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/.

Coordination dynamics and attentional costs of continuous and discontinuous bimanual circle drawing movements

It has been suggested that the temporal control of rhythmic unimianual movements is different between tasks requiring continuous (e.g., circle drawing) and discontinuous movements (e.g., finger tapping). Specifically, for continuous movements temporal regularities are ail emergent property, whereas for tasks that involve discontinuities timing is ail explicit part of the action goal. The present experiment further investigated the control of continuous and discontinuous movements by comparing the coordination dynamics and attentional demands of bimanual continuous circle drawing with bimanual intermittent circle drawing. The intermittent task required participants to insert a 400 ms pause between each cycle while circling. Using dual-task methodology, 15 right-handed participants performed the two circle drawing tasks, while vocally responding to randomly presented auditory probes. The circle drawing tasks were performed in symmetrical and asymmetrical coordination modes and at movement frequencies of 1 Hz and 1.7 Hz. Intermittent circle drawing exhibited superior spatial and temporal accuracy and stability than continuous circle drawing supporting the hypothesis that the two tasks have different underlying control processes. In terms of attentional cost, probe RT was significantly slower during the intermittent circle drawing task than the continuous circle drawing task across both coordination modes and movement frequencies. Of interest was the finding that in the intermittent circling task reaction time (RT) to probes presented during the pause between cycles did not differ from the RT to probes occurring during the circling movement. The differences in attentional demands between the intermittent and continuous circle drawing tasks may reflect the operation of explicit event timing and implicit emergent timing processes, respectively. (C) 2008 Elsevier B.V. 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.

Exercise prevents the effects of experimental arthritis on the metabolism and function of immune cells

Active lymphocytes (LY) and macrophages (M Phi) are involved in the pathophysiology of rheumatoid arthritis (RA) Due to its anti-inflammatory effect. physical exercise may be beneficial in RA by acting on the immune system (IS) Thus, female Wistar rats with type II collagen-induced arthritis (CIA) were submitted to swimming training (6 weeks. 5 days/week. 60 min/day) and some biochemical and immune parameters, such as the metabolism of glucose and glutamine and function of LY and M. were evaluated In addition, plasma levels of some hormones and of interleukin-2 (IL-2) were also determined Results demonstrate that CIA increased lymphocyte proliferation (1.9- and 1 7-fold, respectively, in response to concanavalin A (ConA) and lipopolysaccharide (LPS)), as well as macrophage H(2)O(2) production (1 6-fold), in comparison to control Exercise training prevented the activation of immune cells, induced by CIA. and established a pattern of substrate utilization similar to that described as normal for these cells. Exercise also promoted an elevation of plasma levels of corticosterone (22 2%), progesterone (1 7-fold) and IL-2 (2 6-fold) Our data suggest that chronic exercise is able to counterbalance the effects of CIA on cells of the IS. reinforcing the proposal that the benefits of exercise may not be restricted to aerobic capacity and/or strength improvement Copyright (C) 2010 John Wiley & Sons, Ltd

Experimental chronic low-frequency resistance training produces skeletal muscle hypertrophy in the absence of muscle damage and metabolic stress markers

Volitional animal resistance training constitutes an important approach to modeling human resistance training. However, the lack of standardization protocol poses a frequent impediment to the production of skeletal muscle hypertrophy and the study of related physiological variables (i.e., cellular damage/inflammation or metabolic stress). Therefore, the purposes of the present study were: (1) to test whether a long-term and low frequency experimental resistance training program is capable of producing absolute increases in muscle mass; (2) to examine whether cellular damage/inflammation or metabolic stress is involved in the process of hypertrophy. In order to test this hypothesis, animals were assigned to a sedentary control (C, n = 8) or a resistance trained group (RT, n = 7). Trained rats performed 2 exercise sessions per week (16 repetitions per day) during 12 weeks. Our results demonstrated that the resistance training strategy employed was capable of producing absolute mass gain in both soleus and plantaris muscles (12%, p<0.05). Furthermore, muscle tumor necrosis factor (TNF-alpha) protein expression (soleus muscle) was reduced by 24% (p<0.01) in trained group when compared to sedentary one. Finally, serum creatine kinase (CK) activity and serum lactate concentrations were not affected in either group. Such information may have practical applications if reproduced in situations where skeletal muscle hypertrophy is desired but high mechanical stimuli of skeletal muscle and inflammation are not. Copyright (C) 2010 John Wiley & Sons, Ltd.

Electrodeposition of copper on titanium wires: Taguchi experimental design approach

Electrodeposition of thin copper layer was carried out on titanium wires in acidic sulphate bath. The influence of titanium surface preparation, cathodic current density, copper sulphate and sulphuric acid concentrations, electrical charge density and stirring of the solution on the adhesion of the electrodeposits was studied using the Taguchi statistical method. A L(16) orthogonal array with the six factors of control at two levels each and three interactions was employed. The analysis of variance of the mean adhesion response and signal-to-noise ratio showed the great influence of cathodic current density on adhesion. on the contrary, the other factors as well as the three investigated interactions revealed low or no significant effect. From this study optimized electrolysis conditions were defined. The copper electrocoating improved the electrical conductivity of the titanium wire. This shows that copper electrocoated titanium wires could be employed for both electrical purpose and mechanical reinforcement in superconducting magnets. (C) 2008 Elsevier B.V. All rights reserved.

Establishment of the optimum initial xylose concentration and nutritional supplementation of brewer`s spent grain hydrolysate for xylitol production by Candida guilliermondii

The effects of initial xylose concentration and nutritional supplementation of brewer`s spent grain hydrolysate on xylitol production by Candida guilliermondii were evaluated using experimental design methodology. The hydrolysate containing 55, 75 or 95 g/l xylose, supplemented or not with nutrients (calcium chloride, ammonium sulfate and rice bran extract), was used as fermentation medium. The increase in xylitol yield and productivity was related to the increase of initial xylose concentration, but up to a certain limit. above of which the yeast performance was not improved. The hydrolysate supplementation with nutrients did not interfere with xylose-to-xylitol conversion. By using the statistic tool the best conditions for maximum xylitol production were found. which consisted in using the non-supplemented hydrolysate containing 70 g/l initial xylose concentration. Under these conditions, a xylitol yield of 0.78 g/g and productivity of 0.58 g/(l h) were achieved. (C) 2008 Elsevier Ltd. All rights reserved.

ETHANOL PRODUCTION FROM XYLOSE BY Pichia stipitis NRRL Y-7124 IN A STIRRED TANK BIOREACTOR

The ethanol production by Pichia stipitis was evaluated in a stirred tank bioreactor using semi-defined medium containing xylose (90.0 g/l) as the main carbon source. Experimental assays were performed according to a 2(2) full factorial design to evaluate the influence of aeration (0.25 to 0.75 vvm) and agitation (150 to 250 rpm) conditions on ethanol production. In the studied range of values, the agitation increase and aeration decrease favored ethanol production, which was maximum (26.7 g/l) using 250 rpm and 0.25 vvm, conditions that gave a volumetric oxygen transfer coefficient (k(L)a value) of 4.9 h(-1). Under these conditions, the ethanol yield factor, ethanol productivity, and the process efficiency were 0.32 g/g, 0.32 g/l.h, and 63%, respectively. These results are promising and contribute to the development of a suitable process for ethanol production from xylose by Pichia stipitis.

A contribution for thermoeconomic modelling: A methodology proposal

This work presents a thermoeconomic optimization methodology for the analysis and design of energy systems. This methodology involves economic aspects related to the exergy conception, in order to develop a tool to assist the equipment selection, operation mode choice as well as to optimize the thermal plants design. It also presents the concepts related to exergy in a general scope and in thermoeconomics which combines the thermal sciences principles (thermodynamics, heat transfer, and fluid mechanics) and the economic engineering in order to rationalize energy systems investment decisions, development and operation. Even in this paper, it develops a thermoeconomic methodology through the use of a simple mathematical model, involving thermodynamics parameters and costs evaluation, also defining the objective function as the exergetic production cost. The optimization problem evaluation is developed for two energy systems. First is applied to a steam compression refrigeration system and then to a cogeneration system using backpressure steam turbine. (C) 2010 Elsevier Ltd. All rights reserved.

Simultaneous saccharification and ethanol fermentation of oxalic acid pretreated corncob assessed with response surface methodology

Response surface methodology was used to evaluate optimal time, temperature and oxalic acid concentration for simultaneous saccharification and fermentation (SSF) of corncob particles by Pichia stipitis CBS 6054. Fifteen different conditions for pretreatment were examined in a 2(3) full factorial design with six axial points. Temperatures ranged from 132 to 180 degrees C, time from 10 to 90 min and oxalic acid loadings from 0.01 to 0.038 g/g solids. Separate maxima were found for enzymatic saccharification and hemicellulose fermentation, respectively, with the condition for maximum saccharification being significantly more severe. Ethanol production was affected by reaction temperature more than by oxalic acid and reaction time over the ranges examined. The effect of reaction temperature was significant at a 95% confidence level in its effect on ethanol production. Oxalic acid and reaction time were statistically significant at the 90% level. The highest ethanol concentration (20 g/l) was obtained after 48 h with an ethanol volumetric production rate of 0.42 g ethanol l(-1) h(-1). The ethanol yield after SSF with P. stipitis was significantly higher than predicted by sequential saccharification and fermentation of substrate pretreated under the same condition. This was attributed to the secretion of beta-glucosidase by P. stipitis. During SSF, free extracellular beta-glucosidase activity was 1.30 pNPG U/g with P. stipitis, while saccharification without the yeast was 0.66 pNPG U/g. Published by Elsevier Ltd.

Theoretical and Experimental Study of Polarization Dependent Loss in a Optical Recirculating Loop

An experimental study of the Polarization Dependent Loss (PDL) is performed in an Optical Recirculating Loop (RCL). The RCL enables to simulate the transmission through various optical links using just one optical fiber spool, one in line amplifier, some optical filters and devices in a low cost manner. The total amount of PDL in a Recirculating loop, due to its statistical nature, is different of the simple sum of each element of the recirculating loop because of the alignment variation of the PDL elements with time, depending on the environmental conditions such as fiber stress and temperature. In this paper theoretical studies are also performed using formalism of Jones and Mueller matrices in order to represent the different optical elements in the recirculating loop. The PDL must be correctly characterized in order to evaluate properly the impact on the performance of next generation DWDM systems. Theoretical and experimental results comparison shows that a depolarization of 7% occurs in the experimental setup, probably by the optical amplifier due to the depolarized nature of the amplified spontaneous emission.

Power quality analysis applying a hybrid methodology with wavelet transforms and neural networks

A hybrid system to automatically detect, locate and classify disturbances affecting power quality in an electrical power system is presented in this paper. The disturbances characterized are events from an actual power distribution system simulated by the ATP (Alternative Transients Program) software. The hybrid approach introduced consists of two stages. In the first stage, the wavelet transform (WT) is used to detect disturbances in the system and to locate the time of their occurrence. When such an event is flagged, the second stage is triggered and various artificial neural networks (ANNs) are applied to classify the data measured during the disturbance(s). A computational logic using WTs and ANNs together with a graphical user interface (GU) between the algorithm and its end user is then implemented. The results obtained so far are promising and suggest that this approach could lead to a useful application in an actual distribution system. (C) 2009 Elsevier Ltd. All rights reserved.

A classification methodology for the risk of weed infestation using fuzzy logic

Despite modern weed control practices, weeds continue to be a threat to agricultural production. Considering the variability of weeds, a classification methodology for the risk of infestation in agricultural zones using fuzzy logic is proposed. The inputs for the classification are attributes extracted from estimated maps for weed seed production and weed coverage using kriging and map analysis and from the percentage of surface infested by grass weeds, in order to account for the presence of weed species with a high rate of development and proliferation. The output for the classification predicts the risk of infestation of regions of the field for the next crop. The risk classification methodology described in this paper integrates analysis techniques which may help to reduce costs and improve weed control practices. Results for the risk classification of the infestation in a maize crop field are presented. To illustrate the effectiveness of the proposed system, the risk of infestation over the entire field is checked against the yield loss map estimated by kriging and also with the average yield loss estimated from a hyperbolic model.

Design and assembly of an experimental laboratory for the study of atmosphere-plant interactions in the system of fumigation chambers

An experimental laboratory was designed and assembled at the Botanical Institute of So Paulo, Brazil, in order to research atmosphere-plant interactions through the use of a system of fumigation chambers. A system of three ""closed"" fumigation chambers was designed to be used inside or outside the laboratory. The system was built to be used with a single pollutant or a mix of them. The innovation in this system is to allow chemical reactions inside the chambers that simulate atmospheric chemistry, especially photochemical processes involving high levels of ozone. Assessment of the performance and applicability of the system was based on the response of Nicotiana tabacum Bel W3 exposed to ozone produced alternatively by a generator and inside the chamber by reactions of its precursors. The results showed that the system can be well applied to the study of atmospheric chemistry interactions and the effects on plants.

Experimental results on the nonlinear H(infinity) control via quasi-LPV representation and game theory for wheeled mobile robots

In this paper, nonlinear dynamic equations of a wheeled mobile robot are described in the state-space form where the parameters are part of the state (angular velocities of the wheels). This representation, known as quasi-linear parameter varying, is useful for control designs based on nonlinear H(infinity) approaches. Two nonlinear H(infinity) controllers that guarantee induced L(2)-norm, between input (disturbances) and output signals, bounded by an attenuation level gamma, are used to control a wheeled mobile robot. These controllers are solved via linear matrix inequalities and algebraic Riccati equation. Experimental results are presented, with a comparative study among these robust control strategies and the standard computed torque, plus proportional-derivative, controller.