Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the major component of the transcription machinery. The development of single-molecule techniques, such as magnetic and optical tweezers, atomic-force microscopy and single-molecule fluorescence, increased our understanding of the transcription process and complements traditional biochemical studies. Based on these studies, theoretical models have been proposed to explain and predict the kinetics of the RNAP during the polymerization, highlighting the results achieved by models based on the thermodynamic stability of the transcription elongation complex. However, experiments showed that if more than one RNAP initiates from the same promoter, the transcription behavior slightly changes and new phenomenona are observed. We proposed and implemented a theoretical model that considers collisions between RNAPs and predicts their cooperative behavior during multi-round transcription generalizing the Bai et al. stochastic sequence-dependent model. In our approach, collisions between elongating enzymes modify their transcription rate values. We performed the simulations in Mathematica® and compared the results of the single and the multiple-molecule transcription with experimental results and other theoretical models. Our multi-round approach can recover several expected behaviors, showing that the transcription process for the studied sequences can be accelerated up to 48% when collisions are allowed: the dwell times on pause sites are reduced as well as the distance that the RNAPs backtracked from backtracking sites. © 2013 Costa et al.

Time-frequency analysis combining wavelets and the envelope technique for fault identification in rotary machines

Nowadays the method based on demodulation by envelope finds wide application in industry as a technique for evaluation of bearings and other components in rotating machinery. In recent years the application of Wavelets for fault diagnosis in machinery has also obtained good development. This article demonstrates the effectiveness of the combined application of Wavelets and envelope technique (also known as HFRT High-Frequency Resonance Technique) to remove background noise from signals collected from defect bearings and identification of the characteristic frequencies of defects. A comparison of the results obtained with the isolated application of only one method against the combined technique is performed showing the increased capacity in detection of faults in rolling bearings. © (2013) Trans Tech Publications, Switzerland.

Ergodic crossover in partially self-avoiding stochastic walks

Consider a one-dimensional environment with N randomly distributed sites. An agent explores this random medium moving deterministically with a spatial memory μ. A crossover from local to global exploration occurs in one dimension at a well-defined memory value μ1=log2N. In its stochastic version, the dynamics is ruled by the memory and by temperature T, which affects the hopping displacement. This dynamics also shows a crossover in one dimension, obtained computationally, between exploration schemes, characterized yet by the trajectory size (Np) (aging effect). In this paper we provide an analytical approach considering the modified stochastic version where the parameter T plays the role of a maximum hopping distance. This modification allows us to obtain a general analytical expression for the crossover, as a function of the parameters μ, T, and Np. Differently from what has been proposed by previous studies, we find that the crossover occurs in any dimension d. These results have been validated by numerical experiments and may be of great value for fixing optimal parameters in search algorithms. © 2013 American Physical Society.

Procedimento híbrido envolvendo os métodos primal-dual de pontos interiores e branch and bound em problemas multiobjetivo de aproveitamento de resíduos de cana-de-açúcar

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Improving face recognition with multispectral fusion and support vector machines

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Comparing support vector machines and artificial neural networks in the recognition of steering angle for driving of mobile robots through paths in plantations

The use of mobile robots turns out to be interesting in activities where the action of human specialist is difficult or dangerous. Mobile robots are often used for the exploration in areas of difficult access, such as rescue operations and space missions, to avoid human experts exposition to risky situations. Mobile robots are also used in agriculture for planting tasks as well as for keeping the application of pesticides within minimal amounts to mitigate environmental pollution. In this paper we present the development of a system to control the navigation of an autonomous mobile robot through tracks in plantations. Track images are used to control robot direction by pre-processing them to extract image features. Such features are then submitted to a support vector machine and an artificial neural network in order to find out the most appropriate route. A comparison of the two approaches was performed to ascertain the one presenting the best outcome. The overall goal of the project to which this work is connected is to develop a real time robot control system to be embedded into a hardware platform. In this paper we report the software implementation of a support vector machine and of an artificial neural network, which so far presented respectively around 93% and 90% accuracy in predicting the appropriate route. (C) 2013 The Authors. Published by Elsevier B.V. Selection and peer review under responsibility of the organizers of the 2013 International Conference on Computational Science

Modeling of state machines in VHDL for encapsulation of DNP3 Protocol in P2P ZigBee Network

Several countries have invested in technologies for Smart Grids. Among such protocols designed cover this area, highlights the DNP3 (Distributed Network Protocol version 3). Although the DNP3 be developed for operation over the serial interface, there is a trend in the literature to the use of other interfaces. The Zigbee wireless interface has become more popular in the industrial applications. In order to study the challenges of integrating of these two protocols, this article is presented the analysis of DNP3 protocol stack through state machines The encapsulation of DNP3 messages in P2P (point-to-point) ZigBee Network, may assist in the discovery and solution of failures of availability and security of this integration. The ultimate goal is to merge the features of DNP3 and Zigbee stacks, and display a solution that provides the benefits of wireless environment, without impairment of security required for Smart Grid applications.

Adding Motility Stimulants to Improve Freezing of Buffalo Sperm Recovered from Epididymal Cauda

The cryopreservation of epididymal sperm is important to preserve genetic material from valuable buffalo bulls. This study evaluated the viability of post-thawed sperm samples recovered from the epididymal cauda adding motility inductors. For that, were used epididymides from eight Murrah buffaloes with 18 months of age. Semen samples were submitted to three different conditions: (CT - control) without adding medium, (SPERM) adding Sperm Talp medium, and (FERT) adding Fert Talp medium. Immediately after slaughter, both testicles from each animal were collected and transported at 4 degrees C at maximum six hours interval. In laboratory, the removed epididymides was flushed to obtain sperm and diluted in the freezing extender. Each buffalo sperm were divided and fractions were submitted to all conditions (CT, SPERM and FERT). Semen doses were frozen at -196 degrees C. CT, SPERM and FERT post-thawing results were 13.63 +/- 8.91, 38.77 +/- 8.91 and 42.83 +/- 8.91 for total motility, 7.30 +/- 8.74, 24.87 +/- 8.74 and 29.70 +/- 8.74 for progressive motility, 6.04 +/- 0.92, 6.74 +/- 0.92 and 6.93 +/- 0.92 for percentage of rapid cells (P < 0.05). In conclusion, diluted semen supplementation with Sperm or Fert talp increases the motility of cauda epididymal sperm of buffalo bulls.

Patient Education and Self-Care for the Management of Jaw Pain upon Awakening: A Randomized Controlled Clinical Trial Comparing the Effectiveness of Adding Pharmacologic Treatment with Cyclobenzaprine or Tizanidine

Aims: To compare the effectiveness of adding cyclobenzaprine, tizanidine, or placebo to patient education and a self-care management program for patients with myofascial pain and specifically presenting with jaw pain upon awakening. Methods: Forty-five patients with a diagnosis of myofascial pain based on the guidelines of the American Academy of Orofacial Pain participated in this 3-week study. The subjects were randomly assigned into one of three groups: placebo group, TZA group (tizanidine 4 mg), or CYC group (cyclobenzaprine 10 mg). Patients were evaluated for changes in pain intensity, frequency, and duration by using the modified Severity Symptoms Index and changes in sleep quality with the use of the Pittsburgh Sleep Quality Index. Data were analyzed by ANOVA and post-hoc or nonparametric statistical tests as appropriate. Results: All three groups had a reduction in pain symptoms and improvement of sleep quality based on a comparison of pretreatment and treatment scores. However, no significant differences among the groups were observed at the posttreatment evaluation. Conclusion: The use of tizanidine or cyclobenzaprine in addition to self-care management and patient education was not more effective than placebo for the management of patients with myofascial jaw pain upon awakening.

Reformulation and a Lagrangian heuristic for lot sizing problem on parallel machines

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Markovian versus non-Markovian stochastic quantization of a complex-action model

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A Multi-Stage Stochastic Non-Linear Model for Reactive Power Planning Under Contingencies

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Improved Upper Limits on the Stochastic Gravitational-Wave Background from 2009-2010 LIGO and Virgo Data

Gravitational waves from a variety of sources are predicted to superpose to create a stochastic background. This background is expected to contain unique information from throughout the history of the Universe that is unavailable through standard electromagnetic observations, making its study of fundamental importance to understanding the evolution of the Universe. We carry out a search for the stochastic background with the latest data from the LIGO and Virgo detectors. Consistent with predictions from most stochastic gravitational-wave background models, the data display no evidence of a stochastic gravitational-wave signal. Assuming a gravitational-wave spectrum of Omega(GW)(f) = Omega(alpha)(f/f(ref))(alpha), we place 95% confidence level upper limits on the energy density of the background in each of four frequency bands spanning 41.5-1726 Hz. In the frequency band of 41.5-169.25 Hz for a spectral index of alpha = 0, we constrain the energy density of the stochastic background to be Omega(GW)(f) < 5.6 x 10(-6). For the 600-1000 Hz band, Omega(GW)(f) < 0.14(f/900 Hz)(3), a factor of 2.5 lower than the best previously reported upper limits. We find Omega(GW)(f) < 1.8 x 10(-4) using a spectral index of zero for 170-600 Hz and Omega(GW)(f) < 1.0(f/1300 Hz)(3) for 1000-1726 Hz, bands in which no previous direct limits have been placed. The limits in these four bands are the lowest direct measurements to date on the stochastic background. We discuss the implications of these results in light of the recent claim by the BICEP2 experiment of the possible evidence for inflationary gravitational waves.

Systemic risk in dynamical networks with stochastic failure criterion

Complex non-linear interactions between banks and assets we model by two time-dependent Erdos-Renyi network models where each node, representing a bank, can invest either to a single asset (model I) or multiple assets (model II). We use a dynamical network approach to evaluate the collective financial failure -systemic risk- quantified by the fraction of active nodes. The systemic risk can be calculated over any future time period, divided into sub-periods, where within each sub-period banks may contiguously fail due to links to either i) assets or ii) other banks, controlled by two parameters, probability of internal failure p and threshold T-h ("solvency" parameter). The systemic risk decreases with the average network degree faster when all assets are equally distributed across banks than if assets are randomly distributed. The more inactive banks each bank can sustain (smaller T-h), the smaller the systemic risk -for some Th values in I we report a discontinuity in systemic risk. When contiguous spreading becomes stochastic ii) controlled by probability p(2) -a condition for the bank to be solvent (active) is stochasticthe- systemic risk decreases with decreasing p(2). We analyse the asset allocation for the U.S. banks. Copyright (C) EPLA, 2014

Harmony Search applied for Support Vector Machines Training Optimization

Since the beginning, some pattern recognition techniques have faced the problem of high computational burden for dataset learning. Among the most widely used techniques, we may highlight Support Vector Machines (SVM), which have obtained very promising results for data classification. However, this classifier requires an expensive training phase, which is dominated by a parameter optimization that aims to make SVM less prone to errors over the training set. In this paper, we model the problem of finding such parameters as a metaheuristic-based optimization task, which is performed through Harmony Search (HS) and some of its variants. The experimental results have showen the robustness of HS-based approaches for such task in comparison against with an exhaustive (grid) search, and also a Particle Swarm Optimization-based implementation.