Variabilidade da frequência cardíaca, funções cognitivas e nível de atividade física em pacientes com doença de Alzheimer

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Assessing the gain of biological data integration in gene networks inference

Background: A current challenge in gene annotation is to define the gene function in the context of the network of relationships instead of using single genes. The inference of gene networks (GNs) has emerged as an approach to better understand the biology of the system and to study how several components of this network interact with each other and keep their functions stable. However, in general there is no sufficient data to accurately recover the GNs from their expression levels leading to the curse of dimensionality, in which the number of variables is higher than samples. One way to mitigate this problem is to integrate biological data instead of using only the expression profiles in the inference process. Nowadays, the use of several biological information in inference methods had a significant increase in order to better recover the connections between genes and reduce the false positives. What makes this strategy so interesting is the possibility of confirming the known connections through the included biological data, and the possibility of discovering new relationships between genes when observed the expression data. Although several works in data integration have increased the performance of the network inference methods, the real contribution of adding each type of biological information in the obtained improvement is not clear. Methods: We propose a methodology to include biological information into an inference algorithm in order to assess its prediction gain by using biological information and expression profile together. We also evaluated and compared the gain of adding four types of biological information: (a) protein-protein interaction, (b) Rosetta stone fusion proteins, (c) KEGG and (d) KEGG+GO. Results and conclusions: This work presents a first comparison of the gain in the use of prior biological information in the inference of GNs by considering the eukaryote (P. falciparum) organism. Our results indicates that information based on direct interaction can produce a higher improvement in the gain than data about a less specific relationship as GO or KEGG. Also, as expected, the results show that the use of biological information is a very important approach for the improvement of the inference. We also compared the gain in the inference of the global network and only the hubs. The results indicates that the use of biological information can improve the identification of the most connected proteins.

Assessing the Validity of Brain Glucose Concentration Measurement Using Microdialysis

Brain functions, such as learning, orchestrating locomotion, memory recall, and processing information, all require glucose as a source of energy. During these functions, the glucose concentration decreases as the glucose is being consumed by brain cells. By measuring this drop in concentration, it is possible to determine which parts of the brain are used during specific functions and consequently, how much energy the brain requires to complete the function. One way to measure in vivo brain glucose levels is with a microdialysis probe. The drawback of this analytical procedure, as with many steadystate fluid flow systems, is that the probe fluid will not reach equilibrium with the brain fluid. Therefore, brain concentration is inferred by taking samples at multiple inlet glucose concentrations and finding a point of convergence. The goal of this thesis is to create a three-dimensional, time-dependent, finite element representation of the brainprobe system in COMSOL 4.2 that describes the diffusion and convection of glucose. Once validated with experimental results, this model can then be used to test parameters that experiments cannot access. When simulations were run using published values for physical constants (i.e. diffusivities, density and viscosity), the resulting glucose model concentrations were within the error of the experimental data. This verifies that the model is an accurate representation of the physical system. In addition to accurately describing the experimental brain-probe system, the model I created is able to show the validity of zero-net-flux for a given experiment. A useful discovery is that the slope of the zero-net-flux line is dependent on perfusate flow rate and diffusion coefficients, but it is independent of brain glucose concentrations. The model was simplified with the realization that the perfusate is at thermal equilibrium with the brain throughout the active region of the probe. This allowed for the assumption that all model parameters are temperature independent. The time to steady-state for the probe is approximately one minute. However, the signal degrades in the exit tubing due to Taylor dispersion, on the order of two minutes for two meters of tubing. Given an analytical instrument requiring a five μL aliquot, the smallest brain process measurable for this system is 13 minutes.

Developmental Changes in the Structure and Composition of the Postsynaptic Density

The development of the brain and its underlying circuitry is dependent on the formation of trillions of chemical synapses, which are highly specialized contacts that regulate the flow of information from one neuron to the next. It is through these synaptic connections that neurons wire together into networks capable of performing specific tasks, and activity-dependent changes in their structural and physiological state is one way that the brain is thought to adapt and store information. At the ultrastructural level, developmental and activity-dependent changes in the size and shape of dendritic spines have been well documented, and it is widely believed that structural changes in spines are a hallmark sign of synapse maturation and alteration of synaptic physiology. While changes in spine structure have been studied extensively, changes in one of its most prominent components, the postsynaptic density (PSD), have largely evaded observation. The PSD is a protein-rich organelle on the cytoplasmic side of the postsynaptic membrane, where it sits in direct opposition to the presynaptic terminal. The PSD functions both to cluster neurotransmitter receptors at the cell surface as well as organize the intracellular signaling molecules responsible for transducing extracellular signals to the postsynaptic cell. Much is known about the chemical composition of the PSD, but the structural arrangement of its molecular components is not well documented. Adding to the difficulty of understanding such a complex mass of protein machinery is the fact that its protein composition is known to change in response to synaptic activity, meaning that its structure is plastic and no two PSDs are identical. Here, immuno-gold labeling and electron tomography of PSDs isolated throughout development was used to track changes in both the structure and molecular composition of the PSD. State-of-the-art cryo-electron tomography was used to study the fine structure of the PSD during development, and provides an unprecedented glimpse into its molecular architecture in an un-fixed, unstained and hydrated state. Through this analysis, large structural and compositional changes are apparent and suggest a model by which the PSD is first assembled as a mesh-like lattice of proteins that function as support for the later recruitment of various PSD components. Spatial analysis of the recruitment of proteins into the PSD demonstrated that its assembly has an underlying order.

The Effects of a Physical Activity Intervention on the way Elementary School Girls Play

The rates of childhood and adolescent obesity in the United States have been increasing steadily. American youth continue to eat more (increase energy intake) and reduce physical activity (decrease energy expenditure) resulting in increased body weight and body fatness. One way to help reduce body weight in children is to increase physical activity. The purpose of this study was to determine if an age appropriate before-school physical activity intervention would be successful in increasing energy expenditure, intensity of activity, and behavioral approaches in overweight girls. The subjects were recruited from Parker Memorial School in Tolland, Connecticut, and two testing periods occurred over an eight week period. Video recordings of each physical activity session were analyzed to determine energy expenditure, exercise intensity, and behaviors during exercise. Data was evaluated for normal distribution, and paired t-tests were used to determine statistical significance. This study showed that the age appropriate before school physical activity intervention was able to increase energy expenditure and exercise intensity and have a positive effect on behavioral approaches in overweight girls.

Functional requirements of histone deacetylases in Tup1-Ssn6 repression

The corepressor complex Tup1-Ssn6 regulates many classes of genes in yeast including cell type specific, glucose repressible, and DNA damage inducible. Tup1 and Ssn6 are recruited to target promoters through their interactions with specific DNA binding proteins such as α2, Mig1, and Crt1. Most promoters that are repressed by this corepressor complex exhibit a high degree of nucleosomal organization. This chromatin domain occludes transcription factor access to the promoter element resulting in gene repression. Previous work indicated that Tup1 interacts with underacetylated isoforms of H3 and H4, and that mutation of these histones synergistically compromises repression. These studies predict that Tup1-hypoacetyalted histone interaction is important to the repression mechanism, and in vivo hyperacetylation might compromise the corepressors ability to repress target genes. ^ One way to alter histone acetylation levels in vivo is to alter the balance between histone acetyltransferases and histone deacetylases. To date five histone deacetylases (HDACs) have been identified in yeast Rpd3, Hos1, Hos2, Hos3 and Hda1. Deletion of single or double HDAC genes had little to no effect on Tup1-Ssn6 repression, but simultaneous deletion of three specific activities Rpd3, Hos1, and Hos2 abolished repression in vivo. Promoter regions of Tup1-Ssn6 target genes in these triple deacetylase mutant cells are dramatically hyperacetylated in both H3 and H4. Examination of bulk histone acetylation levels showed that this specific HDAC triple mutant combination (rpd3 hos1 hos2) caused a dramatic and concomitant hyperacetylation of both H3 and H4. The loss of repression in the rpd3 hos1 hos2 cells, but not in other mutants, is consistent with previous observations, which indicate that histones provide redundant functions in the repression mechanism and that high levels of acetylation are required to prevent Tup1 binding. Investigation into a potential direct interaction between the Tup1-Ssn6 corepressor complex and one or more HDAC activities showed that both Rpd3 and Hos2 interact with the corepressor complex in vivo. These findings indicate that Tup1-Ssn6 repression involves the recruitment of histone deacetylase activities to target promoters, where they locally deacetylate histone residues promoting Tup1-histone tail interaction to initiate and/or maintain the repressed state. ^

Cytochrome P450 4F isoforms in different species: Identification, gene regulation and putative roles in inflammation

The cytochrome P450 4F subfamily comprises a group of enzymes that metabolize derivatives of arachidonic acid such as prostaglandins, lipoxins leukotrienes and hydroxyeicosatetraenoic acids, which are important mediators involved in the inflammatory response. Therefore, we speculate that CYP4Fs might be able to modulate the extent of the inflammation by controlling of the tissue levels of these inflammatory mediators, especially, leukotriene B4. One way to provide support for this hypothesis is to test whether the expression of CYP4Fs changes under inflammatory conditions, since these changes are required to adjust the levels of inflammatory mediators. ^ A lipopolysacchride (LPS) induced rat inflammation model was used to analyze the expressions of rat CYP4F4 and CYP4F5 in liver and kidney. LPS administration did not change the constitutive expression level of CYP4F4 and CYP4F5. In liver, the expressions of CYP4F4 and CYP4F5 decreased to 50–60% of the untreated level. The same effect of LPS on CYP4F4 and CYP4F5 expression can be mimicked in hepatocyte primary cultures treated with LPS, indicating a direct of effect of LPS on hepatocytes. LPS treatment also decreased the activity of liver microsomes towards chlorpromazine, however, antibody inhibition study revealed that liver CYP4Fs are not the only players in metabolizing chlorpromazine. To study further the underlying mechanism, CYP4F5 gene was isolated, characterized, and the promoter region was defined. ^ Accumulating evidence showed that peroxisome proliferator-activated receptors (PPARs) play an active role in inflammation. To investigate the possible role of PPARα in regulating CYP4F expression by inflammation or by clofibrate treatment, the expressions of two new mouse 4F isoforms were analyzed in PPARα knockout mice upon LPS or clofibrate challenge. A novel induction of CYP4F15 by LPS and clofibrate was observed in kidney, and this effect is totally dependent on the presence of PPARα. Renal CYP4F16 expression was not affected by LPS or clofibrate in both (+/+) and (−/−) mice. In contrast, hepatic expressions of CYP4F15 and CYP4F16 were reduced significantly in (+/+) mice, but much less in (−/−) mice, suggesting that PPARα is partially responsible for this down-regulation. Clofibrate treatment reduced the expression of CYP4F16 in liver, but has no effect on CYP4F15 and PPARα does not have a role in hepatic CYP4F expression regulated by clofibrate. In general, CYP4Fs are regulated in an isoform-, tissue- and species-specific manner. ^ A human CYP4F isoform, CYP4F11, was isolated. The genomic structure was also solved by using database mining and bioinformatics tools. Localization of CYP4F11 to chromosome 19, 16 kb upstream of CYP4F2, suggests that human CYP4F genes may form a cluster on chromosome 19. This novel human 4F is highly expressed in liver, as well as in kidney, heart and skeletal muscle. Further study of the activity and gene regulation on CYP4F11 will provide us more insights into the physiological functions of CYP4F subfamily. ^

Identification and characterization of the vegetally localized Hermes mRNA

One way developing embryos regulate the expression of their genes is by localizing mRNAs to specific subcellular regions. In the oocyte of the frog, Xenopus laevis, many RNAs are localized specifically to the animal or the vegetal halves of the oocyte. The localization of these RNAs contributes to the primary polarity of the oocyte, the asymmetry that is the basis for patterning and lineage specification in the embryo. I have screened a cDNA library for clones containing the Xlsirt repeat, an element known to target RNAs to the vegetal cortex of the oocyte. I have identified seventeen cDNA clones that contain this element. One of these cDNAs encodes the RNA binding protein Hermes. The Hermes mRNA is localized to the vegetal cortex of the oocyte. Additionally, Hermes protein is also vegetally localized in the oocyte and is found in subcellular structures known to contain localized mRNAs. This suggests that Hermes might interact with localized RNAs. While Hermes protein is present in oocytes, it disappears at germinal vesicle breakdown during maturation. We therefore believe that the time period during which Hermes functions is during oogenesis or maturation prior to the time of Hermes degradation. To determine Hermes function, an antisense depletion strategy was used that involved injecting morpholino oligos (HE-MO) into oocytes. Injection of these morpholinos causes the level of Hennes protein to drop prematurely during maturation. Embryos produced from these oocytes exhibit cleavage defects that are most prevalent in the vegetal blastomeres. The phenotype can be partially rescued by injection of a heterologous Hermes mRNA and is therefore specific to Hermes. The Hermes expression and depletion results are consistent with a model in which Hermes interacts with one or more vegetally localized mRNAs in the oocyte and during the early stages of maturation. The interaction is required for cleavage of the vegetal blastomeres. Therefore, it is likely that at least one mRNA that interacts with Hermes is a cell cycle regulator. ^

3-dimensional binaural sound rendering using acoustic measurements stored in the SOFA format

Several groups all over the world are researching in several ways to render 3D sounds. One way to achieve this is to use Head Related Transfer Functions (HRTFs). These measurements contain the Frequency Response of the human head and torso for each angle. Some years ago, was only possible to measure these Frequency Responses only in the horizontal plane. Nowadays, several improvements have made possible to measure and use 3D data for this purpose. The problem was that the groups didn't have a standard format file to store the data. That was a problem when a third part wanted to use some different HRTFs for 3D audio rendering. Every of them have different ways to store the data. The Spatially Oriented Format for Acoustics or SOFA was created to provide a solution to this problem. It is a format definition to unify all the previous different ways of storing any kind of acoustics data. At the moment of this project they have defined some basis for the format and some recommendations to store HRTFs. It is actually under development, so several changes could come. The SOFA[1] file format uses a numeric container called netCDF[2], specifically the Enhaced data model described in netCDF 4 that is based on HDF5[3]. The SoundScape Renderer (SSR) is a tool for real-time spatial audio reproduction providing a variety of rendering algorithms. The SSR was developed at the Quality and Usability Lab at TU Berlin and is now further developed at the Institut für Nachrichtentechnik at Universität Rostock [4]. This project is intended to be an introduction to the use of SOFA files, providing a C++ API to manipulate them and adapt the binaural renderer of the SSR for working with the SOFA format. RESUMEN. El SSR (SoundScape Renderer) es un programa que está siendo desarrollado actualmente por la Universität Rostock, y previamente por la Technische Universität Berlin. El SSR es una herramienta diseñada para la reproducción y renderización de audio 2D en tiempo real. Para ello utiliza diversos algoritmos, algunos orientados a sistemas formados por arrays de altavoces en diferentes configuraciones y otros algoritmos diseñados para cascos. El principal objetivo de este proyecto es dotar al SSR de la capacidad de renderizar sonidos binaurales en 3D. Este proyecto está centrado en el binaural renderer del SSR. Este algoritmo se basa en el uso de HRTFs (Head Related Transfer Function). Las HRTFs representan la función de transferencia del sistema formado por la cabeza y el torso del oyente. Esta función es medida desde diferentes ángulos. Con estos datos el binaural renderer puede generar audio en tiempo real simulando la posición de diferentes fuentes. Para poder incluir una base de datos con HRTFs en 3D se ha hecho uso del nuevo formato SOFA (Spatially Oriented Format for Acoustics). Este nuevo formato se encuentra en una fase bastante temprana de su desarrollo. Está pensado para servir como formato estándar para almacenar HRTFs y cualquier otro tipo de medidas acústicas, ya que actualmente cada laboratorio cuenta con su propio formato de almacenamiento y esto hace bastante difícil usar varias bases de datos diferentes en un mismo proyecto. El formato SOFA hace uso del contenedor numérico netCDF, que a su vez esta basado en un contenedor más básico llamado HRTF-5. Para poder incluir el formato SOFA en el binaural renderer del SSR se ha desarrollado una API en C++ para poder crear y leer archivos SOFA con el fin de utilizar los datos contenidos en ellos dentro del SSR.

Modelos não lineares resultantes da soma de regressões lineares ponderadas por funções distribuição acumulada

Os controladores eletrônicos de pulverização visam minimizar a variação das taxas de insumos aplicadas no campo. Eles fazem parte de um sistema de controle, e permitem a compensação da variação de velocidade de deslocamento do pulverizador durante a operação. Há vários tipos de controladores eletrônicos de pulverização disponíveis no mercado e uma das formas de selecionar qual o mais eficiente nas mesmas condições, ou seja, em um mesmo sistema de controle, é quantificar o tempo de resposta do sistema para cada controlador específico. O objetivo desse trabalho foi estimar os tempos de resposta para mudanças de velocidade de um sistema eletrônico de pulverização via modelos de regressão não lineares, estes, resultantes da soma de regressões lineares ponderadas por funções distribuição acumulada. Os dados foram obtidos no Laboratório de Tecnologia de Aplicação, localizado no Departamento de Engenharia de Biossistemas da Escola Superior de Agricultura \"Luiz de Queiroz\", Universidade de São Paulo, no município de Piracicaba, São Paulo, Brasil. Os modelos utilizados foram o logístico e de Gompertz, que resultam de uma soma ponderada de duas regressões lineares constantes com peso dado pela função distribuição acumulada logística e Gumbell, respectivamente. Reparametrizações foram propostas para inclusão do tempo de resposta do sistema de controle nos modelos, com o objetivo de melhorar a interpretação e inferência estatística dos mesmos. Foi proposto também um modelo de regressão não linear difásico que resulta da soma ponderada de regressões lineares constantes com peso dado pela função distribuição acumulada Cauchy seno hiperbólico exponencial. Um estudo de simulação foi feito, utilizando a metodologia de Monte Carlo, para avaliar as estimativas de máxima verossimilhança dos parâmetros do modelo.

Estrutura da vegetação e sua relação com a diversidade, abundância e similaridade de coleópteros bioindicadores em diferentes sistemas vegetacionais, Piracicaba, SP

A Mata Atlântica é considerada um dos biomas mais importantes do mundo devido à sua alta biodiversidade e funções ecossistêmicas. Entretanto, encontra-se fragmentada em porções de pequenas dimensões esparsas em uma matriz predominantemente agrícola, composta principalmente por extensas pastagens e monoculturas. Desse modo, os sistemas agroflorestais por apresentarem uma estrutura diferenciada dos monocultivos e similar às condições naturais, podem ser utilizados como uma alternativa para o manejo e a conservação da biodiversidade nos remanescentes florestais. A fragmentação provoca modificações no ambiente que irão refletir na perda e no deslocamento da biodiversidade, estando os insetos entre os grupos mais afetados. Uma das formas de se avaliar o estado de conservação dos fragmentos e o impacto antrópico nos sistemas vegetacionais, é estudar a presença e distribuição de organismos bioindicadores. Dentre esses, os insetos ocupam posição de destaque. Os insetos da família Scarabaeidae e da subfamília Scolytinae são bons indicadores de distúrbios, pois são muito sensíveis ás mudanças ambientais. Neste trabalho hipotetisou-se que a presença desses insetos está relacionada com a estrutura da vegetação e as condições de vida proporcionadas pelas diferentes formas de uso-da-terra. O objetivo desta pesquisa foi avaliar a diversidade de espécies, o padrão de abundância e a similaridade entre as populações de coleópteros (Scarabaeidae e Scolytinae) em diferentes sistemas vegetacionais de diferentes estruturas: i) Fragmento de floresta estacional semidecidual dividido em três áreas: beira do rio, centro e borda; ii) Sistema Agroflorestal (SAF) (interface entre o fragmento e o pasto); iii) Pasto composto de Brachiaria decumbens (L.); iv) Monocultivo de café (Coffea arábica L.); v) Monocultivo de seringueira (Hevea brasiliensis Müell. Arg.); vi) SAF de café e seringueira - todos situados numa região de domínio anterior de floresta estacional semidecidual em Piracicaba-SP. Os sistemas foram caracterizados quanto à sua estrutura e condições micrometeorológicas. Os insetos foram coletados mensalmente entre agosto/2013 e julho/2014 utilizando-se dois tipos de armadilhas: Pitfall e etanol modelo ESALQ-84. Foram coletados 1.047 espécimes distribuídos em 21 espécies da família Scarabaeidae e 1.833 indivíduos de 38 espécies da subfamília Scolytinae. A maior quantidade de espécies de Scarabaeidae foi encontrada na borda do fragmento florestal, enquanto que a maior abundância ocorreu no fragmento florestal perto do rio. A subfamília Scolytinae apresentou a maior riqueza de espécies no sistema agroflorestal misto (borda) e a maior abundância no sistema agroflorestal café-seringueira. A abundância e riqueza de espécies da família Scarabaeidae foram correlacionadas positivamente com a temperatura do ar, temperatura e umidade do solo e a precipitação. Por outro lado, a abundância e a riqueza de espécies da subfamília Scolytinae apresentaram correlação negativa com a temperatura do ar e a temperatura e umidade do solo. Ambos os grupos de insetos apresentaram a maior abundância e riqueza de espécies nas áreas com estrutura vegetacional mais complexa, sendo influenciadas pelas condições microclimáticas dentro de cada local.

The ins and outs of E-cadherin trafficking

One way of controlling the activity of E-cadherin - a protein that is, simultaneously, a major cell-adhesion molecule, a powerful tumour suppressor, a determinant of cell polarity and a partner to the potent catenin signalling molecules - is to keep it on the move. During the past two decades, many insights into the fundamental role of E-cadherin in these processes have been garnered. Studies during the past five years have begun to reveal the importance of intracellular trafficking as a means of regulating the functions of E-cadherin. E-cadherin is trafficked to and from the cell surface by exocytic and multiple endocytic pathways. In this article, we survey the vesicle-trafficking machinery that is responsible for the sorting, transport, actin association and vesicle targeting of E-cadherin to regulate its movement and function during growth and development and, possibly, in cancer.

Objectives for multiple-species conservation planning

The first step in conservation planning is to identify objectives. Most stated objectives for conservation, such as to maximize biodiversity outcomes, are too vague to be useful within a decision-making framework. One way to clarify the issue is to define objectives in terms of the risk of extinction for multiple species. Although the assessment of extinction risk for single species is common, few researchers have formulated an objective function that combines the extinction risks of multiple species. We sought to translate the broad goal of maximizing the viability of species into explicit objectives for use in a decision-theoretic approach to conservation planning. We formulated several objective functions based on extinction risk across many species and illustrated the differences between these objectives with simple examples. Each objective function was the mathematical representation of an approach to conservation and emphasized different levels of threat Our objectives included minimizing the joint probability of one or more extinctions, minimizing the expected number of extinctions, and minimizing the increase in risk of extinction from the best-case scenario. With objective functions based on joint probabilities of extinction across species, any correlations in extinction probabilities bad to be known or the resultant decisions were potentially misleading. Additive objectives, such as the expected number of extinctions, did not produce the same anomalies. We demonstrated that the choice of objective function is central to the decision-making process because alternative objective functions can lead to a different ranking of management options. Therefore, decision makers need to think carefully in selecting and defining their conservation goals.

Statnote 10: the two-way analysis of variance

The two-way design has been variously described as a matched-sample F-test, a simple within-subjects ANOVA, a one-way within-groups ANOVA, a simple correlated-groups ANOVA, and a one-factor repeated measures design! This confusion of terminology is likely to lead to problems in correctly identifying this analysis within commercially available software. The essential feature of the design is that each treatment is allocated by randomization to one experimental unit within each group or block. The block may be a plot of land, a single occasion in which the experiment was performed, or a human subject. The ‘blocking’ is designed to remove an aspect of the error variation and increase the ‘power’ of the experiment. If there is no significant source of variation associated with the ‘blocking’ then there is a disadvantage to the two-way design because there is a reduction in the DF of the error term compared with a fully randomised design thus reducing the ‘power’ of the analysis.

Key Agreement Protocol (KAP) Based on Matrix Power Function

* Work is partially supported by the Lithuanian State Science and Studies Foundation.