Evaluating different methods of microarray data normalization

Abstract Background With the development of DNA hybridization microarray technologies, nowadays it is possible to simultaneously assess the expression levels of thousands to tens of thousands of genes. Quantitative comparison of microarrays uncovers distinct patterns of gene expression, which define different cellular phenotypes or cellular responses to drugs. Due to technical biases, normalization of the intensity levels is a pre-requisite to performing further statistical analyses. Therefore, choosing a suitable approach for normalization can be critical, deserving judicious consideration. Results Here, we considered three commonly used normalization approaches, namely: Loess, Splines and Wavelets, and two non-parametric regression methods, which have yet to be used for normalization, namely, the Kernel smoothing and Support Vector Regression. The results obtained were compared using artificial microarray data and benchmark studies. The results indicate that the Support Vector Regression is the most robust to outliers and that Kernel is the worst normalization technique, while no practical differences were observed between Loess, Splines and Wavelets. Conclusion In face of our results, the Support Vector Regression is favored for microarray normalization due to its superiority when compared to the other methods for its robustness in estimating the normalization curve.

Dental caries related to quality of life in two Brazilian adolescent groups: a cross-sectional randomised study

Objectives: To analyse dental caries-related quality of life (QoL) in adolescent (1519-year-old) subjects in a suburban area (SA) and a downtown area (DA) of Bauru, Sao Paulo, Brazil, in 2009. Methods: This was a cross-sectional, randomised study. The sample consisted of 185 and 147 adolescents from the SA and DA, respectively. The caries index used was that for decayed, missing and filled teeth (DMFT) (World Health Organization criteria). The 14-item Oral Health Impact Profile (OHIP-14) was used to assess QoL. The non-parametric MannWhitney test, Spearmans correlation coefficient and chi-squared test were used in the statistical analysis. Results: The DMFT index, Significant Caries (SiC) Index and percentage of caries-free students were similar (P > 0.05) between these populations, but findings on the Care Index differed (P < 0.05). There was a correlation between the DMFT index and OHIP-14 score in SA subjects (mean DMFT index = 3.01) in the dimensions of physical pain (r = 0.25; P < 0.01) and psychological disability (r = 0.17; P = 0.02). The DMFT index in DA subjects (mean DMFT index = 2.95) showed a correlation with functional limitation (r = 0.19; P = 0.02). The correlation in SA subjects between the caries component (mean = 1.22) of the DMFT index and OHIP-14 was significant only for the physical pain dimension (r = 0.16; P = 0.03). In DA subjects, correlations between the caries component (mean = 0.37) and all dimensions of OHIP-14 were statistically significant (P < 0.05). Conclusions: Despite the similarities in means in the DMFT index, the SiC Index and the caries-free percentage of subjects in both localities, access to dental treatment proved to be less effective for SA adolescents. Physical pain and psychological disability were the most frequent negative manifestations of impact on QoL. The SA adolescents were more negatively affected by dental caries in terms of QoL.

Evaluation of the flexural strength and elastic modulus of resins used for temporary restorations reinforced with particulate glass fibre

Objective: The flexural strength and the elastic modulus of acrylic resins, Dencor, Duralay and Trim Plus II, were evaluated with and without the addition of silanised glass fibre. Materials and methods: To evaluate the flexural strength and elastic modulus, 60 test specimens were fabricated with the addition of 10% ground silanised glass fibres for the experimental group, and 60 without the incorporation of fibres, for the control group, with 20 test specimens being made of each commercial brand of resin (Dencor, Duralay and Trim Plus II) for the control group and experimental group. After the test specimens had been completed, the flexural strength and elastic modulus tests were performed in a universal testing device, using the three-point bending test. For the specimens without fibres the One-Way Analysis of Variance and the complementary Tukey test were used, and for those with fibres it was not normal, so that the non-parametric Mann-Whitney test was applied. Results: For the flexural strength test, there was no statistical difference (p > 0.05) between each commercial brand of resin without fibres [Duralay 84.32(+/- 8.54), Trim plus 85.39(+/- 6.74), Dencor 96.70(+/- 6.52)] and with fibres (Duralay 87.18, Trim plus 88.33, Dencor 98.10). However, for the elastic modulus, there was statistical difference (p > 0.01) between each commercial brand of resin without fibres [Duralay 2380.64 (+/- 168.60), Trim plus 2740.37(+/- 311.74), Dencor 2595.42(+/- 261.22)] and with fibres (Duralay 3750.42, Trim plus 3188.80, Dencor 3400.75). Conclusion: The result showed that the incorporation of fibre did not interfere in the flexural strength values, but it increased the values for the elastic modulus.

The protective effect of Canova homeopathic medicine in cyclophosphamide-treated non-human primates

Background: Canova activates macrophages and indirectly induces lymphocyte proliferation. Here we evaluated the effects of Canova in cyclophosphamide-treated non-human primates. Methods: Twelve Cebus apella were evaluated. Four animals were treated with Canova only. Eight animals were treated with two doses of cyclophosphamide (50 mg/kg) and four of these animals received Canova. Body weight, biochemistry and hematologic analyses were performed for 40 days. Micronucleus and comet assays were performed for the evaluation of DNA damage. Results: We observed that cyclophosphamide induced abnormal WBC count in all animals. However, the group treated with cyclophosphamide plus Canova presented a higher leukocyte count than that which received only cyclophosphamide. Cyclophosphamide induced micronucleus and DNA damage in all animals. The frequency of these alterations was significantly lower in the Canova group than in the group without this medicine. Conclusions: Our results demonstrated that Canova treatment minimizes cyclophosphamide myelotoxicity in C. apella. (C) 2012 Elsevier Ltd. All rights reserved.

Functional Magnetic Resonance Imaging Data Analysis by Autoregressive Estimator

The autoregressive (AR) estimator, a non-parametric method, is used to analyze functional magnetic resonance imaging (fMRI) data. The same method has been used, with success, in several other time series data analysis. It uses exclusively the available experimental data points to estimate the most plausible power spectra compatible with the experimental data and there is no need to make any assumption about non-measured points. The time series, obtained from fMRI block paradigm data, is analyzed by the AR method to determine the brain active regions involved in the processing of a given stimulus. This method is considerably more reliable than the fast Fourier transform or the parametric methods. The time series corresponding to each image pixel is analyzed using the AR estimator and the corresponding poles are obtained. The pole distribution gives the shape of power spectra, and the pixels with poles at the stimulation frequency are considered as the active regions. The method was applied in simulated and real data, its superiority is shown by the receiver operating characteristic curves which were obtained using the simulated data.

Procalcitonin (PCT) and C-reactive Protein (CRP) as severe systemic infection markers in febrile neutropenic adults

Abstract Background Procalcitonin (PCT) is an inflammatory marker that has been used as indicator of severe bacterial infection. We evaluated the concentrations of PCT as a marker for systemic infection compared to C-reactive protein (CRP) in patients neutropenic febrile. Methods 52 adult patients were enrolled in the study. Blood sample was collected in order to determine the serum concentrations of PCT, CRP and other hematological parameters at the onset of fever. The patients were divided into 2 groups, one with severe infection (n = 26) and the other in which the patients did not present such an infection (n = 26). Then PCT and CRP concentrations at the fever onset were compared between groups using non parametric statistical tests, ROC curve, sensitivity, specificity, likelihood ratio, and Spearman's correlation coefficient. Results The mean of PCT was significantly higher in the group with severe infection (6.7 ng/mL versus 0.6 ng/mL – p = 0.0075) comparing with CRP. Serum concentrations of 0.245 ng/mL of PCT displayed 100% de sensitivity and 69.2% specificity. PCT concentrations of 2,145 ng/mL presented a likelihood ratio of 13, which was not observed for any concentration of CRP. Conclusion PCT seems to be an useful marker for the diagnosis of systemic infection in febrile neutropenic patients, probably better than CRP.

Temporomandibular disorders and parafunctional oral habits: an anamnestic study

OBJECTIVE: To assess the frequency and severity of the signs and symptoms of temporomandibular disorders (TMD), the frequency of parafunctional oral habits and the correlation between the variables by means of the patients' perception regarding their problem. METHODS: One hundred patients diagnosed with TMD, through a clinical examination of their masticatory system, answered the questions of a previously published protocol concerning the signs and symptoms most frequently reported in the literature. RESULTS: According to the results from the non parametric statistical analysis, the frequency for the following signs and symptoms was significant: Fatigue and muscle pain, joint sounds, tinnitus, ear fullness, headache, chewing impairment and difficulty to yawn (p<0.01) and otalgia (p<0.05). As to the parafunctional oral habits, there was a significant presence of teeth clenching during the day and night (p<0.01) and teeth grinding at night (p<0.05). The variable correlation analysis showed that there was a positive correlation between symptom frequency and severity; age was correlated with the presence of otalgia, cervical pain and teeth sensitivity, besides being correlated with muscle and joint pain severity. Habit frequency was negatively correlated with age. TMD duration was also positively correlated with the symptoms of tinnitus, ear fullness, muscle and joint pain. CONCLUSION: The study results showed that the anamnestic assessment using ProDTMMulti can predict the severity of the TMD case.

Comparative study of classic friction among different archwire ligation systems

OBJECTIVE: To describe and compare three alternative methods for controlling classical friction: Self-ligating brackets (SLB), special brackets (SB) and special elastomeric ligatures (SEB). METHODS: The study compared Damon MX, Smart Clip, In-Ovation and Easy Clip self-ligating bracket systems, the special Synergy brackets and Morelli's twin bracket with special 8-shaped elastomeric ligatures. New and used Morelli brackets with new and used elastomeric ligatures were used as control. All brackets had 0.022 x 0.028-in slots. 0.014-in nickel-titanium and stainless steel 0.019 x 0.025-in wires were tied to first premolar steel brackets using each archwire ligation method and pulled by an Instron machine at a speed of 0.5 mm/minute. Prior to the mechanical tests the absence of binding in the device was ruled out. Statistical analysis consisted of the Kruskal-Wallis test and multiple non-parametric analyses at a 1% significance level. RESULTS: When a 0.014-in archwire was employed, all ligation methods exhibited classical friction forces close to zero, except Morelli brackets with new and old elastomeric ligatures, which displayed 64 and 44 centiNewtons, respectively. When a 0.019 x 0.025-in archwire was employed, all ligation methods exhibited values close to zero, except the In-Ovation brackets, which yielded 45 cN, and the Morelli brackets with new and old elastomeric ligatures, which displayed 82 and 49 centiNewtons, respectively. CONCLUSIONS: Damon MX, Easy Clip, Smart Clip, Synergy bracket systems and 8-shaped ligatures proved to be equally effective alternatives for controlling classical friction using 0.014-in nickel-titanium archwires and 0.019 x 0.025-in steel archwires, while the In-Ovation was efficient with 0.014-in archwires but with 0.019 x 0.025-in archwires it exhibited friction that was similar to conventional brackets with used elastomeric ligatures.

Proteinuria predicts relapse in adolescent and adult minimal change disease

OBJECTIVE: This study sought to outline the clinical and laboratory characteristics of minimal change disease in adolescents and adults and establish the clinical and laboratory characteristics of relapsing and non-relapsing patients. METHODS: We retrospectively evaluated patients with confirmed diagnoses of minimal change disease by renal biopsy from 1979 to 2009; the patients were aged >13 years and had minimum 1-year follow-ups. RESULTS: Sixty-three patients with a median age (at diagnosis) of 34 (23-49) years were studied, including 23 males and 40 females. At diagnosis, eight (12.7%) patients presented with microscopic hematuria, 17 (27%) with hypertension and 17 (27%) with acute kidney injury. After the initial treatment, 55 (87.3%) patients showed complete remission, six (9.5%) showed partial remission and two (3.1%) were nonresponders. Disease relapse was observed in 34 (54%) patients who were initial responders (n = 61). In a comparison between the relapsing patients (n = 34) and the non-relapsing patients (n = 27), only proteinuria at diagnosis showed any significant difference (8.8 (7.1-12.0) vs. 6.0 (3.6-7.3) g/day, respectively, p = 0.001). Proteinuria greater than 7 g/day at the initial screening was associated with relapsing disease. CONCLUSIONS: In conclusion, minimal change disease in adults may sometimes present concurrently with hematuria, hypertension, and acute kidney injury. The relapsing pattern in our patients was associated with basal proteinuria over 7 g/day.

A comparison of time-motion performance between age groups in judo matches

The aim of this study was to compare time-motion indicators during judo matches performed by athletes from different age groups. The following age groups were analysed: Pre-Juvenile (13-14 years, n=522), Juvenile (15-16 years, n 353); Junior (19 years, n = 349) and Senior (>20 years, n = 587). The time-motion indicators included: Total Combat Time, Standing Combat Time, Displacement Without Contact, Gripping Time, Groundwork Combat Time and Pause Time. Analysis of variance (ANOVA) one-way and the Tukey test, as well as the Kruskal-Wallis test and Mann-Whitney (for non-parametric data), were conducted, using P < 0.05 as significance level. The results showed that all analysed groups obtained a median of 7 (first quantile - 3, third quantile - 12) sequences of combat/pause cycles. In total time of combat, the result was: for Total Combat Time, Standing Combat Time and Gripping Time: Pre-Juvenile and Senior were significantly longer than Juvenile and Junior. Considering Displacement Without Contact, Junior was significantly longer than all other age groups. For Groundwork Combat Time, Senior was significantly longer than all other age groups and Pre-Juvenile was longer than Junior. These results can be used to improve the physiological performance in intermittent practices, as well as technicaltactical training during judo sessions.

Impact of hypoxia on IGF-I, IGF-II, IGFBP-3, ALS and IGFBP-1 regulation and on IGF1R gene expression in children

Hypoxia is one of many factors involved in the regulation of the IGF system. However, no information is available regarding the regulation of the IGF system by acute hypoxia in humans. Objective: The aim of this study was to evaluate the effect of acute hypoxia on the IGF system of children. Design: Twenty-seven previously health children (14 boys and 13 girls) aged 15 days to 9.5 years were studied in two different situations: during a hypoxemic state (HS) due to acute respiratory distress and after full recovery to a normoxemic state (NS). In these two situations oxygen saturation was assessed with a pulse-oximeter and blood samples were collected for serum IGF-I, IGF-II, IGFBP-1, IGFBP-3, ALS and insulin determination by ELISA; fluoroimmunometric assay determination for GH and also for IGF1R gene expression analysis in peripheral lymphocytes by quantitative real-time PCR. Data were paired and analyzed by the Wilcoxon non-parametric test. Results: Oxygen saturation was significantly lower during HS than in NS (P<0.0001). IGF-I and IGF-II levels were lower during HS than in NS (P<0.0001 and P=0.0004. respectively). IGFBP-3 levels were also lower in HS than in NS (P=0.0002) while ALS and basal GH levels were higher during HS (P=0.0015 and P=0.014, respectively). Moreover, IGFBP-1 levels were higher during HS than in NS (P=0.004). No difference was found regarding insulin levels. The expression of IGF1R mRNA as 2(-Delta Delta CT) was higher during HS than in NS (P=0.03). Conclusion: The above results confirm a role of hypoxia in the regulation of the IGF system also in humans. This effect could be direct on the liver and/or mediated by GH and it is not restricted to the hepatocytes but involves other cell lines. During acute hypoxia a combination of alterations usually associated with reduced IGF action was observed. The higher expression of IGF1R mRNA may reflect an up-regulation of the transcriptional process. (C) 2012 Elsevier Ltd. All rights reserved.

Anti-aquaporin-4 antibodies in the context of assorted immune-mediated diseases

Background and purposes: Anti-aquaporin 4 antibodies are specific markers for Devics disease. This study aimed to test if this high specificity holds in the context of a large spectrum of systemic autoimmune and non-autoimmune diseases. Methods: Anti-aquaporin-4 antibodies (NMO-IgG) were determined by indirect immunofluorescence (IIF) on mouse cerebellum in 673 samples, as follows: group I (clinically defined Devic's disease, n = 47); group II [ inflammatory/demyelinating central nervous system (CNS) diseases, n = 41]; group III (systemic and organ-specific autoimmune diseases, n = 250); group IV (chronic or acute viral diseases, n = 35); and group V (randomly selected samples from a general clinical laboratory, n = 300). Results: MNO-IgG was present in 40/47 patients with classic Devic's disease (85.1% sensitivity) and in 13/22 (59.1%) patients with disorders related to Devic's disease. The latter 13 positive samples had diagnosis of longitudinally extensive transverse myelitis (n = 10) and isolated idiopathic optic neuritis (n = 3). One patient with multiple sclerosis and none of the remaining 602 samples with autoimmune and miscellaneous diseases presented NMO-IgG (99.8% specificity). The autoimmune disease subset included five systemic lupus erythematosus individuals with isolated or combined optic neuritis and myelitis and four primary Sjogren's syndrome (SS) patients with cranial/peripheral neuropathy. Conclusions: The available data clearly point to the high specificity of anti-aquaporin-4 antibodies for Devic's disease and related syndromes also in the context of miscellaneous non-neurologic autoimmune and non-autoimmune disorders.

Validation of the Brazilian Portuguese version of the Beck Depression Inventory-II in a community sample

Background: The Beck Depression Inventory (BDI) is used worldwide for detecting depressive symptoms. This questionnaire has been revised (1996) to match the DSM-IV criteria for a major depressive episode. We assessed the reliability and the validity of the Brazilian Portuguese version of the BDI-II for non-clinical adults. Methods: The questionnaire was applied to 60 college students on two occasions. Afterwards, 182 community-dwelling adults completed the BDI-II, the Self-Report Questionnaire, and the K10 Scale. Trained psychiatrists performed face-to-face interviews with the respondents using the Structured Clinical Interview (SCID-I), the Montgomery-angstrom sberg Depression Scale, and the Hamilton Anxiety Scale. Descriptive analysis, signal detection analysis (Receiver Operating Characteristics), correlation analysis, and discriminant function analysis were performed to investigate the psychometric properties of the BDI-II. Results: The intraclass correlation coefficient of the BDI-II was 0.89, and the Cronbach's alpha coefficient of internal consistency was 0.93. Taking the SCID as the gold standard, the cut-off point of 10/11 was the best threshold for detecting depression, yielding a sensitivity of 70% and a specificity of 87%. The concurrent validity (a correlation of 0.63-0.93 with scales applied simultaneously) and the predictive ability of the severity level (over 65% correct classification) were acceptable. Conclusion: The BDI-II is reliable and valid for measuring depressive symptomatology among Portuguese-speaking Brazilian non-clinical populations.

Impact of a participatory program to reduce noise in a Neonatal Unit

This study evaluated the impact of a participatory program to reduce noise in a neonatal intermediate care unit of a university hospital. A time-series quasi-experimental design was used, in which sound pressure levels were measured before and after the intervention was implemented using the Quest-400 dosimeter. Non-parametric statistical tests were used to compare noise with the level of significance fixed at 5%. Results showed significant reduction of sound pressure levels in the neonatal unit after the intervention program was implemented (p<0.0001). The average Leq before the intervention was 62.5dBA and was reduced to 58.8dBA after the intervention. A reduction of 7.1dBA in the average Lmax(from 104.8 to 87.7dBA) and of 30.6dBA in the average Lpeak(from 138.1 to 107.5dBA) was observed. The program was proven to be effective in significantly reducing noise levels in the neonatal unit, although levels were still more intense than recommended.

Influence of cardiopulmonary bypass on cefuroxime plasma concentration and pharmacokinetics in patients undergoing coronary surgery

The aims of this study were to evaluate the influence of cardiopulmonary bypass (CPB) on the plasma concentrations and pharmacokinetics of cefuroxime and to assess whether the cefuroxime dose regimen (a 1.5 g dose, followed by 750 mg every 6 h for 24 h) is adequate for cardiac surgery antibiotic prophylaxis. A prospective, controlled, observational study compared patients undergoing coronary surgery with CPB (CPB group, n = 10) or off-pump surgery (off-pump group, n = 9). After each cefuroxime dose, blood samples were sequentially collected and analysed using high-efficiency chromatography. For demographic data and pharmacokinetic parameters, the authors used Fisher's exact test for nominal variables and Student's t-test and the Mann-Whitney U-test for parametric and non-parametric variables, respectively. Plasma concentrations were compared using ANOVA, and the percentage of patients with a remaining plasma concentration of > 16 mg/l within 6 h after each bolus was quantified in tabular form. After each cefuroxime bolus was administered, both groups presented a significant decrease in plasma concentration over time (P < 0.001), without differences between the groups. The mean CPB time of 59.7 +/- 21.1 min did not change cefuroxime plasma concentrations or pharmacokinetics. The mean clearance +/- SD (ml/kg/min) and median elimination half-life (h) of the CPB group versus the off-pump group were 1.7 +/- 0.7 versus 1.6 +/- 0.6 (P = 0.67), respectively, and 2.2 versus 2.3 (P = 0.49), respectively. Up to 3 h following the first bolus of 1.5 g, but not after 6 h, all patients had plasma concentrations > 16 mg/l (CPB group = 20% and off-pump group = 44%). However, after all 750 mg boluses were administered, concentrations < 16 mg/dl were reached within 3 h. CPB does not influence cefuroxime plasma concentrations. The dosing regimen is adequate for the intraoperative period, but in the immediate postoperative period, it requires further review.