The impact of measurement errors in the identification of regulatory networks

Background: There are several studies in the literature depicting measurement error in gene expression data and also, several others about regulatory network models. However, only a little fraction describes a combination of measurement error in mathematical regulatory networks and shows how to identify these networks under different rates of noise. Results: This article investigates the effects of measurement error on the estimation of the parameters in regulatory networks. Simulation studies indicate that, in both time series (dependent) and non-time series (independent) data, the measurement error strongly affects the estimated parameters of the regulatory network models, biasing them as predicted by the theory. Moreover, when testing the parameters of the regulatory network models, p-values computed by ignoring the measurement error are not reliable, since the rate of false positives are not controlled under the null hypothesis. In order to overcome these problems, we present an improved version of the Ordinary Least Square estimator in independent (regression models) and dependent (autoregressive models) data when the variables are subject to noises. Moreover, measurement error estimation procedures for microarrays are also described. Simulation results also show that both corrected methods perform better than the standard ones (i.e., ignoring measurement error). The proposed methodologies are illustrated using microarray data from lung cancer patients and mouse liver time series data. Conclusions: Measurement error dangerously affects the identification of regulatory network models, thus, they must be reduced or taken into account in order to avoid erroneous conclusions. This could be one of the reasons for high biological false positive rates identified in actual regulatory network models.

GLOBAL WELL-POSEDNESS AND NON-LINEAR STABILITY OF PERIODIC TRAVELING WAVES FOR A SCHRODINGER-BENJAMIN-ONO SYSTEM

The objective of this paper is two-fold: firstly, we develop a local and global (in time) well-posedness theory for a system describing the motion of two fluids with different densities under capillary-gravity waves in a deep water flow (namely, a Schrodinger-Benjamin-Ono system) for low-regularity initial data in both periodic and continuous cases; secondly, a family of new periodic traveling waves for the Schrodinger-Benjamin-Ono system is given: by fixing a minimal period we obtain, via the implicit function theorem, a smooth branch of periodic solutions bifurcating a Jacobian elliptic function called dnoidal, and, moreover, we prove that all these periodic traveling waves are nonlinearly stable by perturbations with the same wavelength.

Non-Cardiac Surgery in Developing Countries: Epidemiological Aspects and Economical Opportunities - The Case of Brazil

Background: Worldwide distribution of surgical interventions is unequal. Developed countries account for the majority of surgeries and information about non-cardiac operations in developing countries is scarce. The purpose of our study was to describe the epidemiological data of non-cardiac surgeries performed in Brazil in the last years. Methods and Findings: This is a retrospective cohort study that investigated the time window from 1995 to 2007. We collected information from DATASUS, a national public health system database. The following variables were studied: number of surgeries, in-hospital expenses, blood transfusion related costs, length of stay and case fatality rates. The results were presented as sum, average and percentage. The trend analysis was performed by linear regression model. There were 32,659,513 non-cardiac surgeries performed in Brazil in thirteen years. An increment of 20.42% was observed in the number of surgeries in this period and nowadays nearly 3 million operations are performed annually. The cost of these procedures has increased tremendously in the last years. The increment of surgical cost was almost 200%. The total expenses related to surgical hospitalizations were more than $10 billion in all these years. The yearly cost of surgical procedures to public health system was more than $1.27 billion for all surgical hospitalizations, and in average, U$445.24 per surgical procedure. The total cost of blood transfusion was near $98 million in all years and annually approximately $10 million were spent in perioperative transfusion. The surgical mortality had an increment of 31.11% in the period. Actually, in 2007, the surgical mortality in Brazil was 1.77%. All the variables had a significant increment along the studied period: r square (r(2)) = 0.447 for the number of surgeries (P = 0.012), r(2) = 0.439 for in-hospital expenses (P = 0.014) and r(2) = 0.907 for surgical mortality (P = 0.0055). Conclusion: The volume of surgical procedures has increased substantially in Brazil through the past years. The expenditure related to these procedures and its mortality has also increased as the number of operations. Better planning of public health resource and strategies of investment are needed to supply the crescent demand of surgery in Brazil.

Identification of protein-coding and non-coding RNA expression profiles in CD34(+) and in stromal cells in refractory anemia with ringed sideroblasts

Background: Myelodysplastic syndromes (MDS) are a group of clonal hematological disorders characterized by ineffective hematopoiesis with morphological evidence of marrow cell dysplasia resulting in peripheral blood cytopenia. Microarray technology has permitted a refined high-throughput mapping of the transcriptional activity in the human genome. Non-coding RNAs (ncRNAs) transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression, and in the regulation of exon-skipping and intron retention. Characterization of ncRNAs in progenitor cells and stromal cells of MDS patients could be strategic for understanding gene expression regulation in this disease. Methods: In this study, gene expression profiles of CD34(+) cells of 4 patients with MDS of refractory anemia with ringed sideroblasts (RARS) subgroup and stromal cells of 3 patients with MDS-RARS were compared with healthy individuals using 44 k combined intron-exon oligoarrays, which included probes for exons of protein-coding genes, and for non-coding RNAs transcribed from intronic regions in either the sense or antisense strands. Real-time RT-PCR was performed to confirm the expression levels of selected transcripts. Results: In CD34(+) cells of MDS-RARS patients, 216 genes were significantly differentially expressed (q-value <= 0.01) in comparison to healthy individuals, of which 65 (30%) were non-coding transcripts. In stromal cells of MDS-RARS, 12 genes were significantly differentially expressed (q-value <= 0.05) in comparison to healthy individuals, of which 3 (25%) were non-coding transcripts. Conclusions: These results demonstrated, for the first time, the differential ncRNA expression profile between MDS-RARS and healthy individuals, in CD34(+) cells and stromal cells, suggesting that ncRNAs may play an important role during the development of myelodysplastic syndromes.

Near infrared spectroscopy for soil bulk density assessment

P>Soil bulk density values are needed to convert organic carbon content to mass of organic carbon per unit area. However, field sampling and measurement of soil bulk density are labour-intensive, costly and tedious. Near-infrared reflectance spectroscopy (NIRS) is a physically non-destructive, rapid, reproducible and low-cost method that characterizes materials according to their reflectance in the near-infrared spectral region. The aim of this paper was to investigate the ability of NIRS to predict soil bulk density and to compare its performance with published pedotransfer functions. The study was carried out on a dataset of 1184 soil samples originating from a reforestation area in the Brazilian Amazon basin, and conventional soil bulk density values were obtained with metallic ""core cylinders"". The results indicate that the modified partial least squares regression used on spectral data is an alternative method for soil bulk density predictions to the published pedotransfer functions tested in this study. The NIRS method presented the closest-to-zero accuracy error (-0.002 g cm-3) and the lowest prediction error (0.13 g cm-3) and the coefficient of variation of the validation sets ranged from 8.1 to 8.9% of the mean reference values. Nevertheless, further research is required to assess the limits and specificities of the NIRS method, but it may have advantages for soil bulk density predictions, especially in environments such as the Amazon forest.

Nitrogen availability patterns in white-sand vegetations of Central Brazilian Amazon

Addressing spatial variability in nitrogen (N) availability in the Central Brazilian Amazon, we hypothesized that N availability varies among white-sand vegetation types (campina and campinarana) and lowland tropical forests (dense terra-firme forests) in the Central Brazilian Amazon, under the same climate conditions. Accordingly, we measured soil and foliar N concentration and N isotope ratios (delta(15)N) throughout the campina-campinarana transect and compared to published dense terra-firme forest results. There were no differences between white-sand vegetation types in regard to soil N concentration, C:N ratio and delta(15)N across the transect. Both white-sand vegetation types showed very low foliar N concentrations and elevated foliar C:N ratios, and no significant difference between site types was observed. Foliar delta(15)N was depleted, varying from -9.6 to 1.6aEuro degrees in the white-sand vegetations. The legume Aldina heterophylla had the highest average delta(15)N values (-1.5aEuro degrees) as well as the highest foliar N concentration (2.1%) while the non-legume species had more depleted delta(15)N values and the average foliar N concentrations varied from 0.9 to 1.5% among them. Despite the high variation in foliar delta(15)N among plants, a significant and gradual (15)N-enrichment in foliar isotopic signatures throughout the campina-campinarana transect was observed. Individual plants growing in the campinarana were significantly enriched in (15)N compared to those in campina. In the white-sand N-limited ecosystems, the differentiation of N use seems to be a major cause of variations observed in foliar delta(15)N values throughout the campina-campinarana transect.

Neutron Activation Analysis: A Primary (Ratio) Method to Determine SI-Traceable Values of Element Content in Complex Samples

The metrological principles of neutron activation analysis are discussed. It has been demonstrated that this method can provide elemental amount of substance with values fully traceable to the SI. The method has been used by several laboratories worldwide in a number of CCQM key comparisons - interlaboratory comparison tests at the highest metrological level - supplying results equivalent to values from other methods for elemental or isotopic analysis in complex samples without the need to perform chemical destruction and dissolution of these samples. The CCOM accepted therefore in April 2007 the claim that neutron activation analysis should have the similar status as the methods originally listed by the CCOM as `primary methods of measurement`. Analytical characteristics and scope of application are given.

Atenolol blunts blood pressure increase during dynamic resistance exercise in hypertensives

center dot Dynamic resistance exercise promotes a sizeable increase in blood pressure during its execution in non medicated hypertensives. WHAT THIS STUDY ADDS center dot Atenolol not only decreases blood pressure level but also mitigates the increase of blood pressure during dynamic resistance exercise in hypertensive patients. An increase in blood pressure during resistance exercise might be at least in part attributed to an increase in cardiac output. AIMS This study was conducted to determine whether atenolol was able to decrease BP level and mitigate BP increase during dynamic resistance exercise performed at three different intensities in hypertensives. METHODS Ten essential hypertensives (systolic/diastolic BP between 140/90 and 160/105 mmHg) were blindly studied after 6 weeks of placebo and atenolol. In each phase, volunteers executed, in a random order, three protocols of knee-extension exercises to fatigue: (i) one set at 100% of 1 RM; (ii) three sets at 80% of 1 RM; and (iii) three sets at 40% of 1 RM. Intra-arterial radial blood pressure was measured throughout the protocols. RESULTS Atenolol decreased systolic BP maximum values achieved during the three exercise protocols (100% = 186 +/- 4 vs. 215 +/- 7, 80% = 224 +/- 7 vs. 247 +/- 9 and 40% = 223 +/- 7 vs. 252 +/- 16 mmHg, P < 0.05). Atenolol also mitigated an increase in systolic BP in the first set of exercises (100% = +38 +/- 5 vs. +54 +/- 9; 80% = +68 +/- 11 vs. +84 +/- 13 and 40% = +69 +/- 7 vs. +84 +/- 14, mmHg, P < 0.05). Atenolol decreased diastolic BP values and mitigated its increase during exercise performed at 100% of 1 RM (126 +/- 6 vs. 145 +/- 6 and +41 +/- 6 vs. +52 +/- 6, mmHg, P < 0.05), but not at the other exercise intensities. CONCLUSIONS Atenolol was effective in both reducing systolic BP maximum values and mitigating BP increase during resistance exercise performed at different intensities in hypertensive subjects.

Heat and exercise acclimation increases intracellular levels of Hsp72 and inhibits exercise-induced increase in intracellular and plasma Hsp72 in humans

In order to verify the effects of heat and exercise acclimation (HA) on resting and exercise-induced expression of plasma and leukocyte heat shock protein 72 (Hsp72) in humans, nine healthy young male volunteers (25.0 +/- 0.7 years; 80.5 +/- 2.0 kg; 180 +/- 2 cm, mean +/- SE) exercised for 60 min in a hot, dry environment (40 +/- 0A degrees C and 45 A +/- 0% relative humidity) for 11 days. The protocol consisted of running on a treadmill using a controlled hyperthermia technique in which the work rate was adjusted to elevate the rectal temperature by 1A degrees C in 30 min and maintain it elevated for another 30 min. Before and after the HA, the volunteers performed a heat stress test (HST) at 50% of their individual maximal power output for 90 min in the same environment. Blood was drawn before (REST), immediately after (POST) and 1 h after (1 h POST) HST, and plasma and leukocytes were separated and stored. Subjects showed expected adaptations to HA: reduced exercise rectal and mean skin temperatures and heart rate, and augmented sweat rate and exercise tolerance. In HST1, plasma Hsp72 increased from REST to POST and then returned to resting values 1 h POST (REST: 1.11 A +/- 0.07, POST: 1.48 A +/- 0.10, 1 h POST: 1.22 A +/- 0.11 ng mL(-1); p < 0.05). In HST2, there was no change in plasma Hsp72 (REST: 0.94 A +/- 0.08, POST: 1.20 A +/- 0.15, 1 h POST: 1.17 A +/- 0.16 ng mL(-1); p > 0.05). HA increased resting levels of intracellular Hsp72 (HST1: 1 A +/- 0.02 and HST2: 4.2 A +/- 1.2 density units, p < 0.05). Exercise-induced increased intracellular Hsp72 expression was observed on HST1 (HST1: REST, 1 A +/- 0.02 vs. POST, 2.9 A +/- 0.9 density units, mean +/- SE, p < 0.05) but was inhibited on HST2 (HST2: REST, 4.2 +/- 1.2 vs. POST, 4.4 +/- 1.1 density units, p > 0.05). Regression analysis showed that the lower the pre-exercise expression of intracellular Hsp72, the higher the exercise-induced increase (R = -0.85, p < 0.05). In conclusion, HA increased resting leukocyte Hsp72 levels and inhibited exercise-induced expression. This intracellular adaptation probably induces thermotolerance. In addition, the non-increase in plasma Hsp72 after HA may be related to lower stress at the cellular level in the acclimated individuals.

Finger blood pressure during leg resistance exercise

Blood pressure (BP) assessment during resistance exercise can be useful to avoid high BP, reducing cardiovascular risk, especially in hypertensive individuals. However, non-invasive accurate technique for this purpose is not available. The aim of this study was to compare finger photoplethysmographic (FPP) and intra-arterial BP values and responses during resistance exercise. Eight non-medicated hypertensive subjects (5 males, 30-60 years) were evaluated during pre-exercise resting period and during three sets of the knee extension exercise performed at 80% of 1RM until fatigue. BP was measured simultaneously by FPP and intra-arterial methods. Data are mean +/- SD. Systolic BP was significantly higher with FPP than with intra-arterial: at pre-exercise (157 +/- 13 vs. 152 +/- 10 mmHg; p < 0.01) and the mean (202 +/- 29 vs. 198 +/- 26 mmHg; p < 0.01), and the maximal (240 +/- 26 vs. 234 +/- 16 mmHg; p < 0.05) values achieved during exercise. The increase in systolic BP during resistance exercise was similar between FPP and intra-arterial (+ 73 +/- 29 vs. + 71 +/- 18 mmHg; p = 0.59). Diastolic BP values and increases were lower with FPP. In conclusion, FPP provides similar values of BP increment during resistance exercise than intra-arterial method. However, it overestimates by 2.6 +/- 6.1% the maximal systolic BP achieved during this mode of exercise and underestimates by 8.8 +/- 5.8% the maximal diastolic BP.

Endurance in judogi grip strength tests: comparison between elite and non-elite judo players

Background and Study Aim: The ability to develop a strong grip and maintain it during a judo match has become an important element for judo athletes. Therefore, the purpose of this investigation was to examine differences between measurements of maximal isometric time on judogi pull-up, and number of repetitions during dynamic judogi pull-up. Material/Methods: The sample was composed by two groups: 16 high-level judo athletes from the male Brazilian National Team and 12 male state-level judo athletes, with at least one athlete per weight category. The tests were compared through analysis of co-variance (body mass as co-variable), followed by a post-hoc test (Scheffe). Significance level was set at 5%. Results: No difference was found in the isometric test: Brazilian Team: 35 +/- 18s; Regional: 39 +/- 14s. However, the Brazilian Team performed a high number of repetitions (12 +/- 5 rep) compared to regional group (9 +/- 4 rep) during the dynamic grip strength endurance test. Conclusions: Thus, dynamic grip strength endurance seems to be a discriminating variable between judo athletes, probably because judo combat involves many elbow extensions and flexions in order to avoid the opponent`s grip and to subdue them.

Non-exhaustive tests for critical power estimation

Objective. - The aim of this study was to propose a new method that allows for the estimation of critical power (CP) from non-exhaustive tests using ratings of perceived exertion (RPE). Methods. - Twenty-two subjects underwent two practice trials for ergometer and Borg 15-point scale familiarization, and adaptation to severe exhaustive exercise. After then, four exercise bouts were performed on different days for the estimation of CP and anaerobic work capacity (AWC) by linear work-time equation, and CP(15), CP(17), AWC(15) and AWC(17) were estimated using the work and time to attainment of RPE15 and RPE17 based on the Borg 15-point scale. Results. - The CP, CP(15) and CP(17) (170-177W) were not significantly different (P>0.05). However, AWC, AWC(15) and AWC(17) were all different from each other. The correlations between CP(15) and CP(17), with CP were strong (R=0.871 and 0.911, respectively), but the AWC(15) and AWC(17) were not significantly correlated with AWC. Conclusion. - Sub-maximal. RPE responses can be used for the estimation of CP from non-exhaustive exercise protocols. (C) 2009 Elsevier Masson SAS. All rights reserved.

Effects of recovery type after a judo match on blood lactate and performance in specific and non-specific judo tasks

The objective of the present study was to verify if active recovery (AR) applied after a judo match resulted in a better performance when compared to passive recovery (PR) in three tasks varying in specificity to the judo and in measurement of work performed: four upper-body Wingate tests (WT); special judo fitness test (SJFT); another match. For this purpose, three studies were conducted. Sixteen highly trained judo athletes took part in study 1, 9 in study 2, and 12 in study 3. During AR judokas ran (15 min) at the velocity corresponding to 70% of 4 mmol l(-1) blood lactate intensity (similar to 50% (V) over dotO(2) peak), while during PR they stayed seated at the competition area. The results indicated that the minimal recovery time reported in judo competitions (15 min) is long enough for sufficient recovery of WT performance and in a specific high-intensity test (SJFT). However, the odds ratio of winning a match increased ten times when a judoka performed AR and his opponent performed PR, but the cause of this phenomenon cannot be explained by changes in number of actions performed or by changes in match`s time structure.

Interesterification of milkfat with soybean oil catalysed by Rhizopus oryzae lipase immobilised on SiO(2)-PVA on packed bed reactor

The potential of the lipase from Rhizopus oryzae immobilised on SiO(2)-PVA to catalyse the interesterification of the milkfat with soybean oil in a packed bed reactor running on continuous mode was evaluated. The reactor operated continuously for 35 days at 45 degrees C, and during 12 days, no significant decrease in the initial lipase activity was verified. Interesterification yields were in the range from 35 to 38% wt, which gave an interesterified product having 59% lower consistency in relation to non-interesterified blend. Results showed the potential of the lipase from Rhizopus oryzae to mediate the interesterification of milkfat with soybean oil in packed bed reactor, attaining a more spreadable product under a cool temperature. The biocatalyst operational stability was assessed and an inactivation profile was found to follow the Arrhenius model, revealing values of 34 days and 0.034 day(-1), for half-life and a deactivation coefficient, respectively.

Profiles of xylose reductase, xylitol dehydrogenase and xylitol production under different oxygen transfer volumetric coefficient values

BACKGROUND: Xylitol is a sugar alcohol (polyalcohol) with many interesting properties for pharmaceutical and food products. It is currently produced by a chemical process, which has some disadvantages such as high energy requirement. Therefore microbiological production of xylitol has been studied as an alternative, but its viability is dependent on optimisation of the fermentation variables. Among these, aeration is fundamental, because xylitol is produced only under adequate oxygen availability. In most experiments with xylitol-producing yeasts, low oxygen transfer volumetric coefficient (K(L)a) values are used to maintain microaerobic conditions. However, in the present study the use of relatively high K(L)a values resulted in high xylitol production. The effect of aeration was also evaluated via the profiles of xylose reductase (XR) and xylitol clehydrogenase (XD) activities during the experiments. RESULTS: The highest XR specific activity (1.45 +/- 0.21 U mg(protein)(-1)) was achieved during the experiment with the lowest K(L)a value (12 h(-1)), while the highest XD specific activity (0.19 +/- 0.03 U mg(protein)(-1)) was observed with a K(L)a value of 25 h(-1). Xylitol production was enhanced when K(L)a was increased from 12 to 50 h(-1), which resulted in the best condition observed, corresponding to a xylitol volumetric productivity of 1.50 +/- 0.08 g(xylitol) L(-1) h(-1) and an efficiency of 71 +/- 6.0%. CONCLUSION: The results showed that the enzyme activities during xylitol bioproduction depend greatly on the initial KLa value (oxygen availability). This finding supplies important information for further studies in molecular biology and genetic engineering aimed at improving xylitol bioproduction. (C) 2008 Society of Chemical Industry