Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays

Background: Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples. Results: We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2 of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log(2) units (6 of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators. Conclusions: This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells.

Elephants in pyjamas: testing the weak central coherence account of autism spectrum disorders using a syntactic disambiguation task

According to the weak central coherence (CC) account individuals with autism spectrum disorders (ASD) exhibit enhanced local processing and weak part-whole integration. CC was investigated in the verbal domain. Adolescents, recruited using a 2 (ASD status) by 2 (language impairment status) design, completed an aural forced choice comprehension task involving syntactically ambiguous sentences. Half the picture targets depicted the least plausible interpretation, resulting in longer RTs across groups. These were assumed to reflect local processing. There was no ASD by plausibility interaction and consequently little evidence for weak CC in the verbal domain when conceptualised as enhanced local processing. Furthermore, there was little evidence that the processing of syntactically ambiguous sentences differed as a function of ASD or language-impairment status.

Investigating subtypes of reward processing deficits as trait markers for depression

Background: Anhedonia, the loss of pleasure in usually enjoyable activities, is a central feature of major depressive disorder (MDD). The aim of the present study was to examine whether young people at a familial risk of depression display signs of anticipatory, motivational or consummatory anhedonia, which would indicate that these deficits may be trait markers for MDD. Methods: The study was completed by 22 participants with a family history of depression (FH+) and 21 controls (HC). Anticipatory anhedonia was assessed by asking participants to rate their anticipated liking of pleasant and unpleasant foods which they imagined tasting when cued with images of the foods. Motivational anhedonia was measured by requiring participants to perform key presses to obtain pleasant chocolate taste rewards or to avoid unpleasant apple tastes. Additionally, physical consummatory anhedonia was examined by instructing participants to rate the pleasantness of the acquired tastes. Moreover, social consummatory anhedonia was investigated by asking participants to make preference-based choices between neutral facial expressions, genuine smiles, and polite smiles. Results: It was found that the FH+ group’s anticipated liking of unpleasant foods was significantly lower than that of the control group. By contrast, no group differences in the pleasantness ratings of the actually experienced tastes or in the amount of performed key presses were observed. However, controls preferred genuine smiles over neutral expressions more often than they preferred polite smiles over neutral expressions, while this pattern was not seen in the FH+ group. Conclusion: These findings suggest that FH+ individuals demonstrate an altered anticipatory response to negative stimuli and show signs of social consummatory anhedonia, which may be trait markers for depression.

Thalamic paraventricular nucleus lesions facilitate central amygdala neuronal responses to acute psychological stress

The thalamic paraventricular nucleus (PVT) is activated by stress and projects to forebrain structures directly implicated in processing stress-related information. Accordingly, it seems likely the PVT plays an important role in modulating stress responses. We examined effects of excitotoxic PVT lesions on forebrain Fos expression patterns normally elicited by an acute psychological stressor. PVT lesions significantly increased stress-induced Fos in a key stress-processing region, the central amygdala.

Relationship between membrane fatty acids and cognitive symptoms and information processing in individuals at ultra-high risk for psychosis

Cognitive symptoms and impairment are central to schizophrenia and often an early sign of this condition. The present study investigated biological correlates of cognitive symptoms and performance in individuals at ultra-high risk (UHR) for psychosis. The study sample comprised 80 neuroleptic-naïve UHR individuals aged 13-25 years. Associations among erythrocyte membrane fatty acid levels, measured by gas chromatography, and cognitive functioning were investigated in UHR patients. Subjects were divided into terciles based on their scores on the cognitive factor of the Positive and Negative Syndrome Scale. The Zahlen-Verbindungs Test (ZVT) (the number-combination test) was also used as a measure of information-processing speed. Exploratory analysis was conducted to investigate the relationship between membrane fatty acid levels with the size of the intracranial area (ICA), a neurodevelopmental measure relevant to schizophrenia, in half of subjects (n=40) using magnetic resonance imaging. The adjusted analysis revealed that omega-9 eicosenoic and erucic acid levels were significantly higher, but omega-3 docosahexaenoic acid levels were significantly lower, in the cognitively impaired than in the cognitively intact group. We found a significant negative association of eicosenoic, erucic, and gamma-linoleic acids with ZVT scores. A negative association between ICA and membrane levels of eicosenoic acid was also found. This is the first study to demonstrate the relationship between membrane fatty acids and cognitive function in neuroleptic-naïve subjects at UHR for psychosis. The study findings indicate that abnormalities in membrane fatty acids may be associated with the neurodevelopmental disruption associated with the cognitive impairments of individuals at UHR for psychosis.

Blood pressure and cognitive function: the role of central aortic and brachial pressures

Central (aortic) blood pressures differ from brachial pressures and may be more relevant to the study of cognitive function, given that blood is delivered to the brain through the central large arteries. Pulse-pressure amplification reflects the augmentation of blood pressure between the central and peripheral arteries, which diminishes with aging. We aimed to determine the association between central blood pressure and cognitive function in independently living adults aged 20 to 82 years (N = 493). In adjusted regression models, higher central systolic pressure and higher central pulse pressure were each associated with poorer processing speed, Stroop processing, and recognition memory. Lower amplification was associated with poorer Stroop processing, working memory, and recognition memory. Higher brachial systolic pressure and brachial pulse pressure were both associated with poorer Stroop processing. In summary, central pressures and amplification were sensitive indicators of cognitive aging, predicting aspects of cognitive performance not predicted by brachial blood pressure.

Emotion processing fails to modulate putative mirror neuron response to trained visuomotor associations

Recent neuroimaging studies have demonstrated that activation of the putative human mirror neuron system (MNS) can be elicited via visuomotor training. This is generally interpreted as supporting an associative learning account of the mirror neuron system (MNS) that argues against the ontogeny of the MNS to be an evolutionary adaptation for social cognition. The current study assessed whether a central component of social cognition, emotion processing, would influence the MNS activity to trained visuomotor associations, which could support a broader role of the MNS in social cognition. Using functional magnetic resonance imaging (fMRI), we assessed repetition suppression to the presentation of stimulus pairs involving a simple hand action and a geometric shape that was either congruent or incongruent with earlier association training. Each pair was preceded by an image of positive, negative, or neutral emotionality. In support of an associative learning account of the MNS, repetition suppression was greater for trained pairs compared with untrained pairs in several regions, primarily supplementary motor area (SMA) and right inferior frontal gyrus (rIFG). This response, however, was not modulated by the valence of the emotional images. These findings argue against a fundamental role of emotion processing in the mirror neuron response, and are inconsistent with theoretical accounts linking mirror neurons to social cognition.

Potential and costs for the production of electrolytic hydrogen in alcohol and sugar cane plants in the central and south regions of Brazil

This project verified the potential for the production of hydrogen via water electrolysis by using the exceeding electrical energy resultant from alcohol and sugar plants that use sugar cane bagasse as fuel. The studies were carried out in cogeneration plants authorized by the Electrical Energy National Agency (ANEEL). The processing history of sugar cane considered was based on the 2006/2007 harvests. The total bagasse produced, electrical energy generated and exceeding electrical energy in a year were calculated. It was obtained an average energy consumption value of 5.2 kWh Nm(-3) and the hydrogen production costs regarding the amount of sugar cane processed that ranged from US$ 0.50 to US$ 0.75 Nm(-3). The results pointed that the costs for the production of hydrogen via the bagasse exceeding energy are close to the production costs that use other sources of energy. As the energy generated from the bagasse is a renewable one, this alternative for the production of hydrogen is economical and environmentally viable. (C) 2008 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.

Condicionamento estrutural das zonasa de cisalhamento da região de Forquilha, domínio Ceará Central: uma abordagem integrada de sensoriamento remoto e geologia estrutural

The studied region, named Forquilha and localized in northwestern Central Ceará domain (northern portion of Borborema Province), presents a lithostratigraphic framework constituted by paleoproterozoic metaplutonics, metasedimentary sequences and neoproterozoic granitoids. The metasedimentary rocks of Ceará group occupy most part of the area. This group is subdivided in two distinct units: Canindé and Independência. Canindé unit is represented basically by biotite paragneisses and muscovite paragneisses, with minor metabasic rocks (amphibolite lens). Independência sequence is composed by garnetiferous paragneisses, sillimanite-garnet-quartz-muscovite schists and quartz-muscovite schists, pure or muscovite quartzites and rare marbles. At least three ductile deformation events were recognized in both units of Ceará group, named D1, D2 and D3. The former one is interpreted as related to a low angle tangential tectonics which mass transport is southward. D2 event is marked by the development of close/isoclinal folds with a N-S oriented axis. Refolding patterns generated by F1 and F2 superposition are found in several places. The latest event (D3) corresponds to a transcurrent tectonics, which led to development of mega-folds and several shear zones, under a transpressional regime. The mapped shear zones are Humberto Monte (ZCHM), Poço Cercado (ZCPC) and Forquilha (ZCF). Digital image processing of enhanced Landsat 7-ETM+ satellite images, combined with field data, demonstrate that these penetrative structures are associated with positive and negative geomorphologic patterns, distributed in linear and curvilinear arrangements with tonal banding, corresponding to the ductile fabric and to crests. Diverse color composites were tested and RGB-531 and RGB-752 provided the best results for lineament analysis of the most prominent shear zones. Spatial filtering techniques (3x3 and 5x5 filters) were also used and the application of Prewitt filters generated the best products. The integrated analysis of morphological and textural aspects from filtered images, variation of tonalities related to the distribution of geologic units in color composites and the superposition over a digital elevation model, contributed to a characterization of the structural framework of the study area. Kinematic compatibility of ZCHM, ZCPC, ZCF shear zones, as well as Sobral-Pedro II (ZCSPII) shear zone, situated to the west of the study area, was one of the goal of this work. Two of these shear zones (ZCHM, ZCPC) display sinistral movements, while the others (ZCSPII, ZCF) exhibit dextral kinematics. 40Ar/39Ar ages obtained in this thesis for ZCSPII and ZCPC, associated with other 40Ar/39Ar data of adjacent areas, indicate that all these shear zones are related to Brasiliano orogeny. The trend of the structures, the opposite shear senses and the similar metamorphic conditions are fitted in a model based on the development of conjugate shear zones in an unconfined transpression area. A WNW-ESE bulk shortening direction is infered. The geometry and kinematic of the studied structures suggest that shortening was largely accommodated by lateral extrusion, with only minor amounts of vertical stretch

The central repeat domain 1 of Kaposi's sarcoma-associated herpesvirus (KSHV) latency associated-nuclear antigen 1 (LANA1) prevents cis MHC class I peptide presentation

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Comportamento sexual de touros Zebuínos e Angus em central de coleta e processamento de sêmen

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Angiotensin II-derived reactive oxygen species underpinning the processing of the cardiovascular reflexes in the medulla oblongata

The brainstem is a major site in the central nervous system involved in the processing of the cardiovascular reflexes such as the baroreflex and the peripheral chemoreflex. The nucleus tractus solitarius and the rostral ventrolateral medulla are 2 important brainstem nuclei, and they play pivotal roles in autonomic cardiovascular regulation. Angiotensin II is one of the neurotransmitters involved in the processing of the cardiovascular reflexes within the brainstem. It is well-known that one of the mechanisms by which angiotensin II exerts its effect is via the activation of pathways that generate reactive oxygen species (ROS). In the central nervous system, ROS are reported to be involved in several pathological diseases such as hypertension, heart failure and sleep apnea. However, little is known about the role of ROS in the processing of the cardiovascular reflexes within the brainstem. The present review mainly discussed some recent findings documenting a role for ROS in the processing of the baroreflex and the peripheral chemoreflex in the brainstem.

Optimisation of High Hydrostatic Pressure Processing of Pêra Rio Orange Juice

The influence of high hydrostatic pressure (HHP) on Pêra Rio orange juice was investigated using response surface methodology. A central composite design was used to evaluate the effects of three processing conditions (independent variables), namely pressure (100-600 MPa), temperature (30-60 °C) and time (30-360 s), on the native microflora and pectin methylesterase (PME) activity of orange juice. Analysis of variance showed that second-order polynomial models fitted well with the experimental data for PME residual activity (R2 = 0.9586, p < 0.001) and aerobic microorganism count (R2 = 0.9879, p < 0.001). The optimum HHP processing conditions to produce orange juice with PME residual activity of less than 20 % and low microorganism count (<2 log cycles CFU/mL) were 550 to 600 MPa, 55 to 60 °C and 330 to 360 s. © 2013 Springer Science+Business Media New York.

Proposed procedure for the collection and processing of regional ports and shipping statistics

Presenta una breve descripción de la situación actual en materia de recopilación de estadísticas de puertos y embarques en el Caribe sobre una base regional. Propone una metodología para la recopilación de datos a nivel nacional y la creación de una oficina central para el procesamiento de datos a nivel regional.

Effects of processing on physical properties of extruded snacks with blends of sour cassava starch and flaxseed flour

The opportunity to supplement common cassava biscuits with a product of higher nutritional value meets consumer expectations. In this work it was studied the effects of process parameters and flaxseed addition on physical properties of expanded snacks. Extrusion process was carried out using a single screw extruder in a factorial central composite rotatable design with four factors: flaxseed flour percentage (0-20%), moisture (12-20%), extrusion temperature (90-130 °C) and screw speed (190-270). The effect of extrusion variables was investigated in terms of expansion index, specific volume, water absorption index, water solubility index, color parameters (L*, a* ,b*) and hardness. The data analysis showed that variable parameters of the extrusion process and flaxseed flour affected physical properties of puffed snacks. Among the experimental conditions used in the present study, expanded snack products with good physical properties can be obtained under the conditions of 10% flaxseed flour, 230 rpm screw speed, temperature of 90 °C and moisture of 12%.