A distributed, cloud-ready, digital content processing and transformation platform and a specific use case

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Big Data Processing in the Cloud: a Hydra/Sufia Experience

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Ionic liquid mediated biomass deconstruction: from analysis challenges to fermentable sugars

Ionic liquids, ILs, have recently been studied with accelerating interest to be used for a deconstruction/fractionation, dissolution or pretreatment processing method of lignocellulosic biomass. ILs are usually utilized combined with heat. Regarding lignocellulosic recalcitrance toward fractionation and IL utilization, most of the studies concern IL utilization in the biomass fermentation process prior to the enzymatic hydrolysis step. It has been demonstrated that IL-pretreatment gives more efficient hydrolysis of the biomass polysaccharides than enzymatic hydrolysis alone. Both cellulose (especially cellulose) and lignin are very resistant towards fractionation and even dissolution methods. As an example, it can be mentioned that softwood, hardwood and grass-type plant species have different types of lignin structures leading to the fact that softwood lignin (guaiacyl lignin dominates) is the most difficult to solubilize or chemically disrupt. In addition to the known conventional biomass processing methods, several ILs have also been found to efficiently dissolve either cellulose and/or wood samples – different ILs are suitable for different purposes. An IL treatment of wood usually results in non-fibrous pulp, where lignin is not efficiently separated and wood components are selectively precipitated, as cellulose is not soluble or degradable in ionic liquids under mild conditions. Nevertheless, new ILs capable of rather good fractionation performance have recently emerged. The capability of the IL to dissolve or deconstruct wood or cellulose depends on several factors, (e.g. sample origin, the particle size of the biomass, mechanical treatments as pulverization, initial biomassto-IL ratio, water content of the biomass, possible impurities of IL, reaction conditions, temperature etc). The aim of this study was to obtain (fermentable) saccharides and other valuable chemicals from wood by a combined heat and IL-treatment. Thermal treatments alone contribute to the degradation of polysaccharides (e.g. 150 °C alone is said to cause the degradation of polysaccharides), thus temperatures below that should be used, if the research interest lies on the IL effectiveness. On the other hand, the efficiency of the IL-treatment can also be enhanced to combine other treatment methods, (e.g. microwave heating). The samples of spruce, pine and birch sawdust were treated with either 1-Ethyl-3-methylimidazolium chloride, Emim Cl, or 1-Ethyl-3-methylimidazolium acetate, Emim Ac, (or with ionized water for comparison) at various temperatures (where focus was between 80 and 120 °C). The samples were withdrawn at fixed time intervals (the main interest treatment time area lied between 0 and 100 hours). Double experiments were executed. The selected mono- and disaccharides, as well as their known degradation products, 5-hydroxymethylfurfural, 5-HMF, and furfural were analyzed with capillary electrophoresis, CE, and high-performance liquid chromatography, HPLC. Initially, even GC and GC-MS were utilized. Galactose, glucose, mannose and xylose were the main monosaccharides that were present in the wood samples exposed to ILs at elevated temperatures; in addition, furfural and 5-HMF were detected; moreover, the quantitative amount of the two latter ones were naturally increasing in line with the heating time or the IL:wood ratio.

Autonomic processing of the cardiovascular reflexes in the nucleus tractus solitarii

The nucleus tractus solitarii (NTS) receives afferent projections from the arterial baroreceptors, carotid chemoreceptors and cardiopulmonary receptors and as a function of this information produces autonomic adjustments in order to maintain arterial blood pressure within a narrow range of variation. The activation of each of these cardiovascular afferents produces a specific autonomic response by the excitation of neuronal projections from the NTS to the ventrolateral areas of the medulla (nucleus ambiguus, caudal and rostral ventrolateral medulla). The neurotransmitters at the NTS level as well as the excitatory amino acid (EAA) receptors involved in the processing of the autonomic responses in the NTS, although extensively studied, remain to be completely elucidated. In the present review we discuss the role of the EAA L-glutamate and its different receptor subtypes in the processing of the cardiovascular reflexes in the NTS. The data presented in this review related to the neurotransmission in the NTS are based on experimental evidence obtained in our laboratory in unanesthetized rats. The two major conclusions of the present review are that a) the excitation of the cardiovagal component by cardiovascular reflex activation (chemo- and Bezold-Jarisch reflexes) or by L-glutamate microinjection into the NTS is mediated by N-methyl-D-aspartate (NMDA) receptors, and b) the sympatho-excitatory component of the chemoreflex and the pressor response to L-glutamate microinjected into the NTS are not affected by an NMDA receptor antagonist, suggesting that the sympatho-excitatory component of these responses is mediated by non-NMDA receptors.

Algorithmic Techniques in Gene Expression Processing. From Imputation to Visualization

The amount of biological data has grown exponentially in recent decades. Modern biotechnologies, such as microarrays and next-generation sequencing, are capable to produce massive amounts of biomedical data in a single experiment. As the amount of the data is rapidly growing there is an urgent need for reliable computational methods for analyzing and visualizing it. This thesis addresses this need by studying how to efficiently and reliably analyze and visualize high-dimensional data, especially that obtained from gene expression microarray experiments. First, we will study the ways to improve the quality of microarray data by replacing (imputing) the missing data entries with the estimated values for these entries. Missing value imputation is a method which is commonly used to make the original incomplete data complete, thus making it easier to be analyzed with statistical and computational methods. Our novel approach was to use curated external biological information as a guide for the missing value imputation. Secondly, we studied the effect of missing value imputation on the downstream data analysis methods like clustering. We compared multiple recent imputation algorithms against 8 publicly available microarray data sets. It was observed that the missing value imputation indeed is a rational way to improve the quality of biological data. The research revealed differences between the clustering results obtained with different imputation methods. On most data sets, the simple and fast k-NN imputation was good enough, but there were also needs for more advanced imputation methods, such as Bayesian Principal Component Algorithm (BPCA). Finally, we studied the visualization of biological network data. Biological interaction networks are examples of the outcome of multiple biological experiments such as using the gene microarray techniques. Such networks are typically very large and highly connected, thus there is a need for fast algorithms for producing visually pleasant layouts. A computationally efficient way to produce layouts of large biological interaction networks was developed. The algorithm uses multilevel optimization within the regular force directed graph layout algorithm.

Diagnosing dementia and normal aging: clinical relevance of brain ratios and cognitive performance in a Brazilian sample

The main objective of the present study was to evaluate the diagnostic value (clinical application) of brain measures and cognitive function. Alzheimer and multiinfarct patients (N = 30) and normal subjects over the age of 50 (N = 40) were submitted to a medical, neurological and cognitive investigation. The cognitive tests applied were Mini-Mental, word span, digit span, logical memory, spatial recognition span, Boston naming test, praxis, and calculation tests. The brain ratios calculated were the ventricle-brain, bifrontal, bicaudate, third ventricle, and suprasellar cistern measures. These data were obtained from a brain computer tomography scan, and the cutoff values from receiver operating characteristic curves. We analyzed the diagnostic parameters provided by these ratios and compared them to those obtained by cognitive evaluation. The sensitivity and specificity of cognitive tests were higher than brain measures, although dementia patients presented higher ratios, showing poorer cognitive performances than normal individuals. Normal controls over the age of 70 presented higher measures than younger groups, but similar cognitive performance. We found diffuse losses of tissue from the central nervous system related to distribution of cerebrospinal fluid in dementia patients. The likelihood of case identification by functional impairment was higher than when changes of the structure of the central nervous system were used. Cognitive evaluation still seems to be the best method to screen individuals from the community, especially for developing countries, where the cost of brain imaging precludes its use for screening and initial assessment of dementia.

Post-processing and analysis of tracked hand trajectories

In this thesis, the suitability of different trackers for finger tracking in high-speed videos was studied. Tracked finger trajectories from the videos were post-processed and analysed using various filtering and smoothing methods. Position derivatives of the trajectories, speed and acceleration were extracted for the purposes of hand motion analysis. Overall, two methods, Kernelized Correlation Filters and Spatio-Temporal Context Learning tracking, performed better than the others in the tests. Both achieved high accuracy for the selected high-speed videos and also allowed real-time processing, being able to process over 500 frames per second. In addition, the results showed that different filtering methods can be applied to produce more appropriate velocity and acceleration curves calculated from the tracking data. Local Regression filtering and Unscented Kalman Smoother gave the best results in the tests. Furthermore, the results show that tracking and filtering methods are suitable for high-speed hand-tracking and trajectory-data post-processing.

Familial predisposition to hypertension and the association between urinary sodium excretion and blood pressure in a population-based sample of young adults

The reasons for the inconsistent association between salt consumption and blood pressure levels observed in within-society surveys are not known. A total of 157 normotensive subjects aged 18 to 35 years, selected at random in a cross-sectional population-based survey, answered a structured questionnaire. They were classified as strongly predisposed to hypertension when two or more first-degree relatives had a diagnosis of hypertension. Anthropometric parameters were obtained and sitting blood pressure was determined with aneroid sphygmomanometers. Sodium and potassium excretion was measured by flame spectrophotometry in an overnight urine sample. A positive correlation between blood pressure and urinary sodium excretion was detected only in the group of individuals strongly predisposed to hypertension, both for systolic blood pressure (r = 0.51, P<0.01) and diastolic blood pressure (r = 0.50, P<0.01). In a covariance analysis, after controlling for age, skin color and body mass index, individuals strongly predisposed to hypertension who excreted amounts of sodium above the median of the entire sample had higher systolic and diastolic blood pressure than subjects classified into the remaining conditions. The influence of familial predisposition to hypertension on the association between salt intake and blood pressure may be an additional explanation for the weak association between urinary sodium excretion and blood pressure observed in within-population studies, since it can influence the association between salt consumption and blood pressure in some but not all inhabitants.

Enhancement of declarative memory associated with emotional content in a Brazilian sample

Several studies have documented that emotional arousal may enhance long-term memory. This is an adaptation of a paradigm previously used in North American and European samples in investigations of the influence of emotion on long-term retention. A sample of 46 healthy adults of high and low educational levels watched a slide presentation of stories. A randomly assigned group watched a story with an arousing content and another group watched a neutral story. The stories were matched for structure and comprehensibility and the set and order of the 11 slides were the same in both conditions. Immediately after viewing the slide presentation, the participants were asked to rate the emotionality of the narrative. The arousing narrative was rated as being more emotional than the neutral narrative (t (44) = -3.6, P<0.001). Ten days later subjects were asked to remember the story and answer a multiple-choice questionnaire about it. The subjects who watched the arousing story had higher scores in the free recall measure (t (44) = -2.59, P<0.01). There were no differences between groups in the multiple-choice test of recognition memory (t (44) = 0.26). These findings confirm that an emotional arousing content enhances long-term declarative memory and indicate the possibility of applying this instrument to clinical samples of various cultural backgrounds.

The cognitive subscale of the "Alzheimer's Disease Assessment Scale" in a Brazilian sample

The cognitive subscale of the "Alzheimer's Disease Assessment Scale" (ADAS-Cog) is widely used for the evaluation of dementia and is very popular in dementia drug trials because of the characteristics of the scale. The objective of the present study was to adapt the ADAS-Cog for use for the Brazilian population. A major problem is that education is variable, a fact that may influence performance in cognitive evaluation. This study was conducted on a control group (CG) of 96 subjects (25 males and 71 females aged 68 ± 8.6 years) and on 44 Alzheimer's disease (AD) patients (19 males and 25 females aged 72 ± 6.4 years) with mild dementia (Clinical Dementia Rating score 1). For statistical analysis groups were divided into three educational levels: I, 0-4 years of schooling (65 CG/20 AD); II, 5-11 years of schooling (19 CG/7 AD), and III, 12 or more years of schooling (12 CG/17 AD). The battery was applied according to original instructions. Total mean score for CG and AD was 10.9 and 22.9 for level I, 7.8 and 22.4 for level II, and 6.2 and 15.4 for level III, respectively. These results indicate that our version of the ADAS-Cog is useful to identify mild dementia, though there may be an overlapping when comparing high education demented with low education non-demented subjects.

Performance of a Brazilian population sample in the Boston Diagnostic Aphasia Examination: A pilot study

Brazilian researchers and health professionals often face the challenge of having to use tests developed in foreign languages and standardized for populations of other countries, especially in the fields of Neuropsychology and Neurolinguistics. This fact promotes a feeling that some scoring systems may be inadequate for our sociocultural reality. In the present study, we describe the performance of a Brazilian population sample submitted to a translated and adapted version of the Boston Diagnostic Aphasia Examination (BDAE). Sixty normal volunteers (21 men and 39 women), all Portuguese native speakers, ranging in age from 15 to 78 years (average 43.7) and with an educational level of 2 to 16 years (average 9.9), were tested using a translated and adapted Portuguese version of the BDAE. Cut-off scores are suggested for our population and the performance of the Brazilian sample is compared to that of American and Colombian samples, with the results being closely similar in all tasks. We also performed a correlation analysis between age, gender and educational level and the influence of these variables on the performance of the subjects. We found no statistically significant differences between genders. Educational level correlated positively with performance, especially in the subtests involving reading and writing. There was a negative correlation between age and performance in two subtests (Visual Confrontation Naming and Sentences to Dictation), but a coexisting effect of educational level could not be ruled out.

The X-X-/E+E+ genotype of the XbaI/EcoRI polymorphisms of the apolipoprotein B gene as a marker of coronary artery disease in a Brazilian sample

Studies that consider polymorphisms within the apolipoprotein B (apo B) gene as risk factors for coronary artery disease (CAD) have reported conflicting results. The aim of the present study was to search for associations between two DNA RFLPs (XbaI and EcoRI) of the apo B gene and CAD diagnosed by angiography. In the present study we compared 116 Brazilian patients (92 men) with CAD (CAD+) to 78 control patients (26 men) without ischemia or arterial damage (CAD-). The allele frequencies at the XbaI (X) and EcoRI (E) sites did not differ between groups. The genotype distributions of CAD+ and CAD- patients were different (chi²(1) = 6.27, P = 0.012) when assigned to two classes (X-X-/E+E+ and the remaining XbaI/EcoRI genotypes). Multivariate logistic regression analysis showed that individuals with the X-X-/E+E+ genotype presented a 6.1 higher chance of developing CAD than individuals with the other XbaI/EcoRI genotypes, independently of the other risk factors considered (sex, tobacco consumption, total cholesterol, hypertension, and triglycerides). We conclude that the X-X-/E+E genotype may be in linkage disequilibrium with an unknown variation in the apo B gene or with a variation in another gene that affects the risk of CAD.

A method for multiple sequential analyses of macrophage functions using a small single cell sample

Microbial pathogens such as bacillus Calmette-Guérin (BCG) induce the activation of macrophages. Activated macrophages can be characterized by the increased production of reactive oxygen and nitrogen metabolites, generated via NADPH oxidase and inducible nitric oxide synthase, respectively, and by the increased expression of major histocompatibility complex class II molecules (MHC II). Multiple microassays have been developed to measure these parameters. Usually each assay requires 2-5 x 10(5) cells per well. In some experimental conditions the number of cells is the limiting factor for the phenotypic characterization of macrophages. Here we describe a method whereby this limitation can be circumvented. Using a single 96-well microassay and a very small number of peritoneal cells obtained from C3H/HePas mice, containing as little as <=2 x 10(5) macrophages per well, we determined sequentially the oxidative burst (H2O2), nitric oxide production and MHC II (IAk) expression of BCG-activated macrophages. More specifically, with 100 µl of cell suspension it was possible to quantify H2O2 release and nitric oxide production after 1 and 48 h, respectively, and IAk expression after 48 h of cell culture. In addition, this microassay is easy to perform, highly reproducible and more economical.

Headache complaints associated with psychiatric comorbidity in a population-based sample

The objective of the present study was to determine the frequency at which people complain of any type of headache, and its relationship with sociodemographic characteristics and psychiatric comorbidity in São Paulo, Brazil. A three-step cluster sampling method was used to select 1,464 subjects aged 18 years or older. They were mainly from families of middle and upper socioeconomic levels living in the catchment area of Instituto de Psiquiatria. However, this area also contains some slums and shantytowns. The subjects were interviewed using the Brazilian version of the Composite International Diagnostic Interview version 1.1. (CIDI 1.1) by a lay trained interviewer. Answers to CIDI 1.1 questions allowed us to classify people according to their psychiatric condition and their headaches based on their own ideas about the nature of their illness. The lifetime prevalence of "a lot of problems with" headache was 37.4% (76.2% of which were attributed to use of medicines, drugs/alcohol, physical illness or trauma, and 23.8% attributed to nervousness, tension or mental illness). The odds ratio (OR) for headache among participants with "nervousness, tension or mental illness" was elevated for depressive episodes (OR, 2.1; 95%CI, 1.4-3.4), dysthymia (OR, 3.4; 95%CI, 1.6-7.4) and generalized anxiety disorder (OR, 4.3; 95%CI, 2.1-8.6), when compared with patients without headache. For "a lot of problems with" headaches attributed to medicines, drugs/alcohol, physical illness or trauma, the risk was also increased for dysthymia but not for generalized anxiety disorder. These data show a high association between headache and chronic psychiatric disorders in this Brazilian population sample.