Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.

Wavelet analysis of MODIS time series to detect expansion and intensification of row-crop agriculture in Brazil

Since 2000, the southwestern Brazilian Amazon has undergone a rapid transformation from natural vegetation and pastures to row-crop agricultural with the potential to affect regional biogeochemistry. The goals of this research are to assess wavelet algorithms applied to MODIS time series to determine expansion of row-crops and intensification of the number of crops grown. MODIS provides data from February 2000 to present, a period of agricultural expansion and intensification in the southwestern Brazilian Amazon. We have selected a study area near Comodoro, Mato Grosso because of the rapid growth of row-crop agriculture and availability of ground truth data of agricultural land-use history. We used a 90% power wavelet transform to create a wavelet-smoothed time series for five years of MODIS EVI data. From this wavelet-smoothed time series we determine characteristic phenology of single and double crops. We estimate that over 3200 km(2) were converted from native vegetation and pasture to row-crop agriculture from 2000 to 2005 in our study area encompassing 40,000 km(2). We observe an increase of 2000 km(2) of agricultural intensification, where areas of single crops were converted to double crops during the study period. (C) 2007 Elsevier Inc. All rights reserved.

Contuse lesion of the rat spinal cord of moderate intensity leads to a higher time-dependent secondary neurodegeneration than severe one - An open-window for experimental neuroprotective interventions

Secondary neurodegeneration takes place in the surrounding tissue of spinal cord trauma and modifies substantially the prognosis, considering the small diameter of its transversal axis. We analyzed neuronal and glial responses in rat spinal cord after different degree of contusion promoted by the NYU Impactor. Rats were submitted to vertebrae laminectomy and received moderate or severe contusions. Control animals were sham operated. After 7 and 30 days post surgery, stereological analysis of Nissl staining cellular profiles showed a time progression of the lesion volume after moderate injury, but not after severe injury. The number of neurons was not altered cranial to injury. However, same degree of diminution was seen in the caudal cord 30 days after both severe and moderate injuries. Microdensitometric image analysis demonstrated a microglial reaction in the white matter 30 days after a moderate contusion and showed a widespread astroglial reaction in the white and gray matters 7 days after both severities. Astroglial activation lasted close to lesion and in areas related to Wallerian degeneration. Data showed a more protracted secondary degeneration in rat spinal cord after mild contusion, which offered an opportunity for neuroprotective approaches. Temporal and regional glial responses corroborated to diverse glial cell function in lesioned spinal cord. (C) 2007 Elsevier Ltd. All rights reserved.

Angiotensin receptor blockade improves the net balance of cardiac Ca(2+) handling-related proteins in sympathetic hyperactivity-induced heart failure

Aims: The clinical benefits of angiotensin II type 1 (AT1) receptor blockers (ARB) in heart failure (HF) include cardiac anti-remodeling and improved ventricular function. However, the cellular mechanisms underlying the benefits of ARB on ventricular function need to be better clarified. In the present manuscript, we evaluated the effects of AT1 receptor blockade on the net balance of Ca(2+) handling proteins in hearts of mice lacking alpha(2A) and alpha(2C) adrenoceptors (alpha(2A)/alpha(2C)ARKO), which develop sympathetic hyperactivity (SH) induced-HF. Main methods: A cohort of male wild-type (WT) and congenic alpha(2A)/alpha(2C)ARKO mice in a C57BL6/J genetic background (5-7 mo of age) was randomly assigned to receive either placebo or ARB (Losartan, 10 mg/kg for 8wks). Ventricular function (VF) was assessed by echocardiography, and cardiac myocyte width and ventricular fibrosis by a computer-assisted morphometric system. Sarcoplasmic reticulum Ca(2+) ATPase (SERCA2), phospholamban (PLN), phospho-Ser(16)-PLN, phospho-Thr(17)-PLN, phosphatase 1 (PP1), Na(+)-Ca(2+) exchanger (NCX), Ca(2+)/calmodulin-dependent protein kinase 11 (CaMKII) and phospho-Thr(286)-CaMKII were analyzed by Western blot. Key findings: alpha(2A)/alpha(2C)ARKO mice displayed ventricular dysfunction, cardiomyocyte hypertrophy and cardiac fibrosis paralleled by decreased SERCA2 and increased phospho-Thr(17)-PLN, CaMKII, phospho-Thr(286)-CaMKII and NCX levels. ARB induced anti-cardiac remodeling effect and improved VF in alpha(2A)/alpha(2C)ARKO associated with increased SERCA2 and phospho-Ser(16)-PLN levels, and SERCA2:NCX ratio. Additionally, ARB decreased phospho-Thr(17)-PLN levels as well as reestablished NCX, CaMKII and phospho-Thr(286)-CaMKII toward WT levels. Significance: Altogether, these data provide new insights on intracellular Ca(2+) regulatory mechanisms underlying improved ventricular function by ARB therapy in HF. (c) 2011 Elsevier Inc. All rights reserved.

Exercise training reduces cardiac angiotensin II levels and prevents cardiac dysfunction in a genetic model of sympathetic hyperactivity-induced heart failure in mice

The role of exercise training (ET) on cardiac renin-angiotensin system (RAS) was investigated in 3-5 month-old mice lacking alpha(2A-) and alpha(2C-)adrenoceptors (alpha(2A)/alpha(2C)ARKO) that present heart failure (HF) and wild type control (WT). ET consisted of 8-week running sessions of 60 min, 5 days/week. In addition, exercise tolerance, cardiac structural and function analysis were made. At 3 months, fractional shortening and exercise tolerance were similar between groups. At 5 months, alpha(2A)/alpha(2C)ARKO mice displayed ventricular dysfunction and fibrosis associated with increased cardiac angiotensin (Ang) II levels (2.9-fold) and increased local angiotensin-converting enzyme activity (ACE 18%). ET decreased alpha(2A)/alpha(2C)ARKO cardiac Ang II levels and ACE activity to age-matched untrained WT mice levels while increased ACE2 expression and prevented exercise intolerance and ventricular dysfunction with little impact on cardiac remodeling. Altogether, these data provide evidence that reduced cardiac RAS explains, at least in part, the beneficial effects of ET on cardiac function in a genetic model of HF.

The role of local and systemic renin angiotensin system activation in a genetic model of sympathetic hyperactivity-induced heart failure in mice

Sympathetic hyperactivity (SH) and renin angiotensin system (RAS) activation are commonly associated with heart failure (HF), even though the relative contribution of these factors to the cardiac derangement is less understood. The role of SH on RAS components and its consequences for the HF were investigated in mice lacking alpha(2A) and alpha(2C) adrenoceptor knockout (alpha(2A)/alpha(2C) ARKO) that present SH with evidence of HF by 7 mo of age. Cardiac and systemic RAS components and plasma norepinephrine (PN) levels were evaluated in male adult mice at 3 and 7 mo of age. In addition, cardiac morphometric analysis, collagen content, exercise tolerance, and hemodynamic assessments were made. At 3 mo, alpha(2A)/alpha(2C)ARKO mice showed no signs of HF, while displaying elevated PN, activation of local and systemic RAS components, and increased cardiomyocyte width (16%) compared with wild-type mice (WT). In contrast, at 7 mo, alpha(2A)/alpha(2C)ARKO mice presented clear signs of HF accompanied only by cardiac activation of angiotensinogen and ANG II levels and increased collagen content (twofold). Consistent with this local activation of RAS, 8 wk of ANG II AT(1) receptor blocker treatment restored cardiac structure and function comparable to the WT. Collectively, these data provide direct evidence that cardiac RAS activation plays a major role underlying the structural and functional abnormalities associated with a genetic SH-induced HF in mice.

Real-Time Voltage Regulation in Power Distribution System Using Fuzzy Control

Two different fuzzy approaches to voltage control in electric power distribution systems are introduced in this paper. The real-time controller in each case would act on power transformers equipped with under-load tap changers. Learning systems are employed to turn the voltage-control relays into adaptive devices. The scope of this study has been limited to the power distribution substation, and the voltage measurements and control actions are carried out on the secondary bus. The capacity of fuzzy systems to handle approximate data, together with their unique ability to interpret qualitative information, make it possible to design voltage-control strategies that satisfy the requirements of the Brazilian regulatory bodies and the real concerns of the electric power distribution companies. Fuzzy control systems based on these two strategies have been implemented and the test results were highly satisfactory.

H(infinity) filtering for rectangular discrete-time descriptor systems

This paper deals with the H(infinity) recursive estimation problem for general rectangular time-variant descriptor systems in discrete time. Riccati-equation based recursions for filtered and predicted estimates are developed based on a data fitting approach and game theory. In this approach, the nature determines a state sequence seeking to maximize the estimation cost, whereas the estimator tries to find an estimate that brings the estimation cost to a minimum. A solution exists for a specified gamma-level if the resulting cost is positive. In order to present some computational alternatives to the H(infinity) filters developed, they are rewritten in information form along with the respective array algorithms. (C) 2009 Elsevier Ltd. All rights reserved.

Failure analysis of low velocity impact on thin composite laminates: Experimental and numerical approaches

The dynamic behavior of composite laminates is very complex because there are many concurrent phenomena during composite laminate failure under impact load. Fiber breakage, delaminations, matrix cracking, plastic deformations due to contact and large displacements are some effects which should be considered when a structure made from composite material is impacted by a foreign object. Thus, an investigation of the low velocity impact on laminated composite thin disks of epoxy resin reinforced by carbon fiber is presented. The influence of stacking sequence and energy impact was investigated using load-time histories, displacement-time histories and energy-time histories as well as images from NDE. Indentation tests results were compared to dynamic results, verifying the inertia effects when thin composite laminate was impacted by foreign object with low velocity. Finite element analysis (FEA) was developed, using Hill`s model and material models implemented by UMAT (User Material Subroutine) into software ABAQUS (TM), in order to simulate the failure mechanisms under indentation tests. (C) 2007 Elsevier Ltd. All rights reserved.

Short-term experimental data of drying shrinkage of ground granulated blast-furnace slag cement concrete

This paper presents results of laboratory testing of unrestrained drying shrinkage during a period of 154 days of different concrete mixtures from the Brazilian production line that utilize ground granulated blast-furnace slag in their compositions. Three concrete mixtures with water/cement ratio of 0.78(M1), 0.41(M2), and 0.37(M3) were studied. The obtained experimental data were compared with the analytical results from prediction models available in the literature: the ACI 209 model (ACI), the B3 model (B3), the Eurocode 2 model (EC2), the GL 2000 model (GL), and the Brazilian NBR 6118 model (NBR), and an analysis of the efficacy of these models was conducted utilizing these experimental data. In addition, the development of the mechanical properties (compressive strength and modulus of elasticity) of the studied concrete mixtures was also measured in the laboratory until 126 days. From this study, it could be concluded that the ACI and the GL were the models that most approximated the experimental drying shrinkage data measured during the analyzed period of time.

Falling sheet envelope method for non-destructive testing time-dependent signals

In this work, an algorithm to compute the envelope of non-destructive testing (NDT) signals is proposed. This method allows increasing the speed and reducing the memory in extensive data processing. Also, this procedure presents advantage of preserving the data information for physical modeling applications of time-dependent measurements. The algorithm is conceived to be applied for analyze data from non-destructive testing. The comparison between different envelope methods and the proposed method, applied to Magnetic Bark Signal (MBN), is studied. (C) 2010 Elsevier Ltd. All rights reserved.

Reliability concepts applied to cutting tool change time

This paper presents a reliability-based analysis for calculating critical tool life in machining processes. It is possible to determine the running time for each tool involved in the process by obtaining the operations sequence for the machining procedure. Usually, the reliability of an operation depends on three independent factors: operator, machine-tool and cutting tool. The reliability of a part manufacturing process is mainly determined by the cutting time for each job and by the sequence of operations, defined by the series configuration. An algorithm is presented to define when the cutting tool must be changed. The proposed algorithm is used to evaluate the reliability of a manufacturing process composed of turning and drilling operations. The reliability of the turning operation is modeled based on data presented in the literature, and from experimental results, a statistical distribution of drilling tool wear was defined, and the reliability of the drilling process was modeled. (C) 2010 Elsevier Ltd. All rights reserved.

Post-failure behaviour of impulsively loaded circular plates

The dynamic plastic response of a simply supported circular plate is analysed. Emphasis is given to the plate behaviour after it has broken free from the supports due to a local material failure. The theoretical rigid plastic analysis predicts various features of the response such as the time to failure, residual kinetic energy and the critical velocity at failure. The residual kinetic energy of the plate could be significant enough to cause secondary impact damage. It is shown that the shape of the plate changes after breaking free from the supports, which is important for forensic investigations. The solution for various cases were proven to be exact in the context of the upper and lower bounds theorems of the theory of plasticity. (C) 2009 Elsevier Ltd. All rights reserved.

Availability analysis of heat recovery steam generators used in thermal power plants

The combined-cycle gas and steam turbine power plant presents three main pieces of equipment: gas turbines, steam turbines and heat recovery steam generator (HRSG). In case of HRSG failure the steam cycle is shut down, reducing the power plant output. Considering that the technology for design, construction and operation of high capacity HRSGs is quite recent its availability should be carefully evaluated in order to foresee the performance of the power plant. This study presents a method for reliability and availability evaluation of HRSGs installed in combined-cycle power plant. The method`s first step consists in the elaboration of the steam generator functional tree and development of failure mode and effects analysis. The next step involves a reliability and availability analysis based on the time to failure and time to repair data recorded during the steam generator operation. The third step, aiming at availability improvement, recommends the fault-tree analysis development to identify components the failure (or combination of failures) of which can cause the HRSG shutdown. Those components maintenance policy can be improved through the use of reliability centered maintenance (RCM) concepts. The method is applied on the analysis of two HRSGs installed in a 500 MW combined-cycle power plant. (C) 2010 Elsevier Ltd. All rights reserved.

Failure assessments of corroded pipelines with axial defects using stress-based criteria: Numerical studies and verification analyses

Conventional procedures used to assess the integrity of corroded piping systems with axial defects generally employ simplified failure criteria based upon a plastic collapse failure mechanism incorporating the tensile properties of the pipe material. These methods establish acceptance criteria for defects based on limited experimental data for low strength structural steels which do not necessarily address specific requirements for the high grade steels currently used. For these cases, failure assessments may be overly conservative or provide significant scatter in their predictions, which lead to unnecessary repair or replacement of in-service pipelines. Motivated by these observations, this study examines the applicability of a stress-based criterion based upon plastic instability analysis to predict the failure pressure of corroded pipelines with axial defects. A central focus is to gain additional insight into effects of defect geometry and material properties on the attainment of a local limit load to support the development of stress-based burst strength criteria. The work provides an extensive body of results which lend further support to adopt failure criteria for corroded pipelines based upon ligament instability analyses. A verification study conducted on burst testing of large-diameter pipe specimens with different defect length shows the effectiveness of a stress-based criterion using local ligament instability in burst pressure predictions, even though the adopted burst criterion exhibits a potential dependence on defect geometry and possibly on material`s strain hardening capacity. Overall, the results presented here suggests that use of stress-based criteria based upon plastic instability analysis of the defect ligament is a valid engineering tool for integrity assessments of pipelines with axial corroded defects. (C) 2008 Elsevier Ltd. All rights reserved.