast levels (maximal, 75, 25%) using 1A degrees and 15` check sizes. Both CRT and TFT displays were luminance and contrast matched, according to the gamma functions based on measurements at several DAC values. Monitor-specific luminance parameters were measured by means of spectroradiometric instruments. Temporal differences between the displays` electronic and radiometric signals were measured with a device specifically built for the purpose. We tested six healthy control subjects with visual acuity of at least 20/20. The tests were performed on each subject three times on different days. We found significant temporal differences between the CRT and the LCD monitors at all contrast levels and spatial frequencies. In average, the latency times were 9.0 ms (+/- 3.3 ms) longer with the TFT stimulator. This value is in accordance with the average of the measured TFT input-output temporal difference values (10.1 +/- A 2.2 ms). According to our findings, measuring the temporal parameters of the TFT monitor with an adequately calibrated measurement setup and correcting the VEP data with the resulting values, the VEP signals obtained with different display types can be transformed to be comparable.

Availability of processed foods in the perimeter of public schools in urban areas

Objective: To assess the availability of food in relation to their degree of industrial processing and the types of food stores in the perimeters of elementary schools. Method: This is a cross-sectional study. 82 food stores located within a 500 m radius buffer of three public schools located in three distinct regions with different socioeconomic levels in the municipality of Santos, state of Sao Paulo, Brazil, were assessed. All streets within a 500-meter radius of the schools were covered, geographic coordinates were recorded and information about the stores and food items available were collected by direct observation and interview with store managers. Available food items were classified in relation to their degree of industrial processing as ultra-processed foods and minimally processed foods. Kernel's density maps were used to assess the degree of agglomeration of stores near the schools. Results: The stores that offered mostly ultra-processed foods were significantly closer to schools than those who offered mostly minimally processed foods. There was a significant difference between the availability of processed food in different types of stores and between the three regions assessed. Conclusions: The data found by this work evidences that children who attend the three public schools assessed are exposed to an environment that encourages the consumption of ultra-processed foods through easier access of these products in the studied stores.

Preparation and characterization of poly(vinyl butyral)-polyaniline-montmorillonite nanocomposites

Poly(vinyl butyral)-polyaniline-sodium montmorillonite nanocomposites were prepared via polymerization of aniline between clay mineral platelets at two different pH levels (2.0 and 5.0), followed by dispersion of the polyaniline-sodium montmorillonite nanocomposite in a poly(vinyl butyral) solution. A comparison was made of the effect of the pH levels and the polyaniline-sodium montmorillonite nanocomposite precursor on the final structures of the poly(vinyl butyral) nanocomposites and their electrical conductivities. X-ray diffraction patterns revealed the formation of nanocomposites at both pH levels. UV-Vis spectra indicated that the polyaniline formed at both pH levels was conductive, with the UV-Vis spectra presenting a band at 420 nm corresponding to the polaronic form and the beginning of a new band at 600 nm indicating the presence of polaronic segments. FTIR spectra revealed the peaks of the groups present in polyaniline and poly(vinyl butyral) nanocomposites. The electrical conductivities of the polyaniline and poly(vinyl butyral) nanocomposites prepared at pH 2.0 were lower than those of the same nanocomposites prepared at pH 5.0, probably due to the lower formation of polyaniline chains in a more acidic dispersion and to the final configuration of polyaniline in the nanocomposites.

Impact of Land Degradation on Soil Microbial Biomass and Activity in Northeast Brazil

Land degradation causes great changes in the soil biological properties. The process of degradation may decrease soil microbial biomass and consequently decrease soil microbial activity. The study was conducted out during 2009 and 2010 at the four sites of land under native vegetation (NV), moderately degraded land (LDL), highly degraded land (HDL) and land under restoration for four years (RL) to evaluate changes in soil microbial biomass and activity in lands with different degradation levels in comparison with both land under native vegetation and land under restoration in Northeast Brazil. Soil samples were collected at 0-10 cm depth. Soil organic carbon (SOC), soil microbial biomass C (MBC) and N (MBN), soil respiration (SR), and hydrolysis of fluorescein diacetate (FDA) and dehydrogenase (DHA) activities were analyzed. After two years of evaluation, soil MBC, MBN, FDA and DHA had higher values in the NV, followed by the RL. The decreases of soil microbial biomass and enzyme activities in the degraded lands were approximately 8-10 times as large as those found in the NV. However, after land restoration, the MBC and MBN increased approximately 5-fold and 2-fold, respectively, compared with the HDL. The results showed that land degradation produced a strong decrease in soil microbial biomass. However, land restoration may promote short- and long-term increases in soil microbial biomass.

Thyroid hormone profile in breast cancer patients in postmenopause

Objective: The aim of this study was to determine thyroid hormone (TH) profile in postmenopausal patients with breast cancer (BC). Subjects and methods: 12 CaM patients stages I or II, without interventions that could interfere with tumor progression were selected, as well as and a control group with 18 postmenopausal women without CaM. We measured serum anti-thyroperoxidase antibody (TPOAB), thyroid-stimulating hormone (TSH), free thyroxine (T4L), estradiol (E2), follicle-stimulating hormone (FSH), and luteinizing hormone (LH), before and after surgery, besides immunohistochemistry for estrogen (ER) and progesterone (PR) receptors. Results: Four patients with CaM showed changes in thyroid hormone profile: two had hyperthyroidism, one hypothyroidism, and one was positive for TPO-AB. All of them positive for ER and PR.TSH levels in breast cancer patients were not different from levels found in the control group (1.89 +/- 1.56 vs. 2.86 +/- 3.12 mIU/mL), but the levels of T4L in patients with CaM were statistically higher than those of the control group (1.83 +/- 0.57 vs. 1.10 +/- 0.20 ng/dL). Conclusion: These results reinforce the need for assessment of thyroid status in CaM patients, since in the absence of E2, changes in clinical HTs can act in E2-controlled processes. Arq Bras Endocrinol Metab. 2012;56(4):238-43

Reliability and construct validity of the karate-specific aerobic test

Chaabene, H, Hachana, Y, Franchini, E, Mkaouer, B, Montassar, M, and Chamari, K. Reliability and construct validity of the karate-specific aerobic test. J Strength Cond Res 26(12): 3454-3460, 2012-The aim of this study was to examine absolute and relative reliabilities and external responsiveness of the Karate-specific aerobic test (KSAT). This study comprised 43 male karatekas, 19 of them participated in the first study to establish test-retest reliability and 40, selected on the bases of their karate experience and level of practice, participated in the second study to identify external responsiveness of the KSAT. The latter group was divided into 2 categories: national-level group (G(n)) and regional-level group (Gr). Analysis showed excellent test-retest reliability of time to exhaustion (TE), with intraclass correlation coefficient ICC(3,1) >0.90, standard error of measurement (SEM) <5%: (3.2%) and mean difference (bias) +/- the 95% limits of agreement: -9.5 +/- 78.8 seconds. There was a significant difference between test-retest session in peak lactate concentration (Peak [La]) (9.12 +/- 2.59 vs. 8.05 +/- 2.67 mmol.L-1; p < 0.05) but not in peak heart rate (HRpeak) and rating of perceived exertion (RPE) (196 +/- 9 vs. 194 +/- 9 b.min(-1) and 7.6 +/- 0.93 vs. 7.8 +/- 1.15; p > 0.05), respectively. National-level karate athletes (1,032 +/- 101 seconds) were better than regional level (841 +/- 134 seconds) on TE performance during KSAT (p < 0.001). Thus, KSAT provided good external responsiveness. The area under the receiver operator characteristics curve was >0.70 (0.86; confidence interval 95%: 0.72-0.95). Significant difference was detected in Peak [La] between national- (6.09 +/- 1.78 mmol.L-1) and regional-level (8.48 +/- 2.63 mmol.L-1) groups, but not in HRpeak (194 +/- 8 vs. 195 +/- 8 b.min(-1)) and RPE (7.57 +/- 1.15 vs. 7.42 +/- 1.1), respectively. The result of this study indicates that KSAT provides excellent absolute and relative reliabilities. The KSAT can effectively distinguish karate athletes of different competitive levels. Thus, the KSAT may be suitable for field assessment of aerobic fitness of karate practitioners.

Effects of Aspergillus spp. exogenous fibrolytic enzymes on in vitro fermentation of tropical forages

BACKGROUND: Cellulose and hemicellulose are quantitatively the most important structural carbohydrates present in ruminant diets. Rumen micro-organisms produce enzymes that catalyse their hydrolysis, but the complex network formed by structural carbohydrates and lignin reduces their digestibility and restricts efficient utilisation of feeds by ruminants. This study aimed to produce two enzymatic extracts, apply them in ruminant diets to determine the best levels for ruminal digestibility and evaluate their effects on in vitro digestibility. RESULTS: In experiment 1 a two-stage in vitro technique was used to examine the effects of different enzymatic levels of Aspergillus japonicus and Aspergillus terricola on tropical forages. Enzyme addition had minor effects on corn silage at the highest enzymatic level. In experiment 2 an in vitro gas production (GP) technique was applied to determine apparent in vitro organic matter digestibility and metabolisable energy. The addition of enzymes in GP showed interesting results. Good data were obtained using sugar cane and Tifton-85 hay supplemented with extracts of A. japonicus and A. terricola respectively. CONCLUSION: Overall, the study suggests that addition of crude extracts containing exogenous fibrolytic enzymes to ruminant diets enhances the effective utilisation of ruminant feedstuffs such as forages. Copyright (c) 2012 Society of Chemical Industry