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.

The impact of the subtropical South Atlantic SST on South American precipitation

The Community Climate Model (CCM3) from the National Center for Atmospheric Research (NCAR) is used to investigate the effect of the South Atlantic sea surface temperature (SST) anomalies on interannual to decadal variability of South American precipitation. Two ensembles composed of multidecadal simulations forced with monthly SST data from the Hadley Centre for the period 1949 to 2001 are analysed. A statistical treatment based on signal-to-noise ratio and Empirical Orthogonal Functions (EOF) is applied to the ensembles in order to reduce the internal variability among the integrations. The ensemble treatment shows a spatial and temporal dependence of reproducibility. High degree of reproducibility is found in the tropics while the extratropics is apparently less reproducible. Austral autumn (MAM) and spring (SON) precipitation appears to be more reproducible over the South America-South Atlantic region than the summer (DJF) and winter (JJA) rainfall. While the Inter-tropical Convergence Zone (ITCZ) region is dominated by external variance, the South Atlantic Convergence Zone (SACZ) over South America is predominantly determined by internal variance, which makes it a difficult phenomenon to predict. Alternatively, the SACZ over western South Atlantic appears to be more sensitive to the subtropical SST anomalies than over the continent. An attempt is made to separate the atmospheric response forced by the South Atlantic SST anomalies from that associated with the El Nino - Southern Oscillation (ENSO). Results show that both the South Atlantic and Pacific SSTs modulate the intensity and position of the SACZ during DJF. Particularly, the subtropical South Atlantic SSTs are more important than ENSO in determining the position of the SACZ over the southeast Brazilian coast during DJF. On the other hand, the ENSO signal seems to influence the intensity of the SACZ not only in DJF but especially its oceanic branch during MAM. Both local and remote influences, however, are confounded by the large internal variance in the region. During MAM and JJA, the South Atlantic SST anomalies affect the magnitude and the meridional displacement of the ITCZ. In JJA, the ENSO has relatively little influence on the interannual variability of the simulated rainfall. During SON, however, the ENSO seems to counteract the effect of the subtropical South Atlantic SST variations on convection over South America.

Impact of cancer-related symptom synergisms on health-related quality of life and performance status

To identify the impact of multiple symptoms and their co-occurrence on health-related quality of life (HRQOL) dimensions and performance status (PS), 115 outpatients with cancer, who were not receiving active cancer treatment and were recruited from, a university hospital in Sao Paulo, Brazil completed the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire-C30, the Beck Depression Inventory, and the Brief Pain Inventory. Karnofsky Performance Status scores also were completed. Application of TwoStep Cluster analysis resulted in two distinct patient subgroups based on 113 patient experiences with pain, depression, fatigue, insomnia, constipation, lack of appetite, dyspnea, nausea, vomiting, and diarrhea. One group had multiple and severe symptom subgroup and another had Less symptoms and with lower severity. Multiple and severe symptoms had worse PS, role functioning, and physical, emotional, cognitive, social, and overall HRQOL. Multiple and severe symptom subgroup was also six times as likely as lower severity to have poor role functioning;five times more likely to have poor emotional;four times more likely to have poor PS, physical, and overall HRQOL, and three times as likely to have poor cognitive and social HRQOL, independent of gender, age, level of education, and economic condition. Classification and Regression Tree analyses were undertaken to identify which co-occurring symptoms would best determine reduction in HRQOL and PS. Pain and fatigue were identified as indicators of reduction on physical HRQOL and PS. Fatigue and insomnia were associated with reduction in cognitive; depression and pain in social; and fatigue and constipation in role functioning. Only depression was associated with reduction in overall HRQOL. These data demonstrate that there is a synergic effect among distinct cancer symptoms that result in reduction in HRQOL dimensions and PS.

The impact of a 17-day training period for an international championship on mucosal immune parameters in top-level basketball players and staff members

This investigation examined the impact of a 17-d training period (that included basketball-specific training, sprints, intermittent running exercises, and weight training, prior to an international championship competition) on salivary immunoglobulin A (SIgA) levels in 10 subjects (athletes and staff members) from a national basketball team, as a biomarker for mucosal immune defence. Unstimulated saliva samples were collected at rest at the beginning of the preparation for the Pan American Games and 1 d before the first game. The recovery interval from the last bout of exercise was 4 h. The SIgA level was measured using enzyme-linked immunosorbent assay and expressed as absolute concentrations, secretion rate, and SIgA level relative to total protein. The decrease in SIgA levels following training was greater in athletes than in support staff; however, no significant differences between the two groups were detected. A decrease in SIgA level, regardless of the method used to express IgA results, was verified for athletes. Only one episode of upper respiratory tract illness symptoms was reported, and it was not associated with changes in SIgA levels. In summary, a situation of combined stress for an important championship was found to decrease the level of SIgA-mediated immune protection at the mucosal surface in team members, with greater changes observed in the athletes.

Reliability and validity of the Impact of Event Scale (IES): version for Brazilian burn victims

Aims. The aims of this study were to assess the internal reliability (internal consistency), construct validity, sensitivity and ceiling and floor effects of the Brazilian-Portuguese version of the Impact of Event Scale (IES). Design. Methodological research design. Method. The Brazilian-Portuguese version of the IES was applied to a group of 91 burned patients at three times: the first week after the burn injury (time one), between the fourth and the sixth months (time two) and between the ninth and the 12th months (time three). The internal consistency, construct validity (convergent and dimensionality), sensitivity and ceiling and floor effects were tested. Results. Cronbach`s alpha coefficients showed high internal consistency for the total scale (0 center dot 87) and for the domains intrusive thoughts (0 center dot 87) and avoidance responses (0 center dot 76). During the hospitalisation (time one), the scale showed low and positive correlations with pain measures immediately before (r = 0 center dot 22; p < 0 center dot 05) and immediately after baths and dressings (r = 0 center dot 21; p < 0 center dot 05). After the discharge, we found strong and negative correlations with self-esteem (r = -0 center dot 52; p < 0 center dot 01), strong and positive with depression (r = 0 center dot 63; p < 0 center dot 01) and low and negative with the Bodily pain (r = -0 center dot 24; p < 0 center dot 05), Social functioning (r = -0 center dot 34; p < 0 center dot 01) and Mental health (r = -0 center dot 27; p < 0 center dot 05) domains of the SF-36 at time two. Regarding the sensitivity, no statistically significant differences were observed between mean scale scores according to burned body surface (p = 0 center dot 21). The floor effect was observed in most of the IES items. Conclusion. The adapted version of the scale showed to be reliable and valid to assess postburn reactions on the impact of the event in the group of patients under analysis. Relevance to clinical practice. The Impact of Event Scale can be used in research and clinical practice to assess nursing interventions aimed at decreasing stress during rehabilitation.

Impact of Childhood Cancer on Parents` Relationships: An Integrative Review

Purpose: The diagnosis of cancer and the treatment decisions associated with it may cause uncertainty, stress, and anxiety among parents. Emotional tensions can affect parents` relationships during the trajectory of the child`s cancer illness. We conducted an integrative review to examine the evidence related to the effects of childhood cancer on parents` relationships. Methods: An integrative literature search of studies published between 1997 and 2009 was conducted in the Cumulative Index to Nursing and Allied Health Literature (CINAHL), Psychology Information (PsycINFO), PubMed, Scopus, CUIDEN, and Latin American and Caribbean Health Science Literature (LILACS). The key words used were neoplasms, child, marriage, spouses, family relations, and nursing. Articles were reviewed if the (a) topic addressed parents` relationships during childhood cancer; (b) participants were mothers, fathers, or both; (c) design was either qualitative or quantitative; (d) language was English, Portuguese, or Spanish; (e) date of publication was between January 1997 and October 2009; and (f) abstract was available. Results: Fourteen articles met the search criteria and were reviewed using Cooper`s framework for integrative reviews. Four themes emerged: (a) changes in the parents` relationship during the trajectory of the child`s illness; (b) difficulty in communication between couples; (c) gender differences in parental stress and coping; and (d) role changes. Conclusions and Implications: Findings revealed positive and negative changes in parents` relationships, communication, stress, and roles. Nurses need to assess the impact of cancer diagnosis and treatments on parent relationships, offer support and encouragement, and allow expression of feelings. Future research is needed to develop and test interventions that increase parents` potentials and strengthen relationships during the challenging trajectory of their children`s cancer and treatment. Clinical Relevance: The multiple sources of stress and uncertainty associated with a child`s cancer diagnosis and treatment affect parents` relationships. Difficulties in communication appear frequently in parents` relationship. Our findings may guide healthcare professionals in identifying parents at risk for developing conflicts, communication problems, and lack of alignment between parents that could interfere with providing optimal care for their child with cancer. Healthcare professionals may promote dialogue and encourage parents to express their feelings, seek mutual support, and establish a partnership in dealing with the child`s illness.

The life impact of burns: the perspective from burn persons in Brazil during their rehabilitation phase

Method. Participants were 18 years of age or older, who had been discharged from hospitalisation between 6 months and 1 year before the interview, or who underwent reconstructive surgery during the previous year, or who were under outpatient follow-up awaiting reconstructive surgery. Data were collected by means of semi-structured interviews. Results. Thirty-eight of the 44 participants (86.4%) reported some type of changes associated with the burn injury, the treatment, or both, regarding the following aspects: work, leisure, relationships, religious ties, educational activities and habits (smoking, using alcohol and drugs and dressing style). The data showed a statistically significant association between burns on at least one of the upper limbs (with or without hands) and changes in work. Conclusions. Some of the aspects mentioned by the participants, such as work and leisure activities, need to be further researched in order to improve our understanding of the impact that these changes causes in the person`s life.

Alternative positional FEM applied to thermomechanical impact of truss structures

This paper presents a formulation to deal with dynamic thermomechanical problems by the finite element method. The proposed methodology is based on the minimum potential energy theorem written regarding nodal positions, not displacements, to solve the mechanical problem. The thermal problem is solved by a regular finite element method. Such formulation has the advantage of being simple and accurate. As a solution strategy, it has been used as a natural split of the thermomechanical problem, usually called isothermal split or isothermal staggered algorithm. Usual internal variables and the additive decomposition of the strain tensor have been adopted to model the plastic behavior. Four examples are presented to show the applicability of the technique. The results are compared with other authors` numerical solutions and experimental results. (C) 2010 Elsevier B.V. All rights reserved.

The recent occurrence, establishment and potential impact of Geophagus proximus (Cichlidae : Perciformes) in the Tiete River reservoirs: an Amazonian fish species introduced in the Parana Basin (Brazil)

The introduction of allochthonous fish species happens constantly in large bodies of freshwater, like as the reservoirs of Parana Basin, located in Brazilian southeast, representing a threat for local biodiversity. The fish species Plagioscion squamosissimus and Cichla ocellaris were introduced from the 1970s in several water bodies of this basin and had successfully established themselves in all six reservoirs located in the middle and lower Tiete River (SP, Brazil), particularly. After six decades from the first recorded species introduction, this hydrographic system remains open to the invasion of further fish species, owing to widespread fish-farming activity and by the channels opened between this system and other reservoirs and river basin. This study was an effort to confirm the Geophagus proximus occurrence in the six Tiete River reservoirs, verifying the actual introduction status and analyzing its potential environmental impacts on local species by the analysis of the population structure (abundance, body dimensions and feeding habits). By the results, this species was confirmed in the Ibitinga, Nova Avanhandava and Tres Irmaos reservoirs. The abundance and feeding analysis shows, respectively, it is successfully established in the Tres Irmaos reservoir with the same feeding habitats of local species, such as Geophagus brasiliensis. It was further shown to be very likely that G. proximus would spread throughout the reservoir system of the middle and lower Tiete River, in the manner of P. squamosissimus and C. ocellaris, and the competition pressure for food resources between G. proximus and the local species which represents a potential environmental impact system. These scientific evidences fortifies the knowledge basin for the implantation of a fish management system, to control and reduce the abundance of the invader and to prevent its becoming established in all the Tiete River Basin, avoiding the disastrous consequences for the native species of Parana River Basin.

Impact of transition oxides on growth stresses and texture of alumina scales formed during oxidation of iron aluminides

The internal stresses and crystallographic texture in alpha-Al(2)O(3) scales grown on iron aluminides at 1100 degrees C were determined in situ using synchrotron X-ray diffraction. In the first hour of oxidation, alpha-Al(2)O(3) was formed by direct nucleation and by conversion from transition oxides (either theta-Al(2)O(3) or a mixed Fe-Al oxide). A sharp texture develops connected with the direct nucleation of alpha-Al(2)O(3), in contrast to the weaker texture observed in alpha-Al(2)O(3) originated by previous transformations, which also yielded tensile stresses in early oxidation stages. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A Power-Quality Index to Assess the Impact of Voltage Harmonic Distortions and Unbalance to Three-Phase Induction Motors

This paper discusses the need to simultaneously monitor voltage unbalance and harmonic distortions in addition to root-mean-square voltage values. An alternative way to obtain the parameters related to voltage unbalance at fundamental frequency as well as voltage harmonic distortions is here proposed, which is based on the representation of instantaneous values at the axes and at the instantaneous Euclidean norm. A new power-quality (PQ) index is then proposed to combine the effects of voltage unbalance and harmonic distortions. This new index is easily implemented into existing electronic power meters. This PQ index is determined from the analysis of temperature rise in induction motor windings, which were tested for long periods of time. This paper also shows that these voltage disturbances, which are harmful to the lifetime expectancy of motors, can be measured by alternative ways in relation to conventional methods. Although this paper deals with induction motors only, the results show the relevance for further studies on other pieces of equipment.

Impact of plastic deformation on magnetoacoustic properties of Fe-2%Si alloy

The paper presents the results of a complementary study including magnetic hysteresis loops B(H), magnetic Barkhausen noise (MBN) and magnetoacoustic emission (MAE) signals measurements for plastically deformed Fe-2%Si samples. The investigated samples had been plastically deformed with plastic strain level (epsilon(p)) up to 8%. The properties of B(H) loops are quantified using the coercivity H(C) and maximum differential permeability mu(rmax) as parameters. The MBN and MAE voltage signals were analysed by means of rms-like voltage (Ub and Ua, respectively) envelopes, plotted as a function of applied field strength. Integrals of the Ub and Ua voltages over half of a period of magnetization were then calculated. It has been found that He and integrals of Ub increase, while mu(rmax) decreases monotonically with increasing epsilon(p). The MAE (Ua) peak voltage at first decreases, then peaks at epsilon(p) approximate to 1.5% and finally decreases again. The integral of the Ua voltage at first increases for low epsilon(p) and then decreases for epsilon(p) > 1.5%. All those various dependence types suggest the possibility of detection of various stages of microstructure change. The above-mentioned results are discussed qualitatively in the paper. Some modelling of the discussed dependency is also presented. (C) 2008 Elsevier Ltd. All rights reserved.

Impact of guar and xanthan gums on proofing and calorimetric parameters of frozen bread dough

The influence of guar and xanthan gum and their combined use on dough proofing rate and its calorimetric properties was investigated. Fusion enthalpy, which is related to the amount of frozen water, was influenced by frozen dough formulation and storage time; specifically gum addition reduced the fusion enthalpy in comparison to control formulation, 76.9 J/g for formulation with both gums and 81.2 J/g for control, at 28th day. Other calorimetric parameters, such as T(g) and freezable water amount, were also influenced by frozen storage time. For all formulations, proofing rate of dough after freezing, frozen storage time and thawing, decreased in comparison to non-frozen dough, indicating that the freezing process itself was more detrimental to the proofing rate than storage time. For all formulations, the mean value of proofing rate was 2.97 +/- 0.24 cm(3) min(-1) per 100 g of non-frozen dough and 2.22 +/- 0.12 cm(3) min(-1) per 100 g of frozen dough. Also the proofing rate of non-frozen dough with xanthan gum decreased significantly in relation to dough without gums and dough with only guar gum. Optical microscopy analyses showed that the gas cell production after frozen storage period was reduced, which is in agreement with the proofing rate results. (C) 2008 Elsevier Ltd. All rights reserved.