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.

Evaluation of children's behavior aged 0-3 years during dental care: A longitudinal analysis

Child temperament has been studied in various researches and may be useful to predict how a child responds to dental treatment, especially very young children. The purpose of the present longitudinal study was to evaluate the behavioral manifestation of children aged 0 to 3 years, considering different types of dental situation. A total of 169 children were selected and the following data were collected: the age of the child, gender, age of the mother, number of dental visits and their respective dates, stimuli offered to the child, and behavioral response to these stimuli. The children and their respective behaviors were divided into five groups according to the dental situation offered: control, missed visits, fluoride varnish, restoration, and dental trauma. The data were submitted to descriptive and inferential analysis using the chi-square test, with the level of significance set at 5%. Analysis of the different situation offered to infants during routine dental care revealed a predominance of collaborating and partially collaborating behavior, and age at the time of dental care influenced the behavior of the infants, irrespective of the stimulus group. The different types of dental situation provoked changes in the behavioral response of the children of certain age groups, especially in the dental trauma group.

Psicologia e odontopediatria: a contribuição da análise funcional do comportamento

Objetivando analisar funcionalmente a atuação do odontopediatra, procedeu-se ao atendimento odontológico de 3 crianças não-colaboradoras, utilizando ansiolítico ou placebo. As sessões foram filmadas e registrou-se os eventos clínicos e comportamentais dos participantes, em intervalos de 15 segundos. Os resultados revelaram que a colaboração das crianças pode ser considerada condição estabelecedora para os comportamentos da profissional. O ansiolítico não demonstrou efeitos sobre o comportamento dos pacientes. Direção, categoria comportamental predominantemente utilizada pela dentista, revelou-se eficaz na evocação de respostas de colaboração para 2 pacientes. Os dados expressam a contribuição da análise funcional do comportamento ao estudo da interação profissional-paciente em odontopediatria.

Behavioral evaluation during dental care in children ages 0 to 3 years

Purpose: Many studies concluded that the behavior of babies complicated dental care because of child immaturity or the difficulty of establishing acceptable communication and comprehension. Methods: The records of 696 babies were randomly selected from the baby clinic of Araçatuba in Brazil. Patient age ranged from 0 to 36 months. They were divided into 6 groups according to age: Group I-0 to 6 months; Group II-7 to 12 months; Group III-13 to 18 months; Group IV-19 to 24 months; Group V-25 to 30 months; Group VI-31 to 36 months. The behavior of the child was evaluated upon entrance in the dental office and during the first 4 clinical appointments with a clinical exam and oral physiotherapy. The baby was classified as collaborator (C) or noncollaborator (NC). Statistical analysis was performed using Pearson's chi-square method (P< .05). Results: The percentage of NC for Groups II, III, IV, and V (66%), was significantly higher than for groups I (30%) and VI (50%). Conclusions: Babies from 0 to 6 months showed a collaborative behavior; babies from 7 to 30 months showed noncollaborative behavior; and babies from 31 to 36 months showed no statistically significant difference between the percentage of C and NC.

Longitudinal behavioral analysis during dental care of children aged 0 to 3 years

Abstract: When and how the dentist intervenes have repercussions on children's physical and emotional patterns. The objective of the present study was to conduct a longitudinal behavioral analysis during dental care of babies aged 0 to 3 years. A total of 216 patients seen at the Baby Clinic of the School of Dentistry at Araçatuba, São Paulo State University (UNESP), were selected. The selection criterion was attendance at ten dental care sessions at bimonthly intervals for routine procedures such as clinical examination and oral hygiene. There was a predominance of cooperative behavior compared to uncooperative behavior when each visit was analyzed separately. The behavior of the patients must have been directly influenced by their psychomotor development. Constant attendance and exposure of the baby to non-stressful dental stimuli are factors that favor a cooperative behavior.

Particle competition and cooperation to prevent error propagation from mislabeled data in semi-supervised learning

Semi-supervised learning is applied to classification problems where only a small portion of the data items is labeled. In these cases, the reliability of the labels is a crucial factor, because mislabeled items may propagate wrong labels to a large portion or even the entire data set. This paper aims to address this problem by presenting a graph-based (network-based) semi-supervised learning method, specifically designed to handle data sets with mislabeled samples. The method uses teams of walking particles, with competitive and cooperative behavior, for label propagation in the network constructed from the input data set. The proposed model is nature-inspired and it incorporates some features to make it robust to a considerable amount of mislabeled data items. Computer simulations show the performance of the method in the presence of different percentage of mislabeled data, in networks of different sizes and average node degree. Importantly, these simulations reveals the existence of the critical points of the mislabeled subset size, below which the network is free of wrong label contamination, but above which the mislabeled samples start to propagate their labels to the rest of the network. Moreover, numerical comparisons have been made among the proposed method and other representative graph-based semi-supervised learning methods using both artificial and real-world data sets. Interestingly, the proposed method has increasing better performance than the others as the percentage of mislabeled samples is getting larger. © 2012 IEEE.

Modelo cinético estocástico para a transcrição considerando colisões entre as moléculas de RNA polimerase

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Combined active and semi-supervised learning using particle walking temporal dynamicscombined active and semi-supervised learning using particle walking temporal dynamics

Both Semi-Supervised Leaning and Active Learning are techniques used when unlabeled data is abundant, but the process of labeling them is expensive and/or time consuming. In this paper, those two machine learning techniques are combined into a single nature-inspired method. It features particles walking on a network built from the data set, using a unique random-greedy rule to select neighbors to visit. The particles, which have both competitive and cooperative behavior, are created on the network as the result of label queries. They may be created as the algorithm executes and only nodes affected by the new particles have to be updated. Therefore, it saves execution time compared to traditional active learning frameworks, in which the learning algorithm has to be executed several times. The data items to be queried are select based on information extracted from the nodes and particles temporal dynamics. Two different rules for queries are explored in this paper, one of them is based on querying by uncertainty approaches and the other is based on data and labeled nodes distribution. Each of them may perform better than the other according to some data sets peculiarities. Experimental results on some real-world data sets are provided, and the proposed method outperforms the semi-supervised learning method, from which it is derived, in all of them.

Redução do medo durante o tratamento odontológico utilizando pontas ultrassônicas

Over the last few years, new technologies have been developed to making cavity preparations, among which the diamond burs CVDentus® (CVDentus, São José dos Campos, Brazil) are outstanding. These points are produced by chemical deposition from the vapor phase, forming a single diamond stone, with greater durability than the conventional diamond burs. Coupled to the ultrasound appliance, they have several clinical applications in Dentistry with advantages over conventional rotary instruments, such as lower pressure, noise, vibration and heat, as well as reducing the need to use local anesthesia, contributing to minimize patient’s fear and anxiety. The aim of this study was to present the complete restorative dental treatment performed with this system in a child patient with a prior history of non-cooperative behavior. The use of this new technology offered the patient greater comfort, making it possible recondition the patient’s attitude to dental treatment, in addition to favoring conservative cavity preparations to be made.

Phase behavior of synthetic amphiphile vesicles investigated by calorimetry and fluorescence methods

The understanding of biological membranes may be improved by investigating physical properties of vesicles from natural or synthetic amphiphiles. The application of vesicles as mimetic agents depends on the knowledgment of their structure and properties. Vesicles having different curvature and size may be obtained using different preparation protocols. We have used differential scanning calorimetry (DSC) and steady-state fluorescence to investigate the gel to liquid-crystal phase transition of vesicles prepared by sonication (SUV) and non-sonication (GUV) of the synthetic dioctadecyldimethylammonium bromide (DODAB) in aqueous solution. DSC thermograms for a non-sonicated dispersion show a well-defined pre- and main transition corresponding to two narrow peaks at 36 and 45°C in the first upscan, while in a second upscan, only the main peak was observed. The sharpness of the peaks indicate a cooperative phase behavior for GUV. For a sonicated DODAB dispersion, the first upscan shows a third peak at 40.3°C, whereas for the second upscan the peaks are not well-defined, indicating a less cooperative phase behavior. Alternatively, the fluorescence quantum yield (Φ f) and the anisotropy (r) of trans, trans, trans-1-[4-(3-carboxypropyl)-phenyl]-6-[4-butylphenyl]-1,3,5-hexatriene (4H4A) and the ratio I 1/I 3 of the first to the third vibronic peaks of the pyrene emission spectrum as function of temperature are used as well to describe the phase behavior of DODAB sonicated and non-sonicated dispersions. It is in good agreement with the DSC results that the cooperativity of the thermotropic process is diminished under sonication of the DODAB dispersion, meaning that sonication changes from homogeneous to heterogeneous populations of the amphiphile aggregates. The pre- and main transitions obtained from these techniques are in fairly good accord with results from the literature.