From software extensions to product lines of dataflow programs

Abstract Dataflow programs are widely used. Each program is a directed graph where nodes are computations and edges indicate the flow of data. In prior work, we reverse-engineered legacy dataflow programs by deriving their optimized implementations from a simple specification graph using graph transformations called refinements and optimizations. In MDE-speak, our derivations were PIM-to-PSM mappings. In this paper, we show how extensions complement refinements, optimizations, and PIM-to-PSM derivations to make the process of reverse engineering complex legacy dataflow programs tractable. We explain how optional functionality in transformations can be encoded, thereby enabling us to encode product lines of transformations as well as product lines of dataflow programs. We describe the implementation of extensions in the ReFlO tool and present two non-trivial case studies as evidence of our work’s generality

ADSNARK: Nearly practical and privacy-preserving proofs on authenticated data

We study the problem of privacy-preserving proofs on authenticated data, where a party receives data from a trusted source and is requested to prove computations over the data to third parties in a correct and private way, i.e., the third party learns no information on the data but is still assured that the claimed proof is valid. Our work particularly focuses on the challenging requirement that the third party should be able to verify the validity with respect to the specific data authenticated by the source — even without having access to that source. This problem is motivated by various scenarios emerging from several application areas such as wearable computing, smart metering, or general business-to-business interactions. Furthermore, these applications also demand any meaningful solution to satisfy additional properties related to usability and scalability. In this paper, we formalize the above three-party model, discuss concrete application scenarios, and then we design, build, and evaluate ADSNARK, a nearly practical system for proving arbitrary computations over authenticated data in a privacy-preserving manner. ADSNARK improves significantly over state-of-the-art solutions for this model. For instance, compared to corresponding solutions based on Pinocchio (Oakland’13), ADSNARK achieves up to 25× improvement in proof-computation time and a 20× reduction in prover storage space.

Metaphorisms in programming

This paper introduces the metaphorism pattern of relational specification and addresses how specification following this pattern can be refined into recursive programs. Metaphorisms express input-output relationships which preserve relevant information while at the same time some intended optimization takes place. Text processing, sorting, representation changers, etc., are examples of metaphorisms. The kind of metaphorism refinement proposed in this paper is a strategy known as change of virtual data structure. It gives sufficient conditions for such implementations to be calculated using relation algebra and illustrates the strategy with the derivation of quicksort as example.

Galanin-mediated behavioural hyperalgesia from the dorsomedial nucleus of the hypothalamus involves two independent descending pronociceptive pathways

Activation of the dorsomedial nucleus of the hypothalamus (DMH) by galanin (GAL) induces behavioural hyperalgesia. Since DMH neurones do not project directly to the spinal cord, we hypothesized that the medullary dorsal reticular nucleus (DRt), a pronociceptive region projecting to the spinal dorsal horn (SDH) and/or the serotoninergic raphe-spinal pathway acting on the spinal 5-HT3 receptor (5HT3R) could relay descending nociceptive facilitation induced by GAL in the DMH. Heat-evoked paw-withdrawal latency (PWL) and activity of SDH neurones were assessed in monoarthritic (ARTH) and control (SHAM) animals after pharmacological manipulations of the DMH, DRt and spinal cord. The results showed that GAL in the DMH and glutamate in the DRt lead to behavioural hyperalgesia in both SHAM and ARTH animals, which is accompanied particularly by an increase in heat-evoked responses of wide-dynamic range neurons, a group of nociceptive SDH neurones. Facilitation of pain behaviour induced by GAL in the DMH was reversed by lidocaine in the DRt and by ondansetron, a 5HT3R antagonist, in the spinal cord. However, the hyperalgesia induced by glutamate in the DRt was not blocked by spinal ondansetron. In addition, in ARTH but not SHAM animals PWL was increased after lidocaine in the DRt and ondansetron in the spinal cord. Our data demonstrate that GAL in the DMH activates two independent descending facilitatory pathways: (i) one relays in the DRt and (ii) the other one involves 5-HT neurones acting on spinal 5HT3Rs. In experimental ARTH, the tonic pain-facilitatory action is increased in both of these descending pathways.

Fundamental studies on natural deep eutectic solvents: physico-chemical, thermal and rheological properties

When combined at particular molar fractions, sugars, aminoacids or organic acids a present a high melting point depression, becoming liquids at room temperature. These are called Natural Deep Eutectic Solvents – NADES and are envisaged to play a major role on the chemical engineering processes of the future. Nonetheless, there is a significant lack of knowledge of its fundamental and basic properties, which is hindering their industrial applications. For this reason it is important to extend the knowledge on these systems, boosting their application development [1]. In this work, we have developed and characterized NADES based on choline chloride, organic acids, amino acids and sugars. Their density, thermal behavior, conductivity and polarity were assessed for different compositions. The conductivity was measured from 0 to 40 °C and the temperature effect was well described by the Vogel-Fulcher-Tammann equation. The morphological characterization of the crystallizable materials was done by polarized optical microscopy that provided also evidence of homogeneity/phase separation. Additionally, the rheological and thermodynamic properties of the NADES and the effect of water content were also studied. The results show these systems have Newtonian behavior and present significant viscosity decrease with temperature and water content, due to increase on the molecular mobility. The anhydrous systems present viscosities that range from higher than 1000Pa.s at 20°C to less than 1Pa.s at 70°C. DSC characterization confirms that for water content as high as 1:1:1 molar ratio, the mixture retains its single phase behavior. The results obtained demonstrate that the NADES properties can be finely tunned by careful selection of its constituents. NADES present the necessary properties for use as extraction solvents. They can be prepared from inexpensive raw materials and tailored for the selective extraction of target molecules. The data produced in this work is hereafter importance for the selection of the most promising candidates avoiding a time consuming and expensive trial and error phase providing also data for the development of models able to predict their properties and the mechanisms that allow the formation of the deep eutectic mixtures.

Estimativa dos parâmetros de compactação de solos usando técnicas de data mining

Dissertação de mestrado integrado em Engenharia Civil

Age effects on EEG correlates of the Wisconsin card sorting test

Body and brain undergo several changes with aging. One of the domains in which these changes are more remarkable relates with cognitive performance. In the present work, electroencephalogram (EEG) markers (power spectral density and spectral coherence) of age-related cognitive decline were sought whilst the subjects performed the Wisconsin Card Sorting Test (WCST). Considering the expected age-related cognitive deficits, WCST was applied to young, mid-age and elderly participants, and the theta and alpha frequency bands were analyzed. From the results herein presented, higher theta and alpha power were found to be associated with a good performance in the WCST of younger subjects. Additionally, higher theta and alpha coherence were also associated with good performance and were shown to decline with age and a decrease in alpha peak frequency seems to be associated with aging. Additionally, inter-hemispheric long-range coherences and parietal theta power were identified as age-independent EEG correlates of cognitive performance. In summary, these data reveals age-dependent as well as age-independent EEG correlates of cognitive performance that contribute to the understanding of brain aging and related cognitive deficits.

Exploring the factor structure of neurocognitive measures in older individuals

Here we focus on factor analysis from a best practices point of view, by investigating the factor structure of neuropsychological tests and using the results obtained to illustrate on choosing a reasonable solution. The sample (n=1051 individuals) was randomly divided into two groups: one for exploratory factor analysis (EFA) and principal component analysis (PCA), to investigate the number of factors underlying the neurocognitive variables; the second to test the "best fit" model via confirmatory factor analysis (CFA). For the exploratory step, three extraction (maximum likelihood, principal axis factoring and principal components) and two rotation (orthogonal and oblique) methods were used. The analysis methodology allowed exploring how different cognitive/psychological tests correlated/discriminated between dimensions, indicating that to capture latent structures in similar sample sizes and measures, with approximately normal data distribution, reflective models with oblimin rotation might prove the most adequate.

The bounds of education in the human brain connectome

Inter-individual heterogeneity is evident in aging; education level is known to contribute for this heterogeneity. Using a cross-sectional study design and network inference applied to resting-state fMRI data, we show that aging was associated with decreased functional connectivity in a large cortical network. On the other hand, education level, as measured by years of formal education, produced an opposite effect on the long-term. These results demonstrate the increased brain efficiency in individuals with higher education level that may mitigate the impact of age on brain functional connectivity.

Interrelationship between partition behavior of organic compounds and proteins in aqueous dextran-Polyethylene glycol and Polyethylene glycol-sodium sulfate two-phase systems

Partition behavior of adenosine and guanine mononucleotides was examined in aqueous dextran-polyethylene glycol (PEG) and PEG-sodium sulfate two-phase systems. The partition coefficients for each series of mononucleotides were analyzed as a functions of the number of phosphate groups and found to be dependent on the nature of nucleic base and on the type of \ATPS\ utilized. It was concluded that an average contribution of a phosphate group into logarithm of partition coefficient of a mononucleotide cannot be used to estimate the difference between the electrostatic properties of the coexisting phases of ATPS. The data obtained in this study were considered together with those for other organic compounds and proteins reported previously, and the linear interrelationship between logarithms of partition coefficients in dextran-PEG, PEG-Na2SO4 and PEG-Na2SO4-0.215 M NaCl (all in 0.01 M Na- or K/Na-phosphate buffer, pH 7.4 or 6.8) was established. Similar relationship was found for the previously reported data for proteins in Dex-PEG, PEG-600-Na2SO4, and PEG-8000-Na2SO4 ATPS. It is suggested that the linear relationships of the kind established in \ATPS\ may be observed for biological properties of compounds as well.

Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data

The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2016.00275

Tapping the wealth of microbial data in high-throughput metabolic model reconstruction

Genome-scale metabolic models are valuable tools in the metabolic engineering process, based on the ability of these models to integrate diverse sources of data to produce global predictions of organism behavior. At the most basic level, these models require only a genome sequence to construct, and once built, they may be used to predict essential genes, culture conditions, pathway utilization, and the modifications required to enhance a desired organism behavior. In this chapter, we address two key challenges associated with the reconstruction of metabolic models: (a) leveraging existing knowledge of microbiology, biochemistry, and available omics data to produce the best possible model; and (b) applying available tools and data to automate the reconstruction process. We consider these challenges as we progress through the model reconstruction process, beginning with genome assembly, and culminating in the integration of constraints to capture the impact of transcriptional regulation. We divide the reconstruction process into ten distinct steps: (1) genome assembly from sequenced reads; (2) automated structural and functional annotation; (3) phylogenetic tree-based curation of genome annotations; (4) assembly and standardization of biochemistry database; (5) genome-scale metabolic reconstruction; (6) generation of core metabolic model; (7) generation of biomass composition reaction; (8) completion of draft metabolic model; (9) curation of metabolic model; and (10) integration of regulatory constraints. Each of these ten steps is documented in detail.

An object-oriented model for rapid prototyping of data path/control systems - a case study

Publicado em "Information control in manufacturing 1998 : (INCOM'98) : advances in industrial engineering : a proceedings volume from the 9th IFAC Symposium, Nancy-Metz, France, 24-26 June 1998. Vol. 2"

Role of sirtuin 3 on mitochondrial dynamics in Huntington's disease striatal cells

Dissertação de mestrado em Genética Molecular

Estimation of statistical cure from cancer using population-based data

Dissertação de mestrado em Estatística