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/.

Survival time of random walk in random environment among soft obstacles

We consider a Random Walk in Random Environment (RWRE) moving in an i.i.d. random field of obstacles. When the particle hits an obstacle, it disappears with a positive probability. We obtain quenched and annealed bounds on the tails of the survival time in the general d-dimensional case. We then consider a simplified one-dimensional model (where transition probabilities and obstacles are independent and the RWRE only moves to neighbour sites), and obtain finer results for the tail of the survival time. In addition, we study also the ""mixed"" probability measures (quenched with respect to the obstacles and annealed with respect to the transition probabilities and vice-versa) and give results for tails of the survival time with respect to these probability measures. Further, we apply the same methods to obtain bounds for the tails of hitting times of Branching Random Walks in Random Environment (BRWRE).

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.

Real-time PCR investigation on the expression of sboA and ituD genes in Bacillus spp

Aims: To investigate the expression of sboA and ituD genes among strains of Bacillus spp. at different pH and temperature. Methods and Results: Different Bacillus strains from the Amazon basin and Bacillus subtilis ATCC 19659 were investigated for the production of subtilosin A and iturin A by qRT-PCR, analysing sboA and ituD gene expression under different culture conditions. Amazonian strains presented a general gene expression level lower than B. subtilis ATCC 19659 for sboA. In contrast, when analysing the expression of ituD gene, the strains from the Amazon, particularly P40 and P45B, exhibited higher levels of expression. Changes in pH (6 and 8) and temperature (37 and 42 degrees C) caused a decrease in sboA expression, but increased ituD expression among strains from Amazonian environment. Conclusions: Temperature and pH have an important influence on the expression of genes sboA (subtilosin A) and ituD (iturin A) among Bacillus spp. The strains P40 and P45B can be useful for the production of antimicrobial peptide iturin A. Significance and Impact of the Study: Monitoring the expression of essential biosynthetic genes by qRT-PCR is a valuable tool for optimization of the production of antimicrobial peptides.

Multifractality in the random parameter model for multivariate time series

The Random Parameter model was proposed to explain the structure of the covariance matrix in problems where most, but not all, of the eigenvalues of the covariance matrix can be explained by Random Matrix Theory. In this article, we explore the scaling properties of the model, as observed in the multifractal structure of the simulated time series. We use the Wavelet Transform Modulus Maxima technique to obtain the multifractal spectrum dependence with the parameters of the model. The model shows a scaling structure compatible with the stylized facts for a reasonable choice of the parameter values. (C) 2009 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.

Time Constraints in the School Environment: What Does a Sleepy Student Tell Us?

In this article, we discuss school schedules and their implications in the context of chronobiological contemporary knowledge, arguing for the need to reconsider time planning in the school setting. We present anecdotal observations regarding chronobiological challenges imposed by the school system throughout different ages and discuss the effects of these schedules in terms of sleepiness and its deleterious consequences on learning, memory, and attention. Different settings (including urban vs. rural habitats) influence timing, which also depends on self-selected sleep schedules. Finally, we criticize the traditional view of a necessary strict stability of sleep-wake habits.

Control of interceptive actions is based on expectancy of time to target arrival

In this study the hypothesis that interceptive movements are controlled on the basis of expectancy of time to target arrival was tested. The study was conducted through assessment of temporal errors and kinematics of interceptive movements to a moving virtual target. Initial target velocity was kept unchanged in part of the trials, and in the others it was decreased 300 ms before the due time of target arrival at the interception position, increasing in 100 ms time to target arrival. Different probabilities of velocity decrease ranging from 25 to 100% were compared. The results revealed that while there were increasing errors between probabilities of 25 and 75% for unchanged target velocity, the opposite relationship was observed for target velocity decrease. Kinematic analysis indicated that movement timing adjustments to target velocity decrease were made online. These results support the conception that visuomotor integration in the interception of moving targets is mediated by an internal forward model whose weights can be flexibly adjusted according to expectancy of time to target arrival.

The influence of peripheral afferent signals on the rating of perceived exertion and time to exhaustion during exercise at different intensities

This study determined which peripheral variables would better predict the rating of perceived exertion (RPE) and time to exhaustion (TE) during exercise at different intensities. Ten men performed exercises at first lactate threshold (LT1), second lactate threshold (LT2), 50% of the distance from LT1 to LT2 (TT(50%)), and 25% of the distance from LT2 to maximal power output (TW(25%)). Lactate, catecholamines, potassium, pH, glucose, (V) over dotO(2), VE, HR, respiratory rate (RR) and RPE were measured and plotted against the exercise duration for the slope calculation. Glucose, dopamine, and noradrenaline predicted RPE in TT(50%) (88%), LT2 (64%), and TW(25%) (77%), but no variable predicted RPE in LT1. RPE (55%), RPE+HR (86%), and RPE+RR (92% and 55%) predicted TE in LT1, TT(50%), LT2, and TW(25%), respectively. At intensities from TT(50%) to TW(25%), variables associated with brain activity seem to explain most of the RPE slope, and RPE (+HR and+RR) seems to predict the TE.

Is acute static stretching able to reduce the time to exhaustion at power output corresponding to maximal oxygen uptake?

Samogin Lopes, FA, Menegon, EM, Franchini, E, Tricoli, V, and de M. Bertuzzi, RC. Is acute static stretching able to reduce the time to exhaustion at power output corresponding to maximal oxygen uptake? J Strength Cond Res 24(6): 1650-1656, 2010-This study analyzed the effect of an acute static stretching bout on the time to exhaustion (T(lim)) at power output corresponding to (V) over dotO(2)max. Eleven physically active male subjects (age 22.3 +/- 2.8 years, (V) over dotO(2)max 2.7 +/- 0.5 L . min(-1)) completed an incremental cycle ergometer test, 2 muscle strength tests, and 2 maximal tests to exhaustion at power output corresponding to (V) over dotO(2)max with and without a previous static stretching bout. The T(lim) was not significantly affected by the static stretching (164 +/- 28 vs. 150 +/- 26 seconds with and without stretching, respectively, p = 0.09), but the time to reach (V) over dotO(2)max (118 +/- 22 vs. 102 +/- 25 seconds), blood-lactate accumulation immediately after exercise (10.7 +/- 2.9 vs. 8.0 +/- 1.7 mmol . L(-1)), and oxygen deficit (2.4 +/- 0.9 vs. 2.1 +/- 0.7 L) were significantly reduced (p <= 0.02). Thus, an acute static stretching bout did not reduce T(lim) at power output corresponding to (V) over dotO(2)max possibly by accelerating aerobic metabolism activation at the beginning of exercise. These results suggest that coaches and practitioners involved with aerobic dependent activities may use static stretching as part of their warm-up routines without fear of diminishing high-intensity aerobic exercise performance.

Time course of strength and power recovery after resistance training with different movement velocities

Ide, BN, Leme, TCF, Lopes, CR, Moreira, A, Dechechi, CJ, Sarraipa, MF, da Mota, GR, Brenzikofer, R, and Macedo, DV. Time course of strength and power recovery after resistance training with different movement velocities. J Strength Cond Res 25(7): 2025-2033, 2011-The purpose of this study was to evaluate the time course of strength and power recovery after a single bout of strength training designed with fast and slow contraction velocities. Nineteen male subjects were randomly divided into 2 groups: the slow-velocity contraction (SV) group and the fast velocity contraction (FV) group. Resistance training protocols consisted of 5 sets of 12 repetition maximum (5 x 12RM) with 50 seconds of rest between sets and 2 minutes between exercises. Contraction velocity was controlled by the execution time for each repetition (SV-6 seconds to complete concentric and eccentric phases and for FV-1.5 seconds). Leg Press 45 degrees 1RM (LP 1RM), horizontal countermovement jump (HCMJ), and right thigh circumference (TC) were accessed in 6 distinct moments: base (1 week before exercise), 0 (immediately after exercises), 24, 48, 72, and 96 hours after exercise protocol. The SV and FV presented significant LP 1RM decrements at 0, and these were still evident 24-48 hours postexercise. The magnitude of decline was significantly (p<0.05) higher for FV. The SV and FV presented significant HCMJ decrements at 0, but only for FV were these still evident 24-72 hours postexercise. The SV and FV presented significant TC increments at 0, and these were still evident 24-48 hours postexercise for SV but for FV it continued up to 96 hours. The magnitude of increase was significantly (p<0.05) higher for FV. In conclusion, the fast contraction velocity protocol resulted in greater decreases in LP 1RM and HCMJ performance, when compared with slow velocity. The results lead us to interpret that this variable may exert direct influence on acute muscle strength and power generation capacity.

A review of time-motion analysis and combat development in mixed martial arts matches at regional level tournaments

Mixed martial arts (MMA) have become a fast-growing worldwide expansion of martial arts competition, requiring high level of skill, physical conditioning, and strategy, and involving a synthesis of combat while standing or on the ground. This study quantified the effort-pause ratio (EP), and classified effort segments of stand-up or groundwork development to identify the number of actions performed per round in MMA matches. 52 MMA athletes participated in the study (M age = 24 yr., SD = 5; average experience in MMA = 5 yr., SD = 3). A one-way analysis of variance with repeated measurements was conducted to compare the type of action across the rounds. A chi-squared test was applied across the percentages to compare proportions of different events. Only one significant difference (p < .05) was observed among rounds: time in groundwork of low intensity was longer in the second compared to the third round. When the interval between rounds was not considered, the EP ratio (between high-intensity effort to low-intensity effort plus pauses) WE S 1:2 to 1:4. This ratio is between ratios typical for judo, wrestling, karate, and taekwondo and reflects the combination of ground and standup techniques. Most of the matches ended in the third round, involving high-intensity actions, predominantly executed during groundwork combat.

Rapid weight loss followed by recovery time does not affect judo-related performance

In this study, we investigated the effects of rapid weight loss followed by a 4-h recovery on judo-related performance. Seven weight-cycler athletes were assigned to a weight loss group (5% body weight reduction by self-selected regime) and seven non-weight-cyclers to a control group (no weight reduction). Body composition, performance, glucose, and lactate were assessed before and after weight reduction (5-7 days apart; control group kept weight stable). The weight loss group had 4 h to re-feed and rehydrate after the weigh-in. Food intake was recorded during the weight loss period and recovery after the weigh-in. Performance was evaluated through a specific judo exercise, followed by a 5-min judo combat and by three bouts of the Wingate test. Both groups significantly improved performance after the weight loss period. No interaction effects were observed. The energy and macronutrient intake of the weight loss group were significantly lower than for the control group. The weight loss group consumed large amounts of food and carbohydrate during the 4-h recovery period. No changes were observed in lactate concentration, but a significant decrease in glucose during rest was observed in the weight loss group. In conclusion, rapid weight loss did not affect judo-related performance in experienced weight-cyclers when the athletes had 4 h to recover. These results should not be extrapolated to inexperienced weight-cyclers.

Influence of gelation time on the morphological and physico-chemical properties of the sol-gel entrapped lipase

Different gelation times (4, 18, 24 and 48 h) were used for the preparation of silica sol-gel supports and encapsulated Candida rugosa lipase using tetraethoxysilane (TEOS) as precursor. The hydrophobic matrices and immobilized lipases produced were characterized with regard to pore volume and size by nitrogen adsorption (BJH method), weight loss upon heating (TGA), differential scanning calorimetry (DSC), scanning electron microscopy (SEM), chemical composition (FTIR) and percentage of hydrolysis (POH%) of olive oil. These structural parameters were found to change with the gelation time, but no direct relation was found between the percentage of oil hydrolysis (POH%) and the gelation time. The best combination of high thermal stability and high POH% (99.5%) occurred for encapsulated lipase produced with 24 h gelation time. (C) 2007 Elsevier B.V. All rights reserved.

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.