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.

LATENT RANK CHANGE DETECTION FOR ANALYSIS OF SPLICE-JUNCTION MICROARRAYS WITH NONLINEAR EFFECTS

Alternative splicing of gene transcripts greatly expands the functional capacity of the genome, and certain splice isoforms may indicate specific disease states such as cancer. Splice junction microarrays interrogate thousands of splice junctions, but data analysis is difficult and error prone because of the increased complexity compared to differential gene expression analysis. We present Rank Change Detection (RCD) as a method to identify differential splicing events based upon a straightforward probabilistic model comparing the over-or underrepresentation of two or more competing isoforms. RCD has advantages over commonly used methods because it is robust to false positive errors due to nonlinear trends in microarray measurements. Further, RCD does not depend on prior knowledge of splice isoforms, yet it takes advantage of the inherent structure of mutually exclusive junctions, and it is conceptually generalizable to other types of splicing arrays or RNA-Seq. RCD specifically identifies the biologically important cases when a splice junction becomes more or less prevalent compared to other mutually exclusive junctions. The example data is from different cell lines of glioblastoma tumors assayed with Agilent microarrays.

Pressure Ulcer Knowledge Among Nurses in a Brazilian University Hospital

To facilitate the implementation of evidence-based skin and pressure ulcer (PU) care practices and related staff education programs in a university hospital in Brazil, a cross-sectional study was conducted to evaluate nurses` knowledge about PU prevention, wound assessment, and staging. Of the 141 baccalaureate nurses (BSN) employed by the hospital at the time of the study, 106 consented to participate. Using a Portuguese version of Pieper`s Pressure Ulcer Knowledge Test (PUKT), participants were asked to indicate whether 33 statements about PU prevention and eight about PU assessment and staging were true or false. For the 33 prevention statements, the average number answered correctly was 26.07 (SD 4.93) and for the eight assessment statements the average was 4.59 (SD 1.62). Nurses working on inpatient clinical nursing units had significantly better scores (P = 0.000). Years of nursing experience had a weak and negative correlation with correct PUKT scores (r = -0.21, P = 0.033) as did years of experience working in the university hospital (r = -.179, P <071). Incorrect responses were most common for statements related to patient positioning, massage, PU assessment, and staging definitions. The results of this study confirm that nurses have an overall understanding of PU prevention and assessment principles but important knowledge deficits exist. Focused continuing education efforts are needed to facilitate the implementation of evidence-based care.

Power imbalance application region method for distributed synchronous generator anti-islanding protection design and evaluation

This paper presents a novel graphical approach to adjust and evaluate frequency-based relays employed in anti-islanding protection schemes of distributed synchronous generators, in order to meet the anti-islanding and abnormal frequency variation requirements, simultaneously. The proposed method defines a region in the power mismatch space, inside which the relay non-detection zone should be located, if the above-mentioned requirements must be met. Such region is called power imbalance application region. Results show that this method can help protection engineers to adjust frequency-based relays to improve the anti-islanding capability and to minimize false operation occurrences, keeping the abnormal frequency variation utility requirements satisfied. Moreover, the proposed method can be employed to coordinate different types of frequency-based relays, aiming at improving overall performance of the distributed generator frequency protection scheme. (C) 2011 Elsevier B.V. All rights reserved.

Aerodynamic study of three-dimensional larynx models using finite element methods

The airflow velocities and pressures are calculated from a three-dimensional model of the human larynx by using the finite element method. The laryngeal airflow is assumed to be incompressible, isothermal, steady, and created by fixed pressure drops. The influence of different laryngeal profiles (convergent, parallel, and divergent), glottal area, and dimensions of false vocal folds in the airflow are investigated. The results indicate that vertical and horizontal phase differences in the laryngeal tissue movements are influenced by the nonlinear pressure distribution across the glottal channel, and the glottal entrance shape influences the air pressure distribution inside the glottis. Additionally, the false vocal folds increase the glottal duct pressure drop by creating a new constricted channel in the larynx, and alter the airflow vortexes formed after the true vocal folds. (C) 2007 Elsevier Ltd. All rights reserved.

Failure Mechanisms in Sand over a Deep Active Trapdoor

An experimental testing program was undertaken to investigate failure mechanisms induced by the active movement of a deep rectangular trapdoor underlying a granular soil. Reduced-scale models were tested under normal gravity as well as under an increased gravitational field using a centrifuge facility. Some models were used to evaluate the performance of both flexible and rigid pipes undergoing a localized loss of support. Failure mechanisms in the longitudinal direction of the models were characterized by a single, well-defined failure surface that developed within the limits of the trapdoor. However, failure mechanisms in the transverse direction of the models were characterized by multiple failure surfaces extending outside the limits of the trapdoor. Significant dilation of the soil located immediately above the trapdoor was identified in the failure of the models. The pattern of the failure mechanisms was found to be affected by the stress level and backfill density. Higher stress levels were found to lead to well-developed failure zones. The influence of backfill density was found to be more relevant in models involving flexible pipes. Pipes embedded within loose backfill were severely damaged after loss of support, while pipes embedded in dense backfill experienced negligible deformations. These results indicate that damage to pipelines caused by ground loss of support can be significantly minimized by controlling the compaction of the fill.

Numerical solution of the two-phase expansion of a metastable flashing liquid jet using the dispersion-controlled dissipative scheme

This paper presents a study of the stationary phenomenon of superheated or metastable liquid jets, flashing into a two-dimensional axisymmetric domain, while in the two-phase region. In general, the phenomenon starts off when a high-pressure, high-temperature liquid jet emerges from a small nozzle or orifice expanding into a low-pressure chamber, below its saturation pressure taken at the injection temperature. As the process evolves, crossing the saturation curve, one observes that the fluid remains in the liquid phase reaching a superheated condition. Then, the liquid undergoes an abrupt phase change by means of an oblique evaporation wave. Across this phase change the superheated liquid becomes a two-phase high-speed mixture in various directions, expanding to supersonic velocities. In order to reach the downstream pressure, the supersonic fluid continues to expand, crossing a complex bow shock wave. The balance equations that govern the phenomenon are mass conservation, momentum conservation, and energy conservation, plus an equation-of-state for the substance. A false-transient model is implemented using the shock capturing scheme: dispersion-controlled dissipative (DCD), which was used to calculate the flow conditions as the steady-state condition is reached. Numerical results with computational code DCD-2D vI have been analyzed. Copyright (C) 2009 John Wiley & Sons, Ltd.

Instrumented indentation testing of an epoxy adhesive used in automobile body assembling

Instrumented indentation has been used to investigate the mechanical properties of BETAMATE 1496 (R) Epoxy adhesive. The properties of the adhesive were analyzed by measuring its hardness and its Young`s modulus in samples extracted from six different positions of the front door of a commercial passenger vehicle in two phases of processing: after application of the adhesive in the door assembling (""pre-cured"" state) and after final cure in the painting oven (""cured"" state). Special attention was given to setting the optimal parameters (""creep"" time and unloading time step) for the instrumented indentation testing for the present application. Young`s modulus values around 1.1 +/- 0.2 GPa and hardness values around 0.15 +/- 0.05 GPa were obtained for all samples, irrespective of the variation of the indentation parameters in the testing procedure and of the relative position of the adhesive in the door frame in both states. (C) 2008 Elsevier Ltd. All rights reserved.

Control charts for individual observations of a bivariate Poisson process

In this paper, three single-control charts are proposed to monitor individual observations of a bivariate Poisson process. The specified false-alarm risk, their control limits, and ARLs were determined to compare their performances for different types and sizes of shifts. In most of the cases, the single charts presented better performance rather than two separate control charts ( one for each quality characteristic). A numerical example illustrates the proposed control charts.

Characterization of tree-rings of Pinus caribaea var. hondurensis Barr. et Golf. trees by X ray densitometry

This work aimed to determining the anatomical structure of wood, through methodology of histology and X-ray densitometry, of resin-tapped and not resin-tapped Pinus caribaea var. hondurensis trees samples, of three diameter classes. Pine trees, in forest plantation established in 1969, in the Ecological Experimental Station of Itirapina, from the Forestry Institute of Sao Paulo State, were measured and stratified into three classes of trunk diameter. The pine trees were resin-tapped since 2004, with the opening of two simultaneous and opposing panels. Sixty samples of pine wood trees were extracted from the tree trunk through a non-destructive method and in the laboratory. Tree rings were determined in the laboratory and wood apparent density by X-ray densitometry. The test results showed that: (i) false tree rings occur in the early wood and late wood of the tree rings due to climate change; (ii) the X-ray densitometry allowed the demarcation of the tree rings limits; (iii) the wood apparent density average was significantly different between the trees in high class diameter and in the medium-low class; (iv) the wood characteristics from the resin-tapped and non resin-tapped faces did not show significant differences.

Suitability of relative humidity as an estimator of leaf wetness duration

Leaf wetness duration (LWD) is a key parameter in agricultural meteorology since it is related to epidemiology of many important crops, controlling pathogen infection and development rates. Because LWD is not widely measured, several methods have been developed to estimate it from weather data. Among the models used to estimate LWD, those that use physical principles of dew formation and dew and/or rain evaporation have shown good portability and sufficiently accurate results, but their complexity is a disadvantage for operational use. Alternatively, empirical models have been used despite their limitations. The simplest empirical models use only relative humidity data. The objective of this study was to evaluate the performance of three RH-based empirical models to estimate LWD in four regions around the world that have different climate conditions. Hourly LWD, air temperature, and relative humidity data were obtained from Ames, IA (USA), Elora, Ontario (Canada), Florence, Toscany (Italy), and Piracicaba, Sao Paulo State (Brazil). These data were used to evaluate the performance of the following empirical LWD estimation models: constant RH threshold (RH >= 90%); dew point depression (DPD); and extended RH threshold (EXT_RH). Different performance of the models was observed in the four locations. In Ames, Elora and Piracicaba, the RH >= 90% and DPD models underestimated LWD, whereas in Florence these methods overestimated LWD, especially for shorter wet periods. When the EXT_RH model was used, LWD was overestimated for all locations, with a significant increase in the errors. In general, the RH >= 90% model performed best, presenting the highest general fraction of correct estimates (F(C)), between 0.87 and 0.92, and the lowest false alarm ratio (F(AR)), between 0.02 and 0.31. The use of specific thresholds for each location improved accuracy of the RH model substantially, even when independent data were used; MAE ranged from 1.23 to 1.89 h, which is very similar to errors obtained with published physical models for LWD estimation. Based on these results, we concluded that, if calibrated locally, LWD can be estimated with acceptable accuracy by RH above a specific threshold, and that the EXT_RH method was unsuitable for estimating LWD at the locations used in this study. (C) 2007 Elsevier B.V. All rights reserved.

Effect of Toasting Intensity at Cooperage on Phenolic Compounds in Acacia (Robinia pseudoacacia) Heartwood

The phenolic composition of heartwood from Robinia pseudoacacia, commonly known as false acacia, before and after toasting in cooperage was studied by HPLC-DAD and HPLC-DAD/ESI-MS/MS. A total of 41 flavonoid and nonflavonoid compounds were identified, some tentatively, and quantified. Seasoned acacia wood showed high concentrations of flavonoid and low levels of nonflavonoid compounds, the main compounds being the dihydroflavonols dihydrorobinetin, fustin, tetrahydroxy, and trihydroxymethoxy dihydroflavonol, the flavonol robinetin, the flavanones robtin and butin, and a leucorobinetinidin, none of which are found in oak wood. The low molecular weight (LMW) phenolic compounds present also differed from those found in oak, since compounds with a beta-resorcylic structure, gallic related compounds, protocatechuic aldehyde, and some hydroxycinnamic compounds are included, but only a little gallic and ellagic acid. Toasting changed the chromatographic profiles of extracts spectacularly. Thus, the toasted acacia wood contributed flavonoids and condensed tannins (prorobinetin type) in inverse proportion to toasting intensity, while LMW phenolic compounds were directly proportional to toasting intensity, except for gallic and ellagic acid and related compounds. Even though toasting reduced differences between oak and acacia, particular characteristics of this wood must be taken into account when considering its use in cooperage: the presence of flavonoids and compounds with beta-resorcylic structure and the absence of hydrolyzable tannins.

Courtyard, Hill House, Chapel Hill, Brisbane

Central courtyard space. Door to master bedroom and ensuite on right.

Entry, Hill House, Chapel Hill, Brisbane

Entry stairs and front door, with garden area beyond.

Entry court, Hill House, Chapel Hill, Brisbane

As seen from front door stairs.