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.

Pedagogical model and school failure

Includes bibliography

A new proposed rodent model of chemically induced prostate carcinogenesis: Distinct time-course prostate cancer progression in the dorsolateral and ventral lobes

Background. Characterization of novel rodent models for prostate cancer studies requires evaluation of either spontaneous and carcinogen-induced tumors as well as tumor incidence in different prostatic lobes. We propose a new short-term rodent model of chemically induced prostate carcinogenesis in which prostate cancer progression occurs differentially in the dorsolateral and ventral lobes. Methods. Adult gerbils were treated with MNU alone or associated with testosterone for 3 or 6 months of treatment. Tumor incidence, latency, localization, and immunohistochemistry (AR, PCNA, smooth muscle α-actin, p63, MGMT, and E-cadherin) were studied in both lobes. Results. Comparisons between both lobes revealed that lesions developed first in the DL while the VL presented longer tumor latency. However, after 6 months, there was a dramatic increase in tumor multiplicity in the VL, mainly in MNU-treated groups. Lesions clearly progressed from a premalignant to a malignant phenotype over time and tumor latency was decreased by MNU + testosterone administration. Three-dimensional reconstruction of the prostatic complex showed that the DL developed tumors exclusively in the periurethral area and showed intense AR, PCNA, and MGMT immunostaining. Moreover, VL lesions emerged throughout the entire lobe. MNU-induced lesions presented markers indicative of an aggressive phenotype: lack of basal cells, rupture of the smooth muscle cell layer, loss of E-cadherin, and high MGMT staining. Conclusions. There are distinct pathways involved in tumor progression in gerbil prostate lobes. This animal provides a good model for prostate cancer since it allows the investigation of advanced steps of carcinogenesis with shorter latency periods in both lobes. Copyright © 2013 Wiley Periodicals, Inc.

Morphologic and biomechanical changes of thoracic and abdominal aorta in a rat model of cigarette smoke exposure

Background: Smoking is the most relevant environmental factor that affects the development of aortic aneurysm. Smokers have elevated levels of elastase activity in the arterial wall, which leads to weakening of the aorta. The aim of this study was to verify whether cigarette smoke exposure itself is capable of altering the aortic wall. Methods: Forty-eight Wistar rats were divided into 2-, 4-, and 6-month experimental periods and into 2 groups: smokers (submitted to smoke exposure at a rate of 40 cigarettes/day) and nonsmokers. At the end of the experimental periods, the aortas were removed and cross-sectioned to obtain histologic specimens for light microscopic and morphometric analyses. The remaining longitudinal segments were stretched to rupture and mechanical parameters were determined. Results: A degenerative process (i.e., a reduction in elastic fibers, the loss of lamellar arrangement, and a reduction of smooth muscle cells) was observed, and this effect was proportional in intensity to the period of tobacco exposure. We observed a progressive reduction in the yield point of the thoracic aorta over time (P < 0.05). There was a decrease in stiffness (P < 0.05) and in failure load (P < 0.05) at 6 months in the abdominal aorta of rats in the smoking group. Conclusions: Chronic exposure to tobacco smoke can affect the mechanical properties of the aorta and can also provoke substantial structural changes of the arterial wall. © 2013 Elsevier Inc. All rights reserved.

A time series sequestration and storage model of atmospheric carbon dioxide

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

The influence of floc size and hydraulic detention time on the performance of a dissolved air flotation (DAF) pilot unit in the light of a mathematical model

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

Nonlinear formulation based on FEM, Mazars damage criterion and Fick's law applied to failure assessment of reinforced concrete structures subjected to chloride ingress and reinforcements corrosion

Structural durability is an important design criterion, which must be assessed for every type of structure. In this regard, especial attention must be addressed to the durability of reinforced concrete (RC) structures. When RC structures are located in aggressive environments, its durability is strongly reduced by physical/chemical/mechanical processes that trigger the corrosion of reinforcements. Among these processes, the diffusion of chlorides is recognized as one of major responsible of corrosion phenomenon start. To accurate modelling the corrosion of reinforcements and to assess the durability of RC structures, a mechanical model that accounts realistically for both concrete and steel mechanical behaviour must be considered. In this context, this study presents a numerical nonlinear formulation based on the finite element method applied to structural analysis of RC structures subjected to chloride penetration and reinforcements corrosion. The physical nonlinearity of concrete is described by Mazars damage model whereas for reinforcements elastoplastic criteria are adopted. The steel loss along time due to corrosion is modelled using an empirical approach presented in literature and the chloride concentration growth along structural cover is represented by Fick's law. The proposed model is applied to analysis of bended structures. The results obtained by the proposed numerical approach are compared to responses available in literature in order to illustrate the evolution of structural resistant load after corrosion start. (C) 2014 Elsevier Ltd. All rights reserved.

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

CHARACTERIZATION OF THE BRAZPD II COHORT AND DESCRIPTION OF TRENDS IN PERITONEAL DIALYSIS OUTCOME ACROSS TIME PERIODS

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Peritoneal dialysis in acute kidney injury: trends in the outcome across time periods

Peritoneal dialysis (PD) should be considered a suitable method of renal replacement therapy in acute kidney injury (AKI) patients. This study is the largest cohort providing patient characteristics, clinical practice, patterns and their relationship to outcomes in a developing country. Its objective was to describe the main determinants of patient and technique survival, including trends over time of PD treatment in AKI patients. This was a Brazilian prospective cohort study in which all adult AKI patients on PD were studied from January/2004 to January/2014. For comparison purposes, patients were divided into 2 groups according to the year of treatment: 2004-2008 and 2009-2014. Patient survival and technique failure (TF) were analyzed using the competing risk model of Fine and Gray. A total of 301 patients were included, 51 were transferred to hemodialysis (16.9%) during the study period. The main cause of TF was mechanical complication (47%) followed by peritonitis (41.2%). There was change in TF during the study period: compared to 2004-2008, patients treated at 2009-2014 had relative risk (RR) reduction of 0.86 (95% CI 0.77-0.96) and three independent risk factors were identified: period of treatment at 2009 and 2014, sepsis and age>65 years. There were 180 deaths (59.8%) during the study. Death was the leading cause of dropout (77.9% of all cases) mainly by sepsis (58.3%), followed cardiovascular disease (36.1%). The overall patient survival was 41% at 30 days. Patient survival improved along study periods: compared to 2004-2008, patients treated at 2009-2014 had a RR reduction of 0.87 (95% CI 0.79-0.98). The independent risk factors for mortality were sepsis, age>70 years, ATN-ISS > 0.65 and positive fluid balance. As conclusion, we observed an improvement in patient survival and TF along the years even after correction for several confounders and using a competing risk approach.

Effect of low-level laser therapy in an experimental model of osteoarthritis in rats evaluated through raman spectroscopy

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

Polymerization kinetics and polymerization stress in resin composites after accelerated aging as a function of the expiration date

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Tragedy on grade crossing: driver failure or systemic fragility?

In 2010, an accident occurred in Americana-SP, Brazil, involving two trains and one bus on a Grade Crossing, when 10 people died and 17 were injured including workers. This paper aims to analyze the accident using the Model of Analysis and Prevention of Work Accidents (MAPA). The method provides observation of work, interviews and analysis of documents to understand precedents of the event in the following stages: to understand the usual work from the involved people, the changes occurred in the system, the operation of barriers, managerial and organizational aspects. By the end, measures are suggested to avoid new occurrences. The accident took place at night in a site with insufficient lighting. The working conditions of bus drivers, train operators and watchmen are inadequate. There were only symbolic barriers (visual and acoustic signals) triggered manually by watchman upon train operator radio communication. The fragility of the barrier system associated to poor lighting and short time to trigger the signaling seem to play a critical role in the event. Contrary to the official report which resulted in guilt of the bus driver, the conclusion of the paper emphasizes the fragility of the safety system and the need of level crossing reproject.

Linear matrix inequality-based robust model predictive control for time-delayed systems

This work addresses the solution to the problem of robust model predictive control (MPC) of systems with model uncertainty. The case of zone control of multi-variable stable systems with multiple time delays is considered. The usual approach of dealing with this kind of problem is through the inclusion of non-linear cost constraint in the control problem. The control action is then obtained at each sampling time as the solution to a non-linear programming (NLP) problem that for high-order systems can be computationally expensive. Here, the robust MPC problem is formulated as a linear matrix inequality problem that can be solved in real time with a fraction of the computer effort. The proposed approach is compared with the conventional robust MPC and tested through the simulation of a reactor system of the process industry.

Glutamate-induced obesity leads to decreased sperm reserves and acceleration of transit time in the epididymis of adult male rats

Background: Given the established fact that obesity interferes with male reproductive functions, the present study aimed to evaluate sperm production in the testis and storage in the epididymis in a glutamate-induced model of obesity. Methods: Male rats were treated neonatally with monosodium glutamate (MSG) at doses of 4 mg/kg subcutaneously, or with saline solution (control group), on postnatal days 2, 4, 6, 8 and 10. On day 120, obesity was confirmed by the Lee index in all MSG-treated rats. After this, all animals from the two experimental groups were anesthetized and killed to evaluate body and reproductive organ weights, sperm parameters, plasma hormone levels (FSH, LH and testosterone), testicular and epididymal histo-morphometry and histopathology. Results: Significant reductions in absolute and relative weights of testis, epididymis, prostate and seminal vesicle were noted in MSG-treated animals. In these same animals plasma testosterone and follicle-stimulating hormone (FSH) concentrations were decreased, as well as sperm counts in the testis and epididymis and seminiferous epithelium height and tubular diameter. The sperm transit time was accelerated in obese rats. However, the number of Sertoli cells per seminiferous tubule and stereological findings on the epididymis were not markedly changed by obesity. Conclusions: Neonatal MSG-administered model of obesity lowers sperm production and leads to a reduction in sperm storage in the epididymis of adult male rats. The acceleration of sperm transit time can have implications for the sperm quality of these rats.