Generador de compiladores basado en analizadores ascendentes

El objetivo fundamental de este proyecto consiste en crear un generador de compilador, basado en analizadores ascendentes. Como base para hacer este analizador se usará el lenguaje Cosel y el módulo Com, que es un generador de compiladores basado en analizadores descendentes y que actualmente se está utilizando en las prácticas de la asignatura de Compiladores I. El nuevo generador, que tiene como entrada una gramática, ha de comprobar si es una gramática ascendente LALR (1) y analizar una cadena de entrada de símbolos usando dicha gramática.

Bioinformática: identificar genes en una interfaz gráfica vía web para la comparación de genomas

Este trabajo desarrolla el proceso de diseño e implementación de una interfaz web que permite la exploración en detalle de las relaciones entre genomas completos. La interfaz permite la comparación simultánea de nueve genomas, representando en cada gráfica las relaciones entre cada par de genomas junto los genes identificados de cada uno de ellos. Es capaz de trabajar con genomas del dominio Eukaryota y se adapta a la capacidad de cómputo de la máquina cliente. La información representada son MUMs (Maximal Unique Matching, secuencia máxima y única encontrada en ambos genomas) y SuperMUMs (agrupación de MUMs mediante Approximate String Matching). Los datos son previamente calculados y accesibles desde un servidor web.

Evaluación de un nuevo método de sutura para la cirugía endoscopica transluminal a través de orificios naturales en un modelo animal

Natural Orifice Transluminal Endoscopic Surgery (NOTES) is a novel, potentially less invasive alternative to laparoscopic surgery. However, the problems of transluminal access and closure represent significant obstacles to its successful introduction in humans. Objective: to evaluate the feasibility and safety of a novel device designed for transluminal access and closure in a survival porcine model. Subjects: Four adult female Yorkshire pigs were used in the study. Interventions: While under general anesthesia, the animals were prepared with multiple tap water enemas followed by instillation of an antibiotic suspension and povidone-iodine lavage. At a distance of 15 to 20 cm from the anus, the prototype device (LSI Solutions, Victor, NY, USA) deployed a circumscribing purse-string suture around the planned incision site and subsequently used a blade mechanism to create a 2.5-cm linear incision. The transcolonic incision was then closed by cinching and securing the purse-string suture with a titanium knot by use of a separate hand-activated suture-locking device. Main Outcome Measurements: The animals were monitored daily for signs of peritonitis and sepsis and were survived for 14 days. The peritoneal cavity was examined for peritonitis, and the colonic incision site was examined for wound dehiscence, pericolic abscess formation, and gross adhesions. Tissue samples from both incisional and random peritoneal sites were obtained for histologic examination. Results: Transcolonic incision and closure were successful in all 4 animals. The device performed in a rapid and reproducible fashion. All animals recovered without septic complications. At necropsy, there was no evidence of peritonitis, abscesses, or wound dehiscence. Salpingocolonic and colovesicular adhesions were noted in 3 of 4 animals. Histologic examination revealed microabscesses at the incision site in all animals. Conclusions: The prototype incision and closure device represents a promising solution to the problems of transluminal access for NOTES. The presence of incision-related adhesions and microabscesses signal the need for further refinement in aseptic technique. 

Generation of polycyclic aromatic hydrocarbons (PAHs) during woodworking operations.

Occupational exposures to wood dust have been associated with an elevated risk of sinonasal cancer (SNC). Wood dust is recognized as a human carcinogen but the specific cancer causative agent remains unknown. One possible explanation is a co-exposure to; wood dust and polycyclic aromatic hydrocarbons (PAHs). PAHs could be generated during incomplete combustion of wood due to heat created by use of power tools. To determine if PAHs are generated from wood during common wood working operations, PAH concentrations in wood dust samples collected in an experimental chamber operated under controlled conditions were analyzed. In addition, personal air samples from workers exposed to wood dust (n = 30) were collected. Wood dust was generated using three different power tools: vibrating sander, belt sander, and saw; and six wood materials: fir, Medium Density Fiberboard (MDF), beech, mahogany, oak and wood melamine. Monitoring of wood workers was carried out by means of personal sampler device during wood working operations. We measured 21 PAH concentrations in wood dust samples by capillary gas chromatography-ion trap mass spectrometry (GC-MS). Total PAH concentrations in wood dust varied greatly (0.24-7.95 ppm) with the lowest being in MDF dust and the highest in wood melamine dust. Personal PAH exposures were between 37.5-119.8 ng m(-3) during wood working operations. Our results suggest that PAH exposures are present during woodworking operations and hence could play a role in the mechanism of cancer induction related to wood dust exposure.

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This article provides an overview of the scientific and training resources SIB has consistently been offering to the life science community for more than 15 years.

Human immunodeficiency virus type 1: drug resistance in treated and untreated Brazilian children

Twenty-two vertically human immunodeficiency virus type 1 (HIV-1) infected Brazilian children were studied for antiretroviral drug resistance. They were separated into 2 groups according to the administration of antiretroviral therapy into those who presented disease symptoms or without symptoms and no therapy. Viral genome sequencing reactions were loaded on an automated DNA sampler (TruGene, Visible Genetics) and compared to a database of wild type HIV-1. In the former group 8 of 12 children presented isolates with mutations conferring resistance to protease inhibitors (PIs), 7 presented isolates resistant to nucleoside reverse transcriptase inhibitors (NRTIs) and 2 presented isolates resistant to non-nucleoside reverse transcriptase inhibitors (NNRTIs). Ten children were included in the antiretroviral naïve group. Eight were susceptible to NRTIs and all of them were susceptible to PIs; one presented the V108I mutation, which confers low-level resistance to NNRTIs. The data report HIV mutant isolates both in treated and untreated infants. However, the frequency and the level of drug resistance were more frequent in the group receiving antiretroviral therapy, corroborating the concept of selective pressure acting on the emergence of resistant viral strains. The children who presented alterations at polymorphism sites should be monitored for the development of additional mutations occurring at relevant resistance codons.

Localization of breakage points in knotted strings

It is a common macroscopic observation that knotted ropes or fishing lines under tension easily break at the knot. However, a more precise localization of the breakage point in knotted macroscopic strings is a difficult task. In the present work, the tightening of knots was numerically simulated, a comparison of strength of different knots was experimentally performed and a high velocity camera was used to precisely localize the site where knotted macroscopic strings break. In the case of knotted spaghetti, the breakage occurs at the position with high curvature at the entry to the knot. This localization results from joint contributions of loading, bending and friction forces into the complex process of knot breakage. The present simulations and experiments are in agreement with recent molecular dynamics simulations of a knotted polymer chain and with experiments performed on actin and DNA filaments. The strength of the knotted string is greatly reduced (down to 50%) by the presence of a knot, therefore reducing the resistance to tension of all materials containing chains of any sort. The present work with macroscopic strings revels some important aspects, which are not accessible by experiments with microscopic chains.

The transventricular-transseptal access to the aortic root: a new route for extrapleural trans-catheter aortic stent-valve implantation.

Objective: The aim of this study was to investigate the feasibility of transventricular-transseptal approach (TVSA) for extrapleural transcatheter aortic valved stent implantation via a subxyphoidian access. Methods: In five porcine experiments (52.3 +/- 10.9 kg) the right ventricle was exposed via subxyphoidian access. Under the guidance of intracardiac echocardiography (ICE) and fluoroscopy, the transseptal access from right ventricle to left ventricle was created progressively by puncture and dilation with dilators (8F-26F). Valved stents built in-house from commercial tanned pericardium and self-expandable Nitinol stents were loaded into a cartridge. A delivery sheath was then introduced from the right ventricle into the left ventricle and then into the ascending aorta. The cartridge was connected and the valved stent was deployed in the aortic position. Then, the ventricular septal access was sealed with an Amplatzer septal occluder device and the right ventricular access was closed by tying prepared purse-string suture directly. Thirty minutes after the whole procedure, the animals were sacrificed for macroscopic evaluation of the position of valved stent and septal closure device. Result: Procedural success of TVSA was 100% at the first attempt. Mean procedure time was 49 +/- 4 min. Progressive dilatation of the transseptal access resulted in a measurable ventricular septal defect (VSD) after dilator sizes 18F and more. All valved stents were delivered at the target site over the native aortic valve with good acute valve function and no paravalvular leaks. During the procedure, premature beats (5/5) and supraventriclar tachycardias (5/5) were observed, but no atrial-ventricular block (0/5) occurred. Heart rate before (after) was 90 +/- 3 beats min(-1) (100 +/- 2 beats min(-1): p < 0.05), whereas blood pressure was 60 + 1 mm Hg (55 + 2 mm Hg (p < 0.05)). Total blood loss was 280 + 10 ml. The Amplatzer septal occluder devices were fully deployed and the ventricular septal accesses were sealed successfully, without detectable residual shunt. Conclusion: Trans-catheter implantation of aortic valved stent via extrapleural transventricular-transseptal access is technically feasible and has the potential for a simplified procedure under local anaesthesia. (C) 2010 European Association for Cardio-Thoracic Surgery. Published by Elsevier B. V. All rights reserved.

Indoor air microbiological evaluation of offices, hospitals, industries, and shopping centers

In this study it was compared the MAS-100 and the Andersen air samplers' performances and a similar trend in both instruments was observed. It was also evaluated the microbial contamination levels in 3060 samples of offices, hospitals, industries, and shopping centers, in the period of 1998 to 2002, in Rio de Janeiro city. Considering each environment, 94.3 to 99.4% of the samples were the allowed limit in Brazil (750 CFU/m³). The industries' results showed more important similarity among fungi and total heterotrophs distributions, with the majority of the results between zero and 100 CFU/m³. The offices' results showed dispersion around 300 CFU/m³. The hospitals' results presented the same trend, with an average of 200 CFU/m³. Shopping centers' environments showed an average of 300 CFU/m³ for fungi, but presented a larger dispersion pattern for the total heterotrophs, with the highest average (1000 CFU/m³). It was also investigated the correlation of the sampling period with the number of airborne microorganisms and with the environmental parameters (temperature and air humidity) through the principal components analysis. All indoor air samples distributions were very similar. The temperature and air humidity had no significant influence on the samples dispersion patterns.

The effect of a smoking ban introduction to environmental tobacco smoke exposure in Swiss hospitality workers : Abstracts of the 23rd Annual Conference of the International Society of Environmental Epidemiology (ISEE), September 13-16, 2011, Barcelona, Spain

Background and Aims: To protect the population from environmental tobacco smoke (ETS) Switzerland introduced a nationwide rather heterogeneous smoking ban in May 2010. The exposure situation of non-smoking hospitality workers before and after implementation of the new law is being assessed in a prospective cohort study. Methods: Exposure to ETS was measured using a novel method developed by the Institute for Work and Health in Lausanne. It is a passive sampler called MoNIC (Monitor of NICotine). The nicotine of the ETS is fixed onto a filter and transformed into salt of not volatile nicotine. Subsequently the number of passively smoked cigarettes is calculated. Badges were placed at the workplace as well as distributed to the participants for personal measuring. Additionally a salivary sample was taken to determine nicotine concentration. Results: At baseline Spearman's correlation between workplace and personal badge was 0.47. The average cigarette equivalents per day at the workplace obtained by badge significantly dropped from 5.1 (95%- CI: 2.4 to 7.9) at baseline to 0.3 (0.2 to 0.4) at first follow-up (n=29) three months later (p<0.001). For personal badges the number of passively smoked cigarettes declined from 1.5 (2.7 to 0.4) per day to 0.5 (0.3 to 0.8) (n=16).Salivary nicotine concentration in a subset of 13 participants who had worked on the day prior to the examination was 2.63 ng/ml before and 1.53 ng/ml after the ban (p=0.04). Spearman's correlation of salivary nicotine was 0.56 with workplace badge and 0.79 with personal badge concentrations. Conclusions: Workplace measurements clearly reflect the smoking regulation in a venue. The MoNIC badge proves to be a sensitive measuring device to determine personal ETS exposure and it is a demonstrative measure for communication with lay audiences and study participants as the number of passively smoked cigarettes is an easily conceivable result.

Increased neurotransmitter release at the neuromuscular junction in a mouse model of polyglutamine disease.

In Huntington's disease (HD), the expansion of polyglutamine (polyQ) repeats at the N terminus of the ubiquitous protein huntingtin (htt) leads to neurodegeneration in specific brain areas. Neurons degenerating in HD develop synaptic dysfunctions. However, it is unknown whether mutant htt impacts synaptic function in general. To investigate that, we have focused on the nerve terminals of motor neurons that typically do not degenerate in HD. Here, we have studied synaptic transmission at the neuromuscular junction of transgenic mice expressing a mutant form of htt (R6/1 mice). We have found that the size and frequency of miniature endplate potentials are similar in R6/1 and control mice. In contrast, the amplitude of evoked endplate potentials in R6/1 mice is increased compared to controls. Consistent with a presynaptic increase of release probability, synaptic depression under high-frequency stimulation is higher in R6/1 mice. In addition, no changes were detected in the size and dynamics of the recycling synaptic vesicle pool. Moreover, we have found increased amounts of the synaptic vesicle proteins synaptobrevin 1,2/VAMP 1,2 and cysteine string protein-α, and the SNARE protein SNAP-25, concomitant with normal levels of other synaptic vesicle markers. Our results reveal that the transgenic expression of a mutant form of htt leads to an unexpected gain of synaptic function. That phenotype is likely not secondary to neurodegeneration and might be due to a primary deregulation in synaptic protein levels. Our findings could be relevant to understand synaptic toxic effects of proteins with abnormal polyQ repeats.

Properties of ideal composite knots.

The shortest tube of constant diameter that can form a given knot represents the 'ideal' form of the knot. Ideal knots provide an irreducible representation of the knot, and they have some intriguing mathematical and physical features, including a direct correspondence with the time-averaged shapes of knotted DNA molecules in solution. Here we describe the properties of ideal forms of composite knots-knots obtained by the sequential tying of two or more independent knots (called factor knots) on the same string. We find that the writhe (related to the handedness of crossing points) of composite knots is the sum of that of the ideal forms of the factor knots. By comparing ideal composite knots with simulated configurations of knotted, thermally fluctuating DNA, we conclude that the additivity of writhe applies also to randomly distorted configurations of composite knots and their corresponding factor knots. We show that composite knots with several factor knots may possess distinct structural isomers that can be interconverted only by loosening the knot.

Quantization of energy and writhe in self-repelling knots

Probably the most natural energy functional to be considered for knotted strings is that given by electrostatic repulsion. In the absence of counter-charges, a charged, knotted string evolving along the energy gradient of electrostatic repulsion would progressively tighten its knotted domain into a point on a perfectly circular string. However, in the presence of charge screening self-repelling knotted strings can be stabilized. It is known that energy functionals in which repulsive forces between repelling charges grow inversely proportionally to the third or higher power of their relative distance stabilize self-repelling knots. Especially interesting is the case of the third power since the repulsive energy becomes scale invariant and does not change upon Mobius transformations (reflections in spheres) of knotted trajectories. We observe here that knots minimizing their repulsive Mobius energy show quantization of the energy and writhe (measure of chirality) within several tested families of knots.

CagA phosphorylation EPIYA-C motifs and the vacA i genotype in Helicobacter pylori strains of asymptomatic children from a high-risk gastric cancer area in northeastern Brazil

Helicobacter pylori infection is one of the most common infections worldwide and is associated with gastric diseases. Virulence factors such as VacA and CagA have been shown to increase the risk of these diseases. Studies have suggested a causal role of CagA EPIYA-C in gastric carcinogenesis and this factor has been shown to be geographically diverse. We investigated the number of CagA EPIYA motifs and the vacA i genotypes in H. pylori strains from asymptomatic children. We included samples from 40 infected children (18 females and 22 males), extracted DNA directly from the gastric mucus/juice (obtained using the string procedure) and analysed the DNA using polymerase chain reaction and DNA sequencing. The vacA i1 genotype was present in 30 (75%) samples, the i2 allele was present in nine (22.5%) samples and both alleles were present in one (2.5%) sample. The cagA-positive samples showed distinct patterns in the 3’ variable region of cagA and 18 of the 30 (60%) strains contained 1 EPIYA-C motif, whereas 12 (40%) strains contained two EPIYA-C motifs. We confirmed that the studied population was colonised early by the most virulent H. pylori strains, as demonstrated by the high frequency of the vacA i1 allele and the high number of EPIYA-C motifs. Therefore, asymptomatic children from an urban community in Fortaleza in northeastern Brazil are frequently colonised with the most virulent H. pylori strains.

Selective attention to emotional stimuli: What IQ and Openness do, and emotional intelligence does not

We examined how general intelligence, personality, and emotional intelligence-measured as an ability using the MSCEIT-predicted performance on a selective-attention task requiring participants to ignore distracting emotion information. We used a visual prime in which participants saw a pair of faces depicting emotions; their task was to focus on one of the faces (the target) while ignoring the other (the distractor). Next, participants categorized a string of letters (word or nonword), which was either congruent to the target or the distractor. The speed of response to categorizing the string was recorded. Given the emotional nature of the stimuli and the emotional information processing involved in the task, we were surprised to see that none of the MSCEIT branches predicted performance. However, general intelligence and openness to experience reduced response time.