Integració de tècniques per a la comprovació eficient de restriccions d'integritat en la generació de programari per entorns web

Estudi elaborat a partir d’una estada al Politecnico de Milano, Itàlia, entre gener i juny del 2006. Un dels principals objectius de l’Enginyeria del Programari és automatitzar el màxim possible el procés de desenvolupament del programari, reduint costos mitjançant la generació automàtica del programari a partir de la seva especificació. Per assolir-ho, entre altres, cal resoldre el problema de la comprovació eficient de restriccions, que són una part fonamental de l’especificació del programari. Aquest és precisament l’àmbit en què s’està desenvolupant una tesi que presentarà un mètode que poden integrar totes les eines generadores de codi per tal d’assolir una implementació eficient de les restriccions d’integritat. En l’actual fase del projecte s’ha treballat per validar el mètode de la tesi, optimitzant-lo pel cas específic de les aplicacions web i estendre’l per poder tractar també aplicacions basades en workflows. Pel que fa a l’optimització del mètode per aplicacions web, s’han definit una sèrie de paràmetres que permeten configurar la implementació del mètode tenint en compte les necessitats específiques de rendiment de cada aplicació web en particular. Respecte als workflows (cada cop més populars i que s’usen com a definició d’alt nivell per a les aplicacions a desenvolupar) s’ha estudiat quins són els tipus de restriccions que impliquen i com després es pot aplicar el mètode de la tesi sobre aquestes restriccions per tal de generar de forma eficient també les aplicacions basades en workflows.

Decoloración de tintes por lacasa

Informe de investigación realizado a partir de una estancia en el Instituto de Biotecnología Medioambiental de la Universidad Tecnológica de Graz, Austria, entre Julio y Agosto de 2006. Se ha estudiado la decoloración de varios tintes sintéticos de estructuras químicas diferentes (Rojo Congo, Azul de Naftol, Indigo Carmín, Lanaset Gris, Azul de Nilo) por la enzima lacasa inmovilizada. La inmovilización de la enzima lacasa se llevó a cabo sobre esferas de alúmina (Al2O3) de 3 mm de diámetro debido a la resistecia mecánica de este material. La lacasa y la proteína inmovilizada se determinaron como la diferencia entre las concentraciones iniciales y residuales (obtenidas en los lavados). El porcentaje de lacasa inmovilizada fue del 68% y la cantidad de proteína inmovilizada por gramo de soporte de 5,6 mg. La enzima lacasa inmovilizada fue capaz de decolorar tintes de diferente estructura sin la necesidad de añadir mediadores redox, lo cual la hace una enzima muy adecuada para su aplicación en la decoloración de efluentes procedentes de la industria textil. De todas formas, son necesarios más estudios para optimizar la técnica de inmovilización así como el proceso de decoloración. Es interesante destacar que aunque hay muchos estudios basados en la oxidación de tintes textiles por lacasa la mayoría utilizan la enzima libre y hay muy poca información disponible sobre la aplicación de lacasas inmovilizadas, por lo que el presente estudio constituye una aportación muy interesante y novedosa.

Expression of Staphylococcus aureus clumping factor A in Lactococcus lactis subsp. cremoris using a new shuttle vector.

Staphylococcus aureus harbors redundant adhesins mediating tissue colonization and infection. To evaluate their intrinsic role outside of the staphylococcal background, a system was designed to express them in Lactococcus lactis subsp. cremoris 1363. This bacterium is devoid of virulence factors and has a known genetic background. A new Escherichia coli-L. lactis shuttle and expression vector was constructed for this purpose. First, the high-copy-number lactococcal plasmid pIL253 was equipped with the oriColE1 origin, generating pOri253 that could replicate in E. coli. Second, the lactococcal promoters P23 or P59 were inserted at one end of the pOri253 multicloning site. Gene expression was assessed by a luciferase reporter system. The plasmid carrying P23 (named pOri23) expressed luciferase constitutively at a level 10,000 times greater than did the P59-containing plasmid. Transcription was absent in E. coli. The staphylococcal clumping factor A (clfA) gene was cloned into pOri23 and used as a model system. Lactococci carrying pOri23-clfA produced an unaltered and functional 130-kDa ClfA protein attached to their cell walls. This was indicated both by the presence of the protein in Western blots of solubilized cell walls and by the ability of ClfA-positive lactococci to clump in the presence of plasma. ClfA-positive lactococci had clumping titers (titer of 4,112) similar to those of S. aureus Newman in soluble fibrinogen and bound equally well to solid-phase fibrinogen. These experiments provide a new way to study individual staphylococcal pathogenic factors and might complement both classical knockout mutagenesis and modern in vivo expression technology and signature tag mutagenesis.

Predicting hematologic toxicity in patients undergoing radioimmunotherapy with 90Y-ibritumomab tiuxetan or 131I-tositumomab.

This study aimed at identifying clinical factors for predicting hematologic toxicity after radioimmunotherapy with (90)Y-ibritumomab tiuxetan or (131)I-tositumomab in clinical practice. Hematologic data were available from 14 non-Hodgkin lymphoma patients treated with (90)Y-ibritumomab tiuxetan and 18 who received (131)I-tositumomab. The percentage baseline at nadir and 4 wk post nadir and the time to nadir were selected as the toxicity indicators for both platelets and neutrophils. Multiple linear regression analysis was performed to identify significant predictors (P < 0.05) of each indicator. For both platelets and neutrophils, pooled and separate analyses of (90)Y-ibritumomab tiuxetan and (131)I-tositumomab data yielded the time elapsed since the last chemotherapy as the only significant predictor of the percentage baseline at nadir. The extent of bone marrow involvement was not a significant factor in this study, possibly because of the short time elapsed since the last chemotherapy of the 7 patients with bone marrow involvement. Because both treatments were designed to deliver a comparable bone marrow dose, this factor also was not significant. None of the 14 factors considered was predictive of the time to nadir. The R(2) value for the model predicting percentage baseline at nadir was 0.60 for platelets and 0.40 for neutrophils. This model predicted the platelet and neutrophil toxicity grade to within ±1 for 28 and 30 of the 32 patients, respectively. For the 7 patients predicted with grade I thrombocytopenia, 6 of whom had actual grade I-II, dosing might be increased to improve treatment efficacy. The elapsed time since the last chemotherapy can be used to predict hematologic toxicity and customize the current dosing method in radioimmunotherapy.

Scheduling of straddle carriers in a container terminal

Report for the scientific sojourn at the University of California at Berkeley between September 2007 to February 2008. The globalization combined with the success of containerization has brought about tremendous increases in the transportation of containers across the world. This leads to an increasing size of container ships which causes higher demands on seaport container terminals and their equipment. In this situation, the success of container terminals resides in a fast transhipment process with reduced costs. For these reasons it is necessary to optimize the terminal’s processes. There are three main logistic processes in a seaport container terminal: loading and unloading of containerships, storage, and reception/deliver of containers from/to the hinterland. Moreover there is an additional process that ensures the interconnection between previous logistic activities: the internal transport subsystem. The aim of this paper is to optimize the internal transport cycle in a marine container terminal managed by straddle carriers, one of the most used container transfer technologies. Three sub-systems are analyzed in detail: the landside transportation, the storage of containers in the yard, and the quayside transportation. The conflicts and decisions that arise from these three subsystems are analytically investigated, and optimization algorithms are proposed. Moreover, simulation has been applied to TCB (Barcelona Container Terminal) to test these algorithms and compare different straddle carrier’s operation strategies, such as single cycle versus double cycle, and different sizes of the handling equipment fleet. The simulation model is explained in detail and the main decision-making algorithms from the model are presented and formulated.

Navegación, guiado y control de vehículos aeroespaciales

El objetivo del proyecto es diseñar una plataforma de ensayos para la simulación de vuelos de vehículos aeroespaciales. La plataforma permitirá diseñar y evaluar los algoritmos de navegación, guiado y control de los vehículos aeroespaciales modelados en la plataforma de simulación, focalizando el trabajo de los ingenieros en el modelado de vehículos y en el desarrollo de sistemas de control digital. La memoria recoge las fases de un proyecto de ingeniería del software, describiendo el plan de proyecto, el análisis del sistema, la especificación de requisitos y el diseño del mismo.

Estimation of glomerular filtration rate in hospitalised patients: are we overestimating renal function?

QUESTIONS UNDER STUDY AND PRINCIPLES: Estimating glomerular filtration rate (GFR) in hospitalised patients with chronic kidney disease (CKD) is important for drug prescription but it remains a difficult task. The purpose of this study was to investigate the reliability of selected algorithms based on serum creatinine, cystatin C and beta-trace protein to estimate GFR and the potential added advantage of measuring muscle mass by bioimpedance. In a prospective unselected group of patients hospitalised in a general internal medicine ward with CKD, GFR was evaluated using inulin clearance as the gold standard and the algorithms of Cockcroft, MDRD, Larsson (cystatin C), White (beta-trace) and MacDonald (creatinine and muscle mass by bioimpedance). 69 patients were included in the study. Median age (interquartile range) was 80 years (73-83); weight 74.7 kg (67.0-85.6), appendicular lean mass 19.1 kg (14.9-22.3), serum creatinine 126 μmol/l (100-149), cystatin C 1.45 mg/l (1.19-1.90), beta-trace protein 1.17 mg/l (0.99-1.53) and GFR measured by inulin 30.9 ml/min (22.0-43.3). The errors in the estimation of GFR and the area under the ROC curves (95% confidence interval) relative to inulin were respectively: Cockcroft 14.3 ml/min (5.55-23.2) and 0.68 (0.55-0.81), MDRD 16.3 ml/min (6.4-27.5) and 0.76 (0.64-0.87), Larsson 12.8 ml/min (4.50-25.3) and 0.82 (0.72-0.92), White 17.6 ml/min (11.5-31.5) and 0.75 (0.63-0.87), MacDonald 32.2 ml/min (13.9-45.4) and 0.65 (0.52-0.78). Currently used algorithms overestimate GFR in hospitalised patients with CKD. As a consequence eGFR targeted prescriptions of renal-cleared drugs, might expose patients to overdosing. The best results were obtained with the Larsson algorithm. The determination of muscle mass by bioimpedance did not provide significant contributions.

Evaluation by ELISA of Anisakis simplex Larval Antigen Purified by Affinity Chromatography

In order to improve the specificity and sensitivity of the techniques for the human anisakidosis diagnosis, a method of affinity chromatography for the purification of species-specific antigens from Anisakis simplex third-stage larvae (L3) has been developed. New Zealand rabbits were immunized with A. simplex or Ascaris suum antigens or inoculated with Toxocara canis embryonated eggs. The IgG specific antibodies were isolated by means of protein A-Sepharose CL-4B beads columns. IgG anti-A. simplex and -A. suum were coupled to CNBr-activated Sepharose 4B. For the purification of the larval A. simplex antigens, these were loaded into the anti-A. simplex column and bound antigens eluted. For the elimination of the epitopes responsible for the cross-reactions, the A. simplex specific proteins were loaded into the anti-A. suum column. To prove the specificity of the isolated proteins, immunochemical analyses by polyacrylamide gel electrophoresis were carried out. Further, we studied the different responses by ELISA to the different antigenic preparations of A. simplex used, observing their capability of discriminating among the different antisera raised in rabbits (anti-A. simplex, anti-A. suum, anti-T. canis). The discriminatory capability with the anti-T. canis antisera was good using the larval A. simplex crude extract (CE) antigen. When larval A. simplex CE antigen was loaded into a CNBr-activated Sepharose 4B coupled to IgG from rabbits immunized with A. simplex CE antigen, its capability for discriminate between A. simplex and A. suum was improved, increasing in the case of T. canis. The best results were obtained using larval A. simplex CE antigen loaded into a CNBr-activated Sepharose 4B coupled to IgG from rabbits immunized with adult A. suum CE antigen. When we compared the different serum dilution and antigenic concentration, we selected the working serum dilution of 1/400 and 1 µg/ml of antigenic concentration.

Sistema per protegir la privadesa dels usuaris dels motors de cerca d'Internet

Actualment seria impensable la existència d'una xarxa d'informació com Internet sense la existència dels motors de cerca. Gràcies a ells, qualsevol usuari tenim al nostre abast la possibilitat d'obtenir informació sobre qualsevol tema només enviant una consulta des dels nostres ordinadors i rebent una resposta en qüestió de segons. Entre els usuaris dels cercadors d'Internet és molt habitual que les consultes facin referència a la empresa on treballem, la ciutat on vivim, els llocs que visitem, o inclús sobre problemes que tenim o malalties que patim amb l'objectiu de trobar opinions, consells o solucions. En resum, els usuaris, a través de les nostres consultes, proporcionem a diari als motors de cerca informació sobre nosaltres mateixos i sobre la nostra identitat que, juntament amb la adreça IP de la màquina des d'on fem les nostres consultes, ens fa perdre l'anonimat dins dels seus sistemes. Sobre aquesta problemàtica és del que tracta el present Projecte de Final de Carrera. En ell s'ha implementat una solució de la proposta especificada per Alexandre Viejo i Jordi Castellà-Roca en la seva publicació "Using social networks to disort users' profiles generated by web search engines", en la qual es documenten una sèrie de protocols de seguretat i d'algorismes de protecció i distribució que garanteixen la privacitat de la identitat dels usuaris dins dels motors de cerca aprofitant per aquest fi la relació existent entre aquests usuaris a través de les xarxes socials.

Generación automática de código con WebRatio

L'aportació d'aquest PFC consistirà en el desenvolupament d'un programa informàtic que verifiqui els fonaments teòrics i els algorismes proposats pels seus autors i proporcionar una eina per a l'experimentació.

Estructura de datos avanzadas : clases disjuntas, montículos, árboles de búsqueda

En aquest treball s'amplia la implementació en Java de les estructures de dades iniciada per Esteve Mariné, utilitzant el seu disseny bàsic. Concretament, s'ha fet la programació de les estructures de a) classes disjuntes, utilitzant els algorismes de llistes encadenades i amb estructura d'arbre, b) monticles, amb els algorismes binari, binomial i de Fibonacci, i c) arbres de recerca basats en l'algorisme d'arbre binari vermell-negre, el qual complementa els dos ja existents amb algorismes d'encadenaments i AVL. Per a examinar l'evolució de les estructures, s'ha preparat un visualitzador gràfic interactiu amb l'usuari que permet fer les operacions bàsiques de l'estructura. Amb aquest entorn és possible desar les estructures, tornar a reproduir-les i desfer i tornar a repetir les operacions fetes sobre l'estructura. Finalment, aporta una metodologia, amb visualització mitjançant gràfics, de l'avaluació comparativa dels algorismes implementats, que permet modificar els paràmetres d'avaluació com ara nombre d'elements que s'han de tractar, algorismes que s'han de comparar i nombre de repeticions. Les dades obtingudes es poden exportar per a analitzar-les posteriorment.

Collective intelligence

Estudio e implantación de algoritmos de recomendación, búsqueda, ranking y aprendizaje.

Added Value of Deep Sequencing Relative to Population Sequencing in Heavily Pre-Treated HIV-1-Infected Subjects.

OBJECTIVE: To explore the potential of deep HIV-1 sequencing for adding clinically relevant information relative to viral population sequencing in heavily pre-treated HIV-1-infected subjects. METHODS: In a proof-of-concept study, deep sequencing was compared to population sequencing in HIV-1-infected individuals with previous triple-class virological failure who also developed virologic failure to deep salvage therapy including, at least, darunavir, tipranavir, etravirine or raltegravir. Viral susceptibility was inferred before salvage therapy initiation and at virological failure using deep and population sequencing genotypes interpreted with the HIVdb, Rega and ANRS algorithms. The threshold level for mutant detection with deep sequencing was 1%. RESULTS: 7 subjects with previous exposure to a median of 15 antiretrovirals during a median of 13 years were included. Deep salvage therapy included darunavir, tipranavir, etravirine or raltegravir in 4, 2, 2 and 5 subjects, respectively. Self-reported treatment adherence was adequate in 4 and partial in 2; one individual underwent treatment interruption during follow-up. Deep sequencing detected all mutations found by population sequencing and identified additional resistance mutations in all but one individual, predominantly after virological failure to deep salvage therapy. Additional genotypic information led to consistent decreases in predicted susceptibility to etravirine, efavirenz, nucleoside reverse transcriptase inhibitors and indinavir in 2, 1, 2 and 1 subject, respectively. Deep sequencing data did not consistently modify the susceptibility predictions achieved with population sequencing for darunavir, tipranavir or raltegravir. CONCLUSIONS: In this subset of heavily pre-treated individuals, deep sequencing improved the assessment of genotypic resistance to etravirine, but did not consistently provide additional information on darunavir, tipranavir or raltegravir susceptibility. These data may inform the design of future studies addressing the clinical value of minority drug-resistant variants in treatment-experienced subjects.

Phylogenetic analysis of Biomphalaria tenagophila (Orbigny, 1835) (Mollusca: Gastropoda)

Mitochondrial DNA of Biomphalaria tenagophila, a mollusc intermediate host of Schistosoma mansoni in Brazil, was sequenced and characterised. The genome size found for B. tenagophila was 13,722 bp and contained 13 messenger RNAs, 22 transfer RNAs (tRNA) and two ribosomal RNAs (rRNA). In addition to sequencing, the mitochondrial DNA (mtDNA) genome organization of B. tenagophila was analysed based on its content and localization of both coding and non-coding regions, regions of gene overlap and tRNA nucleotide sequences. Sequences of protein, rRNA 12S and rRNA 16S nucleotides as well as gene organization were compared between B. tenagophila and Biomphalaria glabrata, as the latter is the most important S. mansoni intermediate host in Brazil. Differences between such species were observed regarding rRNA composition. The complete sequence of the B. tenagophila mitochondrial genome was deposited in GenBank (accession EF433576). Furthermore, phylogenetic relationships were estimated among 28 mollusc species, which had their complete mitochondrial genome deposited in GenBank, using the neighbour-joining method, maximum parsimony and maximum likelihood bootstrap. B. tenagophila was positioned at a branch close to B. glabrata and Pulmonata molluscs, collectively comprising a paraphyletic group, contrary to Opistobranchia, which was positioned at a single branch and constituted a monophyletic group.

Uncertainty Quantification Of A Semi-Supervised Support Vector Regression Reservoir Model

Uncertainty quantification of petroleum reservoir models is one of the present challenges, which is usually approached with a wide range of geostatistical tools linked with statistical optimisation or/and inference algorithms. Recent advances in machine learning offer a novel approach to model spatial distribution of petrophysical properties in complex reservoirs alternative to geostatistics. The approach is based of semisupervised learning, which handles both ?labelled? observed data and ?unlabelled? data, which have no measured value but describe prior knowledge and other relevant data in forms of manifolds in the input space where the modelled property is continuous. Proposed semi-supervised Support Vector Regression (SVR) model has demonstrated its capability to represent realistic geological features and describe stochastic variability and non-uniqueness of spatial properties. On the other hand, it is able to capture and preserve key spatial dependencies such as connectivity of high permeability geo-bodies, which is often difficult in contemporary petroleum reservoir studies. Semi-supervised SVR as a data driven algorithm is designed to integrate various kind of conditioning information and learn dependences from it. The semi-supervised SVR model is able to balance signal/noise levels and control the prior belief in available data. In this work, stochastic semi-supervised SVR geomodel is integrated into Bayesian framework to quantify uncertainty of reservoir production with multiple models fitted to past dynamic observations (production history). Multiple history matched models are obtained using stochastic sampling and/or MCMC-based inference algorithms, which evaluate posterior probability distribution. Uncertainty of the model is described by posterior probability of the model parameters that represent key geological properties: spatial correlation size, continuity strength, smoothness/variability of spatial property distribution. The developed approach is illustrated with a fluvial reservoir case. The resulting probabilistic production forecasts are described by uncertainty envelopes. The paper compares the performance of the models with different combinations of unknown parameters and discusses sensitivity issues.