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.

Rationalization, Kunstwollen and technical means of expressivity. The example of the romantic piano

This article seeks to retrace some of the empirical, historical and sociological elements of Max Weber Sociology of music. Even if he is first and foremost interested in the process of rationalisation throughout western civilisation, his Sociology of music is founded on the idea of the technical medium, which he explores in several different directions. This idea will be examined here by means of several examples drawn from western music, particularly from the romantic piano repertoire.

Electromyographic standardized indices in healthy Brazilian young adults and data reproducibility

P>The determination of normal parameters is an important procedure in the evaluation of the stomatognathic system. We used the surface electromyography standardization protocol described by Ferrario et al. (J Oral Rehabil. 2000;27:33-40, 2006;33:341) to determine reference values of the electromyographic standardized indices for the assessment of muscular symmetry (left and right side, percentage overlapping coefficient, POC), potential lateral displacing components (unbalanced contractile activities of contralateral masseter and temporalis muscles, TC), relative activity (most prevalent pair of masticatory muscles, ATTIV) and total activity (integrated areas of the electromyographic potentials over time, IMPACT) in healthy Brazilian young adults, and the relevant data reproducibility. Electromyography of the right and left masseter and temporalis muscles was performed during maximum teeth clenching in 20 healthy subjects (10 women and 10 men, mean age 23 years, s.d. 3), free from periodontal problems, temporomandibular disorders, oro-facial myofunctional disorder, and with full permanent dentition (28 teeth at least). Data reproducibility was computed for 75% of the sample. The values obtained were POC Temporal (88 center dot 11 +/- 1 center dot 45%), POC masseter (87 center dot 11 +/- 1 center dot 60%), TC (8 center dot 79 +/- 1 center dot 20%), ATTIV (-0 center dot 33 +/- 9 center dot 65%) and IMPACT (110 center dot 40 +/- 23 center dot 69 mu V/mu V center dot s %). There were no statistical differences between test and retest values (P > 0 center dot 05). The Technical Errors of Measurement (TEM) for 50% of subjects assessed during the same session were 1 center dot 5, 1 center dot 39, 1 center dot 06, 3 center dot 83 and 10 center dot 04. For 25% of the subjects assessed after a 6-month interval, the TEM were 0 center dot 80, 1 center dot 03, 0 center dot 73, 12 center dot 70 and 19 center dot 10. For all indices, there was good reproducibility. These electromyographic indices could be used in the assessment of patients with stomatognathic dysfunction.

Innovation concept for measurement gross error detection and identification in power system state estimation

In this study, the innovation approach is used to estimate the measurement total error associated with power system state estimation. This is required because the power system equations are very much correlated with each other and as a consequence part of the measurements errors is masked. For that purpose an index, innovation index (II), which provides the quantity of new information a measurement contains is proposed. A critical measurement is the limit case of a measurement with low II, it has a zero II index and its error is totally masked. In other words, that measurement does not bring any innovation for the gross error test. Using the II of a measurement, the masked gross error by the state estimation is recovered; then the total gross error of that measurement is composed. Instead of the classical normalised measurement residual amplitude, the corresponding normalised composed measurement residual amplitude is used in the gross error detection and identification test, but with m degrees of freedom. The gross error processing turns out to be very simple to implement, requiring only few adaptations to the existing state estimation software. The IEEE-14 bus system is used to validate the proposed gross error detection and identification test.

Direct measurement of instantaneous source speed for a HDR brachytherapy unit using an optical fiber based detector

Purpose: Several attempts to determine the transit time of a high dose rate (HDR) brachytherapy unit have been reported in the literature with controversial results. The determination of the source speed is necessary to accurately calculate the transient dose in brachytherapy treatments. In these studies, only the average speed of the source was measured as a parameter for transit dose calculation, which does not account for the realistic movement of the source, and is therefore inaccurate for numerical simulations. The purpose of this work is to report the implementation and technical design of an optical fiber based detector to directly measure the instantaneous speed profile of a (192)Ir source in a Nucletron HDR brachytherapy unit. Methods: To accomplish this task, we have developed a setup that uses the Cerenkov light induced in optical fibers as a detection signal for the radiation source moving inside the HDR catheter. As the (192)Ir source travels between two optical fibers with known distance, the threshold of the induced signals are used to extract the transit time and thus the velocity. The high resolution of the detector enables the measurement of the transit time at short separation distance of the fibers, providing the instantaneous speed. Results: Accurate and high resolution speed profiles of the 192Ir radiation source traveling from the safe to the end of the catheter and between dwell positions are presented. The maximum and minimum velocities of the source were found to be 52.0 +/- 1.0 and 17.3 +/- 1:2 cm/s. The authors demonstrate that the radiation source follows a uniformly accelerated linear motion with acceleration of vertical bar a vertical bar = 113 cm/s(2). In addition, the authors compare the average speed measured using the optical fiber detector to those obtained in the literature, showing deviation up to 265%. Conclusions: To the best of the authors` knowledge, the authors directly measured for the first time the instantaneous speed profile of a radiation source in a HDR brachytherapy unit traveling from the unit safe to the end of the catheter and between interdwell distances. The method is feasible and accurate to implement on quality assurance tests and provides a unique database for efficient computational simulations of the transient dose. (C) 2010 American Association of Physicists in Medicine. [DOI: 10.1118/1.3483780]

Calibration of the dietary data obtained from the Brazilian center of the Natural History of HPV Infection in Men study: the HIM Study

The objective of this study was to estimate the regressions calibration for the dietary data that were measured using the quantitative food frequency questionnaire (QFFQ) in the Natural History of HPV Infection in Men: the HIM Study in Brazil. A sample of 98 individuals from the HIM study answered one QFFQ and three 24-hour recalls (24HR) at interviews. The calibration was performed using linear regression analysis in which the 24HR was the dependent variable and the QFFQ was the independent variable. Age, body mass index, physical activity, income and schooling were used as adjustment variables in the models. The geometric means between the 24HR and the calibration-corrected QFFQ were statistically equal. The dispersion graphs between the instruments demonstrate increased correlation after making the correction, although there is greater dispersion of the points with worse explanatory power of the models. Identification of the regressions calibration for the dietary data of the HIM study will make it possible to estimate the effect of the diet on HPV infection, corrected for the measurement error of the QFFQ.

Calibração dos dados dietéticos obtidos no centro brasileiro do estudo Natural History of HPV Infection in Men: o Estudo HIM

O objetivo foi estimar as regressões de calibração dos dados dietéticos mensurados pelo questionário quantitativo de freqüência alimentar (QQFA) utilizado no Natural History of HPV Infection in Men: o Estudo HIM. Uma amostra de 98 indivíduos do estudo HIM respondeu, por meio de entrevista, a um QQFA e três recordatórios de 24 horas (R24h). A calibração foi feita por meio de análise de regressão linear, tendo os R24h como variável dependente e o QQFA como variável independente. Idade, índice de massa corporal, atividade física, renda e escolaridade foram utilizadas como variáveis de ajuste nos modelos. As médias geométricas dos R24h e do QQFA corrigido pela calibração são estatisticamente iguais. Os gráficos de dispersão entre os instrumentos demonstraram aumento da correlação após a correção dos dados, porém observa-se maior dispersão dos pontos de acordo com a piora do poder explicativo dos modelos. A identificação das regressões de calibração dos dados dietéticos do estudo HIM permitirá a estimativa do efeito da dieta sobre a infecção por HPV, corrigida pelo erro de medida do QQFA

On the analysis of notched concrete beams: From measurement with digital image correlation to identification with boundary element method of a cohesive model

A way of coupling digital image correlation (to measure displacement fields) and boundary element method (to compute displacements and tractions along a crack surface) is presented herein. It allows for the identification of Young`s modulus and fracture parameters associated with a cohesive model. This procedure is illustrated to analyze the latter for an ordinary concrete in a three-point bend test on a notched beam. In view of measurement uncertainties, the results are deemed trustworthy thanks to the fact that numerous measurement points are accessible and used as entries to the identification procedure. (C) 2010 Elsevier Ltd. All rights reserved.

Reliability of electromyographic amplitude values of the upper limb muscles during closed kinetic chain exercises with stable and unstable surfaces

The purpose of the present study was to evaluate the intra and interday reliability of surface electromyographic amplitude values of the scapular girdle muscles and upper limbs during 3 isometric closed kinetic chain exercises, involving upper limbs with the fixed distal segment extremity on stable base of support and on a Swiss ball (relatively unstable). Twenty healthy adults performed the exercises push-up, bench-press and wall-press with different effort levels (80% and 100% maximal load). Subjects performed three maximal voluntary contractions (MVC) in muscular testing position of each muscle to obtain a reference value for root mean square (RMS) normalization. Individuals were instructed to randomly perform three isometric contraction series, in which each exercise lasted 6 s with a 2-min resting-period between series and exercises. Intra and interday reliabilities were calculated through the intraclass correlation coefficient (ICC 2.1), standard error of the measurement (SEM). Results indicated an excellent intraday reliability of electromyographic amplitude values (ICC >= 0.75). The interday reliability of normalized RMS values ranged between good and excellent (ICC 0.52-0.98). Finally, it is suggested that the reliability of normalized electromyographic amplitude values of the analyzed muscles present better values during exercises on a stable surface. However, load levels used during the exercises do not seem to have any influence on variability levels, possibly because the loads were quite similar. (C) 2007 Elsevier Ltd. All rights reserved.

Prevalence and risk factors of apical periodontitis in endodontically treated teeth in a selected population of Brazilian adults

The aim of this study was to assess the prevalence and risk factors of apical periodontitis in endodontically treated teeth in a selected population of Brazilian adults. A total of 1,372 periapical radiographs of endodontically treated teeth were analyzed based on the quality of root filling, status of coronal restoration and presence of posts associated with apical periodontitis (AP). Data were analyzed statistically using odds ratio, confidence intervals and chi-square test. The prevalence of AP with adequate endodontic treatment was low (16.5%). This percentage dropped to 12.1% in cases with adequate root filling and adequate coronal restoration. Teeth with adequate endodontic treatment and poor coronal restoration had an AP prevalence of 27.9%. AP increased to 71.7% in teeth with poor endodontic treatment associated with poor coronal restoration. When poor endodontic treatment was combined with adequate coronal restoration, AP prevalence was 61.8%. The prevalence of AP was low when associated with high technical quality of root canal treatment. Poor coronal restoration increased the risk of AP even when endodontic treatment was adequate (OR=2.80; 95%CI=1.87-4.22). The presence of intracanal posts had no influence on AP prevalence.

Critical applications of SW 846 US EPA methods to evaluation of marine samples quality

Technical evaluation of analytical data is of extreme relevance considering it can be used for comparisons with environmental quality standards and decision-making as related to the management of disposal of dredged sediments and the evaluation of salt and brackish water quality in accordance with CONAMA 357/05 Resolution. It is, therefore, essential that the project manager discusses the environmental agency's technical requirements with the laboratory contracted for the follow-up of the analysis underway and even with a view to possible re-analysis when anomalous data are identified. The main technical requirements are: (1) method quantitation limits (QLs) should fall below environmental standards; (2) analyses should be carried out in laboratories whose analytical scope is accredited by the National Institute of Metrology (INMETRO) or qualified or accepted by a licensing agency; (3) chain of custody should be provided in order to ensure sample traceability; (4) control charts should be provided to prove method performance; (5) certified reference material analysis or, if that is not available, matrix spike analysis, should be undertaken and (6) chromatograms should be included in the analytical report. Within this context and with a view to helping environmental managers in analytical report evaluation, this work has as objectives the discussion of the limitations of the application of SW 846 US EPA methods to marine samples, the consequences of having data based on method detection limits (MDL) and not sample quantitation limits (SQL), and present possible modifications of the principal method applied by laboratories in order to comply with environmental quality standards.

Allometric models for estimating the phytomass of a secondary Atlantic Forest area of southeastern Brazil

The purpose of this study was to develop and validate equations to estimate the aboveground phytomass of a 30 years old plot of Atlantic Forest. In two plots of 100 m², a total of 82 trees were cut down at ground level. For each tree, height and diameter were measured. Leaves and woody material were separated in order to determine their fresh weights in field conditions. Samples of each fraction were oven dried at 80 °C to constant weight to determine their dry weight. Tree data were divided into two random samples. One sample was used for the development of the regression equations, and the other for validation. The models were developed using single linear regression analysis, where the dependent variable was the dry mass, and the independent variables were height (h), diameter (d) and d²h. The validation was carried out using Pearson correlation coefficient, paired t-Student test and standard error of estimation. The best equations to estimate aboveground phytomass were: lnDW = -3.068+2.522lnd (r² = 0.91; s y/x = 0.67) and lnDW = -3.676+0.951ln d²h (r² = 0.94; s y/x = 0.56).

Echocardiographic study of paediatric patients with mucopolysaccharidosis

Principle Mucopolysaccharidosis is an inborn error of metabolism causing glucosaminoglycans tissue storage. Cardiovascular involvement is variable but contributes significantly towards the morbidity and mortality of the patients. Objective To characterise the echocardiographic abnormalities in children and adolescents with different types of mucopolysaccharidosis. Method Echocardiograms and medical records of 28 patients aged 2–14 years, seen from 2003 to 2005, were revised. At that time, the enzymatic replacement therapy was still not available in our institution.Results Echocardiographic alterations were detected in 26 patients (93 per cent), whereas 16 (57 per cent) had abnormal auscultation, and only 6 (21 per cent) presented with cardiovascular complaint. Mitral valve thickening with dysfunction (regurgitation, stenosis, or double lesion) was diagnosed in 60.8 per cent, left ventricular hypertrophy in 43 per cent and aortic valve thickening with regurgitation in 35.8 per cent of the patients. There was no systolic dysfunction and mild left diastolic dysfunction was shown in 21.5 per cent of the patients. Pulmonary hypertension was present in 36 per cent of the patients, causing the only two deaths recorded. There was a strong association between the accumulation of dermatan sulphate and the presence of mitral valve dysfunction (p = 0.0003), aortic valve dysfunction (p = 0.006), and pulmonary hypertension (p = 0.006). Among individuals with two or more examinations, 82 per cent had a worsening evolution. Conclusions Echocardiographic alterations in children with Mucopolysaccharidosis are frequent and have a progressive character Left valve lesions, ventricular hypertrophy, and pulmonary hypertension were the most common findings and there was an association between the accumulation of dermatan sulphate and cardiovascular involvement. Unlike in adults, pulmonary hypertension was the main cause of death, not left ventricle systolic dysfunction

Precision of distances and ordering of microsatellite markers in consensus linkage maps of chromosomes 1, 3 and 4 from two reciprocal chicken populations using bootstrap sampling

Some factors complicate comparisons between linkage maps from different studies. This problem can be resolved if measures of precision, such as confidence intervals and frequency distributions, are associated with markers. We examined the precision of distances and ordering of microsatellite markers in the consensus linkage maps of chromosomes 1, 3 and 4 from two F 2 reciprocal Brazilian chicken populations, using bootstrap sampling. Single and consensus maps were constructed. The consensus map was compared with the International Consensus Linkage Map and with the whole genome sequence. Some loci showed segregation distortion and missing data, but this did not affect the analyses negatively. Several inversions and position shifts were detected, based on 95% confidence intervals and frequency distributions of loci. Some discrepancies in distances between loci and in ordering were due to chance, whereas others could be attributed to other effects, including reciprocal crosses, sampling error of the founder animals from the two populations, F(2) population structure, number of and distance between microsatellite markers, number of informative meioses, loci segregation patterns, and sex. In the Brazilian consensus GGA1, locus LEI1038 was in a position closer to the true genome sequence than in the International Consensus Map, whereas for GGA3 and GGA4, no such differences were found. Extending these analyses to the remaining chromosomes should facilitate comparisons and the integration of several available genetic maps, allowing meta-analyses for map construction and quantitative trait loci (QTL) mapping. The precision of the estimates of QTL positions and their effects would be increased with such information.

Polydimethylsiloxane: a new contrast material for localization of occult breast lesions

Background. The radioguided localization of occult breast lesions (ROLL) technique often utilizes iodinated radiographic contrast to assure that the local injection of (99m)Tc-MAA corresponds to the location of the lesion under investigation. However, for this application, this contrast has several shortcomings. The objective of this study was to evaluate the safety, effectiveness and technical feasibility of the use of polydimethylsiloxane (PDMS) as radiological contrast and tissue marker in ROLL. Materials and methods. The safety assessment was performed by the acute toxicity study in Wistar rats (n = 50). The radiological analysis of breast tissue (n = 32) from patients undergoing reductive mammoplasty was used to verify the effectiveness of PDMS as contrast media. The technical feasibility was evaluated through the scintigraphic and histologic analysis. Results. We found no toxic effects of PDMS for this use during the observational period. It has been demonstrated in human breast tissue that the average diameter of the tissue marked by PDMS was lower than when marked by the contrast medium (p <0.001). PDMS did not interfere with the scintigraphic uptake (p = 0.528) and there was no injury in histological processing of samples. Conclusions. This study demonstrated not only the superiority of PDMS as radiological contrast in relation to the iodinated contrast, but also the technical feasibility for the same applicability in the ROLL.