Gene Classification Based on Amino Acid Motifs and Residues: The DLX (distal-less) Test Case

BACKGROUND:Comparative studies using hundreds of sequences can give a detailed picture of the evolution of a given gene family. Nevertheless, retrieving only the sequences of interest from public databases can be difficult, in particular, when working with highly divergent sequences. The difficulty increases substantially when one wants to include in the study sequences from many (or less well studied) species whose genomes are non-annotated or incompletely annotated. METHODOLOGY/PRINCIPAL FINDINGS:In this work we evaluate the usefulness of different approaches of gene retrieval and classification, using the distal-less (DLX) gene family as a test case. Furthermore, we evaluate whether the use of a large number of gene sequences from a wide range of animal species, the use of multiple alternative alignments, and the use of amino acids aligned with high confidence only, is enough to recover the accepted DLX evolutionary history. CONCLUSIONS/SIGNIFICANCE:The canonical DLX homeobox gene sequence here derived, together with the characteristic amino acid variants here identified in the DLX homeodomain region, can be used to retrieve and classify DLX genes in a simple and efficient way. A program is made available that allows the easy retrieval of synteny information that can be used to classify gene sequences. Maximum likelihood trees using hundreds of sequences can be used for gene identification. Nevertheless, for the DLX case, the proposed DLX evolutionary is not recovered even when multiple alignment algorithms are used

Protective Ag :TiO2 thin films for pressure sensors in orthopedic prosthesis: the importance of composition, structural and morphological features on the biological response of the coatings

DC reactive magnetron sputtered Ag:TiO2 nanocomposite thin films were developed to be used as protective coatings in pressure sensor devices. The coatings, with Ag content varying from 0 to about 30 at.%, were prepared and characterized in order to study their biological response. The as-deposited samples were annealed in vacuum at 500 °C in order to evaluate the influence of their morphological and structural differences over the response elicited upon contact with simulated bodily fluids and cultured human cells, as well as selected microorganisms. The results showed that the annealing treatment produced less porous films with an enhanced structure, with a significant reduction in structural defects and improved crystallinity. Additionally, samples with higher Ag contents (≥12.8 at.%) exhibited Ag agglomerates/clusters at the surface, a result anticipated from the XRD data. The crystallization of the TiO2 matrix was also observed by XRD analysis, albeit delayed by the dispersion of Ag into the matrix. Biological characterization showed that the antimicrobial activity and cytotoxicity of the coatings were directly related with their composition, closely followed by the particular structural and morphological features, namely those resulting from annealing process.This research is partially sponsored by FEDER funds through the program COMPETE—Programa Operacional Factores de Competitividade and by national funds through FCT—Fundação para a Ciência e a Tecnologia, under the projects PEst-C/EME/UI0285/2011, PTDC/SAU-ENB/116850/2010, PTDC/CTM-NAN/112574/2009P. T Matamá acknowledges FCT for Grant SFRH/BPD/47555/2008

Inter-hemispheric EEG coherence analysis in Parkinson's disease : Assessing brain activity during emotion processing

Parkinson’s disease (PD) is not only characterized by its prominent motor symptoms but also associated with disturbances in cognitive and emotional functioning. The objective of the present study was to investigate the influence of emotion processing on inter-hemispheric electroencephalography (EEG) coherence in PD. Multimodal emotional stimuli (happiness, sadness, fear, anger, surprise, and disgust) were presented to 20 PD patients and 30 age-, education level-, and gender-matched healthy controls (HC) while EEG was recorded. Inter-hemispheric coherence was computed from seven homologous EEG electrode pairs (AF3–AF4, F7–F8, F3–F4, FC5–FC6, T7–T8, P7–P8, and O1–O2) for delta, theta, alpha, beta, and gamma frequency bands. In addition, subjective ratings were obtained for a representative of emotional stimuli. Interhemispherically, PD patients showed significantly lower coherence in theta, alpha, beta, and gamma frequency bands than HC during emotion processing. No significant changes were found in the delta frequency band coherence. We also found that PD patients were more impaired in recognizing negative emotions (sadness, fear, anger, and disgust) than relatively positive emotions (happiness and surprise). Behaviorally, PD patients did not show impairment in emotion recognition as measured by subjective ratings. These findings suggest that PD patients may have an impairment of inter-hemispheric functional connectivity (i.e., a decline in cortical connectivity) during emotion processing. This study may increase the awareness of EEG emotional response studies in clinical practice to uncover potential neurophysiologic abnormalities

Modelling the Effect of Temperature on Respiration Rate of Fresh Cut Papaya (Carica papaya L.) Fruits.

A respiration rate (RR) model based on Peleg’s equation was developed for predicting RRs of fresh cut papaya. Respiration data for fresh cut papaya at 3/4 maturity were generated at temperatures 5, 10, 15, 20, 25 and 30°C using a closed system. RRs was found to be significantly influenced by storage temperature and increased from 0.021 to 0.289 mL[O2]/kg·h and 0.063 to 0.393 mL[CO2]/kg·h as a function of O2 and CO2 gas concentrations, respectively. Peleg’s constant K 1 and K 2 were obtained from linear regression analysis using GraphPad Prism 5.0 software and regression coefficients have good fit with values close to unity. The model was verified to assess the capability of its predictability of the RRs over the temperatures. There was good agreement with the experimentally estimated RRs. Information derived from the model can contribute in the design of successful modified atmospheric systems for storage of fresh cut papaya

Quantum dynamics in strong fluctuating fields

A large number of multifaceted quantum transport processes in molecular systems and physical nanosystems can be treated in terms of quantum relaxation processes which couple to one or several fluctuating environments. A thermal equilibrium environment can conveniently be modelled by a thermal bath of harmonic oscillators. An archetype situation provides a two-state dissipative quantum dynamics, commonly known under the label of a spin-boson dynamics. An interesting and nontrivial physical situation emerges, however, when the quantum dynamics evolves far away from thermal equilibrium. This occurs, for example, when a charge transferring medium possesses nonequilibrium degrees of freedom, or when a strong time-dependent control field is applied externally. Accordingly, certain parameters of underlying quantum subsystem acquire stochastic character. Herein, we review the general theoretical framework which is based on the method of projector operators, yielding the quantum master equations for systems that are exposed to strong external fields. This allows one to investigate on a common basis the influence of nonequilibrium fluctuations and periodic electrical fields on quantum transport processes. Most importantly, such strong fluctuating fields induce a whole variety of nonlinear and nonequilibrium phenomena. A characteristic feature of such dynamics is the absence of thermal (quantum) detailed balance.Comment: review article, Advances in Physics (2005), in pres

Screening of cannabis-related problems among youth: the CPQ-A-S and CAST questionnaires

<p>Abstract</p> <p>Background</p> <p>Cannabis use among young people is a significant problem, making particularly necessary validated screening instruments that permit secondary prevention. The purpose of this study was to analyze and compare the psychometric properties of the CAST and CPQ-A-S questionnaires, two screening instruments specifically addressing the youth population.</p> <p>Methods</p> <p>Information was obtained on sociodemographics, frequency of substance use, psychopathological symptoms and cannabis-use problems, and the CPQ-A-S and CAST were applied, as well as an infrequency scale for discarding responses made randomly. The sample was made up of 144 young people aged 16 to 20 that had used cannabis in the last month, of which 71.5% were boys. Mean age of the sample was 17.38 years (SD = 1.16).</p> <p>Results</p> <p>The results show that from the psychometric point of view both the CAST and the CPQ-A-S are good screening instruments.</p> <p>Conclusions</p> <p>The CAST is shorter and presents slightly better internal consistency than the CPQ-A-S. Both instruments show high sensitivity and specificity in the detection of young people dependent on cannabis according to the DSM IV-TR criteria. The CPQ-A-S appears to show greater capacity for detecting psychopathological distress associated with use. Both questionnaires yield significant odds ratios as predictors of frequent cannabis use and of the DSM IV-TR abuse and dependence criteria. In general, the CPQ-A-S emerges as a better predictor than the CAST.</p