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.

Els germans Petrides a Barcelona : dos trompistes bohemis al Teatre de la Santa Creu (1794-1798)

Aquest treball documenta l’estada a Barcelona, entre el 1794 i 1798, dels germans Joseph i Peter Petrides, trompistes nascuts a Praga. L’excepcional trajectòria d’ambdós a la capital catalana, com a membres de l’orquestra del Teatre de la Santa Creu i com a solistes destacats, il·lustra el desenvolupament de l’ofici de músic a la ciutat durant l’última dècada del segle XVIII.

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. 

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.

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.

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.

Impaired adipose tissue expandability and lipogenic capacities as ones of the main causes of metabolic disorders.

Obesity is considered a major health problem. However, mechanisms involved and its comorbidities are not elucidated. Recent theories concerning the causes of obesity have focused on a limit to the functional capacity of adipose tissue, comparing it with other vital organs. This assumption has been the central point of interest in our laboratory. We proposed that the failure of adipose tissue is initiated by the difficulty of this tissue to increase its cellularity due to excess in fat contribution, owing to genetic or environmental factors. Nevertheless, why the adipose tissue reduces its capacity to make new adipocytes via mesenchymal cells of the stroma has not yet been elucidated. Thus, we suggest that this tissue ceases fulfilling its main function, the storage of excess fat, thereby affecting some of the key factors involved in lipogenesis, some of which are reviewed in this paper (PPARγ, ROR1, FASN, SCD1, Rab18, BrCa1, ZAG, and FABP4). On the other hand, mechanisms involved in adipose tissue expandability are also impaired, predominating hypertrophy via an increase in apoptosis and a decrease in adipogenesis and angiogenesis. However, adipose tissue failure is only part of this great orchestra, only a chapter of this nightmare.

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.

Measuring Pavement Profile at the Slip-Form Paver, May 2005

Pavement profile or smoothness has been identified nationally as a good measure of highway user satisfaction. This has led highway engineers to measure profiles of both operating and new highways. Operational highway profiles are often measured with high-speed inertial profilers. New highway profiles are usually measured with profilographs in order to establish incentives or disincentives for pavement construction. In most cases, these two processes do not measure the same value from the “cradle to grave” life of pavements. In an attempt to correct the inconsistency between measuring techniques, lightweight profilers intended to produce values to be used for construction acceptance are being made that measure the same profile as high-speed inertial profilers. Currently, two profiler systems have been identified that can measure pavement profile during construction. This research has produced a field evaluation of the two systems. The profilers evaluated in this study are able to detect roughness in the final profile, including localized roughness and roughness at joints. Dowel basket ripple is a significant source of pavement surface roughness. The profilers evaluated in this study are able to detect dowel basket ripple with enough clarity to warn the paving crew. String-line disturbances degrade smoothness. The profilers evaluated in this study are able to detect some string-line disturbances during paving operations. The profilers evaluated in this study are not currently able to produce the same absolute International Roughness Index (IRI) values on the plastic concrete that can be measured by inertial profilers on the hardened concrete. Construction application guidelines are provided.

Stringless Portland Cement Concrete Paving, February 2004

This report describes results from a study evaluating the use of stringless paving using a combination of global positioning and laser technologies. CMI and Geologic Computer Systems developed this technology and successfully implemented it on construction earthmoving and grading projects. Concrete paving is a new area for considering this technology. Fred Carlson Co. agreed to test the stringless paving technology on two challenging concrete paving projects located in Washington County, Iowa. The evaluation was conducted on two paving projects in Washington County, Iowa, during the summer of 2003. The research team from Iowa State University monitored the guidance and elevation conformance to the original design. They employed a combination of physical depth checks, surface location and elevation surveys, concrete yield checks, and physical survey of the control stakes and string line elevations. A final check on profile of the pavement surface was accomplished by the use of the Iowa Department of Transportation Light Weight Surface Analyzer (LISA). Due to the speed of paving and the rapid changes in terrain, the laser technology was abandoned for this project. Total control of the guidance and elevation controls on the slip-form paver were moved from string line to global positioning systems (GPS). The evaluation was a success, and the results indicate that GPS control is feasible and approaching the desired goals of guidance and profile control with the use of three dimensional design models. Further enhancements are needed in the physical features of the slipform paver oil system controls and in the computer program for controlling elevation.