Wavelet analysis of human DNA

This paper studies the human DNA in the perspective of signal processing. Six wavelets are tested for analyzing the information content of the human DNA. By adopting real Shannon wavelet several fundamental properties of the code are revealed. A quantitative comparison of the chromosomes and visualization through multidimensional and dendograms is developed.

Histogram-based DNA analysis for the visualization of chromosome, genome and species information

We describe a novel approach to explore DNA nucleotide sequence data, aiming to produce high-level categorical and structural information about the underlying chromosomes, genomes and species. The article starts by analyzing chromosomal data through histograms using fixed length DNA sequences. After creating the DNA-related histograms, a correlation between pairs of histograms is computed, producing a global correlation matrix. These data are then used as input to several data processing methods for information extraction and tabular/graphical output generation. A set of 18 species is processed and the extensive results reveal that the proposed method is able to generate significant and diversified outputs, in good accordance with current scientific knowledge in domains such as genomics and phylogenetics.

Analysis and visualization of chromosome information

This paper analyzes the DNA code of several species in the perspective of information content. For that purpose several concepts and mathematical tools are selected towards establishing a quantitative method without a priori distorting the alphabet represented by the sequence of DNA bases. The synergies of associating Gray code, histogram characterization and multidimensional scaling visualization lead to a collection of plots with a categorical representation of species and chromosomes.

Evaluation of dynamic pass-through of carbon prices into electricity prices – a cointegrated VECM analysis

This paper addresses the impact of the CO2 opportunity cost on the wholesale electricity price in the context of the Iberian electricity market (MIBEL), namely on the Portuguese system, for the period corresponding to the Phase II of the European Union Emission Trading Scheme (EU ETS). In the econometric analysis a vector error correction model (VECM) is specified to estimate both long–run equilibrium relations and short–run interactions between the electricity price and the fuel (natural gas and coal) and carbon prices. The model is estimated using daily spot market prices and the four commodities prices are jointly modelled as endogenous variables. Moreover, a set of exogenous variables is incorporated in order to account for the electricity demand conditions (temperature) and the electricity generation mix (quantity of electricity traded according the technology used). The outcomes for the Portuguese electricity system suggest that the dynamic pass–through of carbon prices into electricity prices is strongly significant and a long–run elasticity was estimated (equilibrium relation) that is aligned with studies that have been conducted for other markets.

Proteomic analysis of the influence of the adipocyte secretome on Glioma Gl261 cells

Glioma is the most frequent form of malignant brain tumor in the adults and childhood. There is a global tendency toward a higher incidence of gliomas in highly developed and industrialized countries. Simultaneously obesity is reaching epidemic proportions in such developed countries. It has been highly accepted that obesity may play an important role in the biology of several types of cancer. We have developed an in vitro method for the understanding of the influence of obesity on glioma mouse cells (Gl261). 3T3-L1 mouse pre-adipocytes were induced to the maturity. The conditioned medium was harvested and used into the Gl261 cultures. Using two-dimension electrophoresis it was analyzed the proteome content of Gl261 in the presence of conditioned medium (CGl) and in its absence (NCGl). The differently expressed spots were collected and analyzed by means of mass spectroscopy (MALDI-TOF-MS). Significantly expression pattern changes were observed in eleven proteins and enzymes. RFC1, KIF5C, ANXA2, N-RAP, RACK1 and citrate synthase were overexpressed or only present in the CGl. Contrariwise, STI1, hnRNPs and phosphoglycerate kinase 1 were significantly underexpressed in CGl. Aldose reductase and carbonic anhydrase were expressed only in NCGl. Our results show that obesity remodels the physiological and metabolic behavior of glioma cancer cells. Also, proteins found differently expressed are implicated in several signaling pathways that control matrix remodeling, proliferation, progression, migration and invasion. In general our results support the idea that obesity may increase glioma malignancy, however, some interesting paradox finding were also reported and discussed.

Forest soil short term response to prescribed fire: an approach by Principal Components Analysis

In the current context of serious climate changes, where the increase of the frequency of some extreme events occurrence can enhance the rate of periods prone to high intensity forest fires, the National Forest Authority often implements, in several Portuguese forest areas, a regular set of measures in order to control the amount of fuel mass availability (PNDFCI, 2008). In the present work we’ll present a preliminary analysis concerning the assessment of the consequences given by the implementation of prescribed fire measures to control the amount of fuel mass in soil recovery, in particular in terms of its water retention capacity, its organic matter content, pH and content of iron. This work is included in a larger study (Meira-Castro, 2009(a); Meira-Castro, 2009(b)). According to the established praxis on the data collection, embodied in multidimensional matrices of n columns (variables in analysis) by p lines (sampled areas at different depths), and also considering the quantitative data nature present in this study, we’ve chosen a methodological approach that considers the multivariate statistical analysis, in particular, the Principal Component Analysis (PCA ) (Góis, 2004). The experiments were carried out in a soil cover over a natural site of Andaluzitic schist, in Gramelas, Caminha, NW Portugal, who was able to maintain itself intact from prescribed burnings from four years and was submit to prescribed fire in March 2008. The soils samples were collected from five different plots at six different time periods. The methodological option that was adopted have allowed us to identify the most relevant relational structures inside the n variables, the p samples and in two sets at the same time (Garcia-Pereira, 1990). Consequently, and in addition to the traditional outputs produced from the PCA, we have analyzed the influence of both sampling depths and geomorphological environments in the behavior of all variables involved.

Comparison of Disposable Pipette Extraction and Dispersive Solid-Phase Extraction in the QuEChERS Method for Analysis of Pesticides in Strawberries

In this study, we sought to assess the applicability of GC–MS/MS for the identification and quantification of 36 pesticides in strawberry from integrated pest management (IPM) and organic farming (OF). Citrate versions of QuEChERS (quick, easy, cheap, effective, rugged and safe) using dispersive solid-phase extraction (d-SPE) and disposable pipette extraction (DPX) for cleanup were compared for pesticide extraction. For cleanup, a combination of MgSO4, primary secondary amine and C18 was used for both the versions. Significant differences were observed in recovery results between the two sample preparation versions (DPX and d-SPE). Overall, 86% of the pesticides achieved recoveries (three spiking levels 10, 50 and 200 µg/kg) in the range of 70–120%, with <13% RSD. The matrix effects were also evaluated in both the versions and in strawberries from different crop types. Although not evidencing significant differences between the two methodologies were observed, however, the DPX cleanup proved to be a faster technique and easy to execute. The results indicate that QuEChERS with d-SPE and DPX and GC–MS/MS analysis achieved reliable quantification and identification of 36 pesticide residues in strawberries from OF and IPM.

Strategic Bidding in Electricity Markets: An agent-based simulator with game theory for scenario analysis

Electricity markets are complex environments, involving a large number of different entities, with specific characteristics and objectives, making their decisions and interacting in a dynamic scene. Game-theory has been widely used to support decisions in competitive environments; therefore its application in electricity markets can prove to be a high potential tool. This paper proposes a new scenario analysis algorithm, which includes the application of game-theory, to evaluate and preview different scenarios and provide players with the ability to strategically react in order to exhibit the behavior that better fits their objectives. This model includes forecasts of competitor players’ actions, to build models of their behavior, in order to define the most probable expected scenarios. Once the scenarios are defined, game theory is applied to support the choice of the action to be performed. Our use of game theory is intended for supporting one specific agent and not for achieving the equilibrium in the market. MASCEM (Multi-Agent System for Competitive Electricity Markets) is a multi-agent electricity market simulator that models market players and simulates their operation in the market. The scenario analysis algorithm has been tested within MASCEM and our experimental findings with a case study based on real data from the Iberian Electricity Market are presented and discussed.

Is mental practice an effective adjunct therapeutic strategy for upper limb motor restoration after stroke? A systematic review and meta- analysis

Stroke is one of the most common conditions requiring rehabilitation, and its motor impairments are a major cause of permanent disability. Hemiparesis is observed by 80% of the patients after acute stroke. Neuroimaging studies showed that real and imagined movements have similarities regarding brain activation, supplying evidence that those similarities are based on the same process. Within this context, the combination of mental practice (MP) with physical and occupational therapy appears to be a natural complement based on neurorehabilitation concepts. Our study seeks to investigate if MP for stroke rehabilitation of upper limbs is an effective adjunct therapy. PubMed (Medline), ISI knowledge (Institute for Scientific Information) and SciELO (Scientific Electronic Library) were terminated on 20 February 2015. Data were collected on variables as follows: sample size, type of supervision, configuration of mental practice, setting the physical practice (intensity, number of sets and repetitions, duration of contractions, rest interval between sets, weekly and total duration), measures of sensorimotor deficits used in the main studies and significant results. Random effects models were used that take into account the variance within and between studies. Seven articles were selected. As there was no statistically significant difference between the two groups (MP vs control), showed a - 0.6 (95% CI: -1.27 to 0.04), for upper limb motor restoration after stroke. The present meta-analysis concluded that MP is not effective as adjunct therapeutic strategy for upper limb motor restoration after stroke.

From Mind to Body: Is Mental Practice Effective on Strength Gains? A Meta-Analysis

Mental practice is an internal reproduction of a motor act (whose intention is to promote learning and improving motor skills). Some studies have shown that other cognitive strategies also increase the strength and muscular resistance in healthy people by the enhancement of the performance during dynamic tasks. Mental training sessions may be primordial to improving muscle strength in different subjects. The aim of this study was to systematically review and meta-analiyze studies that assessed whether mental practice is effective in improving muscular strength. We conducted an electronic-computed search in Pub-Med/Medline and ISI Web of Knowledge, Scielo and manual searchs, searching papers written in English between 1991 and 2014. There were 44 studies in Pub-Med/Medline, 631 in ISI Web of Knowledge, 11 in Scielo and 3 in manual searchs databases. After exclusion of studies for duplicate, unrelated to the topic by title and summary, different samples and methodologies, a meta-analysis of 4 studies was carried out to identify the dose-response relationship. We did not find evidence that mental practice is effective in increasing strength in healthy individuals. There is no evidence that mental practice alone can be effective to induce strength gains or to optimize the training effects.