Dynamic estimation of three-dimensional cerebrovascular deformation from rotational angiography

Purpose: The objective of this study is to investigate the feasibility of detecting and quantifying 3D cerebrovascular wall motion from a single 3D rotational x-ray angiography (3DRA) acquisition within a clinically acceptable time and computing from the estimated motion field for the further biomechanical modeling of the cerebrovascular wall. Methods: The whole motion cycle of the cerebral vasculature is modeled using a 4D B-spline transformation, which is estimated from a 4D to 2D + t image registration framework. The registration is performed by optimizing a single similarity metric between the entire 2D + t measured projection sequence and the corresponding forward projections of the deformed volume at their exact time instants. The joint use of two acceleration strategies, together with their implementation on graphics processing units, is also proposed so as to reach computation times close to clinical requirements. For further characterizing vessel wall properties, an approximation of the wall thickness changes is obtained through a strain calculation. Results: Evaluation on in silico and in vitro pulsating phantom aneurysms demonstrated an accurate estimation of wall motion curves. In general, the error was below 10% of the maximum pulsation, even in the situation when substantial inhomogeneous intensity pattern was present. Experiments on in vivo data provided realistic aneurysm and vessel wall motion estimates, whereas in regions where motion was neither visible nor anatomically possible, no motion was detected. The use of the acceleration strategies enabled completing the estimation process for one entire cycle in 5-10 min without degrading the overall performance. The strain map extracted from our motion estimation provided a realistic deformation measure of the vessel wall. Conclusions: The authors' technique has demonstrated that it can provide accurate and robust 4D estimates of cerebrovascular wall motion within a clinically acceptable time, although it has to be applied to a larger patient population prior to possible wide application to routine endovascular procedures. In particular, for the first time, this feasibility study has shown that in vivo cerebrovascular motion can be obtained intraprocedurally from a 3DRA acquisition. Results have also shown the potential of performing strain analysis using this imaging modality, thus making possible for the future modeling of biomechanical properties of the vascular wall.

Distributed all-atom simulations of intrinsically unstructured proteins

The Computational Biophysics Group at the Universitat Pompeu Fabra (GRIB-UPF) hosts two unique computational resources dedicated to the execution of large scale molecular dynamics (MD) simulations: (a) the ACMD molecular-dynamics software, used on standard personal computers with graphical processing units (GPUs); and (b) the GPUGRID. net computing network, supported by users distributed worldwide that volunteer GPUs for biomedical research. We leveraged these resources and developed studies, protocols and open-source software to elucidate energetics and pathways of a number of biomolecular systems, with a special focus on flexible proteins with many degrees of freedom. First, we characterized ion permeation through the bactericidal model protein Gramicidin A conducting one of the largest studies to date with the steered MD biasing methodology. Next, we addressed an open problem in structural biology, the determination of drug-protein association kinetics; we reconstructed the binding free energy, association, and dissaciociation rates of a drug like model system through a spatial decomposition and a Makov-chain analysis. The work was published in the Proceedings of the National Academy of Sciences and become one of the few landmark papers elucidating a ligand-binding pathway. Furthermore, we investigated the unstructured Kinase Inducible Domain (KID), a 28-peptide central to signalling and transcriptional response; the kinetics of this challenging system was modelled with a Markovian approach in collaboration with Frank Noe’s group at the Freie University of Berlin. The impact of the funding includes three peer-reviewed publication on high-impact journals; three more papers under review; four MD analysis components, released as open-source software; MD protocols; didactic material, and code for the hosting group.

Taking on new challenges in multi-word unit processing for Machine Translation

This paper discusses the qualitativecomparative evaluation performed on theresults of two machine translation systemswith different approaches to the processing ofmulti-word units. It proposes a solution forovercoming the difficulties multi-word unitspresent to machine translation by adopting amethodology that combines the lexicongrammar approach with OpenLogos ontologyand semantico-syntactic rules. The paper alsodiscusses the importance of a qualitativeevaluation metrics to correctly evaluate theperformance of machine translation engineswith regards to multi-word units.

ParallelKnoppix - Rapid deployment of a linux cluster for MPI parallel processing using non-dedicated computers

This note describes ParallelKnoppix, a bootable CD that allows creation of a Linux cluster in very little time. An experienced user can create a cluster ready to execute MPI programs in less than 10 minutes. The computers used may be heterogeneous machines, of the IA-32 architecture. When the cluster is shut down, all machines except one are in their original state, and the last can be returned to its original state by deleting a directory. The system thus provides a means of using non-dedicated computers to create a cluster. An example session is documented.

Estudi sobre equalització electrònica per a sistemes de comunicació per fibra òptica

Estudi realitzat a partir d’una estada a Bell Labs (Lucent Technologies), New Jersey (Estats Units), entre el 15 de setembre de 2005 i el 15 de gener de 2006. Els sistemes de transmissió per fibra òptica fonamenten les principals xarxes de comunicacions. A mesura que la demanda d’ample de banda per usuari creixi, seran necessaris nous sistemes que siguin capaços de cobrir les necessitats a curt i llarg termini. La tecnologia dels sistemes òptics limita fortament la complexitat dels sistemes de transmissió / recepció en comparació, per exemple, als sistemes d’ones de ràdio. La tendència és la de dissenyar sistemes avançats amb detecció directa i mirar d’aplicar tècniques bàsiques de processat del senyal. Una d’aquestes tècniques és l’equalització electrònica, és a dir, fer ús de les tècniques de processament del senyal per tal de compensar la distorsió introduïda pel canal, deguda per una o diverses degradacions típiques: dispersió cromàtica, efectes no lineals, dispersió del mode de polarització (PMD) ... Dins d’un entorn comercial d’empresa, s’ha avaluat el funcionament dels sistemes d’equalització FFE-DFE aixi com MLSE en presència de dispersió cromàtica i/o dispersió del mode de polarització (PMD) en transmissions NRZ/RZ.

Desenvolupament de mesures per comparar transculturalment xarxes personals (USA i Estats Units)

Estudi elaborat a partir d’una estada a la Universitat de Florida durant Abril i Maig de 2006. “Application to Immigrant Populations in South Florida and Northeastern Spain" ha permès recollir les xarxes personals d’immigrants en els dos països mitjançant un qüestionari implementat amb un software desenvolupat ex professo per recollir i presentar visualment les dades. Es van revisar i assemblar les entrevistes i qüestionaris realitzats a Catalunya i a Estats Units (Miami i Nova York, especialment). Fins al moment s’han revisat i analitzat uns 450 casos. Un cop depurada i analitzada la informació obtinguda s’ha pogut disposar per primer cop de mesures globals pels diferents col•lectius estudiats. L'objectiu global del projecte és entendre les implicacions que les estructures de les xarxes personals tenen en relació a un conjunt de conductes (de salut, d'ús de la llengua, etx) i les autoconcepcions. En aquest sentit era necessari desenvolupar un seguit de mesures que permetessin comparar i documentar la variació de les estructures de les xarxes personals a diferents cultures, nivells socioeconòmics, gènere, religió, etc. i incorporar-les com a variables independents als models explicatius.En aquest moments s’està desenvolupant un índex basat en variables estructurals (número de components de la xarxa, densitat, grau d’intermediació, etc.) i variables de composició (proporció de persones diferents del país d’origen, entre d'altres). La idea és disposar d’un índex d’heterogeneïtat de la xarxa social comparable entre els diferents col•lectius. Malgrat que el treball continua, la principal conclusió a la que s’ha arribat és que al menys a Espanya a mida que passa el temps augmenta el nivell d’heterogeneïtat de les xarxes personals. És a dir, que desprès d’un ràpid procés de canvi i una fase de transnacionalitat la tendència és a reduir aquest nivell (pels costos socials i econòmics que comporta) depenent, naturalment, de factors com l’origen temporal (primera onada o successives), el tipus de col•lectiu i el sexe.

Effect of high pressure processing on the microbiology of skin-vacuum packaged sliced meat products: cooked pork ham, dry cured pork ham and marinated beef loin

High hydrostatic pressure is being increasingly investigated in food processing. It causes microbial inactivation and therefore extends the shelf life and enhances the safety of food products. Yeasts, molds, and vegetative cells of bacteria can be inactivated by pressures in the range of 200 to 700 MPa. Microorganisms are more or less sensitive to pressure depending on several factors such as type, strain and the phase or state of the cells. In general, Gram-positive organisms are usually more resistant than Gram-negative. High pressure processing modifies the permeability of the cell membrane, the ion exchange and causes changes in morphology and biochemical reactions, protein denaturations and inhibition of genetic mechanisms. High pressure has been used successfully to extend the shelf life of high-acid foods such as refrigerated fruit juices, jellies and jams. There is now an increasing interest in the use of this technology to extend the shelf life of low-acid foods such as different types of meat products.

Bioequivalence of meat products treated with high pressure processing

The effects of high pressure on the composition of food products have not been evaluated extensively. Since, it is necessary to take in consideration the possible effects in basis to the changes induced in the bio molecules by the application of high pressures. The main effect on protein is the denaturation, because the covalent bonds are not affected; however hydrogen bonding, hydrophobic and intermolecular interactions are modified or destroyed. 1 High pressure can modify the activity of some enzymes. If this is done the proteolysis and lipolysis could be more or less intense and the content of free amino acids and fatty acids will be different. This could be related to the bioavailability of these compounds. Low pressures (100 MPa) have been shown to activate some enzymes (monomeric enzymes). Higher pressures induce loss of the enzyme activity. However some enzymes are very stable (ex. Lipase ~ 600 - 1000 MPa). Lipoxygenase is less stable, and there is little information about the effects on antioxidant enzymes. Other important issue is the influence of high pressure on oxidation susceptibility. This could modify the composition of lipids if the degree of the oxidation would have been higher or lower than in the traditional product. Pressure produces the damage of cell membranes favouring the contact between substrates and enzymes, exposure to oxidation of membrane fatty acids and loos of the efficiency of vitamin E. These effects can also affect to protein oxidation. In this study different compounds were analysed to establish the differences between non-treated and high-pressure treated products.

Desenvolupament de dipòsits institucionals als Estats Units a partir de l'inici del 2005

Aquest article analitza la situació dels dipòsits institucionals als EUA mitjançant una enquesta realitzada per la CNI a les seves institucions acadèmiques. Amb aquesta enquesta s'obtingué informació sobre el grau d'implementació dels dipòsits i la seva extensió, així com del tipus de materials. A més, va servir per conèixer l'opinió de les institucions sobre els dipòsits, i va quedar palès que la major part de les que no en posseeixen, tenen previst posar-ne un en funcionament, tot i que els preocupi el cost de manteniment. L'article també tracta la responsabilitat administrativa dels dipòsits, les polítiques que els gestionen, la possibilitat de compartir dipòsits entre institucions i la procedència dels materials que contenen.

Some variational problems from image processing

"Vegeu el resum a l'inici del document del fitxer adjunt."

Uranium reserve, nuclear fuel cycle delusion, CO2 emission from the sea, and electricity supply: reflections after the fuel meltdown of Fukushima nuclear power units

The Great Tohoku-Kanto earthquake and resulting tsunami has brought considerable attention to the issue of the construction of new power plants. We argue in this paper, nuclear power is not a sustainable solution to energy problems. First, we explore the stock of uranium-235 and the different schemes developed by the nuclear power industry to exploit this resource. Second, we show that these methods, fast breeder and MOX fuel reactors, are not feasible. Third, we show that the argument that nuclear energy can be used to reduce CO2 emissions is false: the emissions from the increased water evaporation from nuclear power generation must be accounted for. In the case of Japan, water from nuclear power plants is drained into the surrounding sea, raising the water temperature which has an adverse affect on the immediate ecosystem, as well as increasing CO2 emissions from increased water evaporation from the sea. Next, a short exercise is used to show that nuclear power is not even needed to meet consumer demand in Japan. Such an exercise should be performed for any country considering the construction of additional nuclear power plants. Lastly, the paper is concluded with a discussion of the implications of our findings.

Diseño y Desarrollo de un cliente Web Processing Services (WPS) para gvSIG

Configuració d'un entorn de desenvolupament en el IDE Eclipse. Introducció als SIG. Usos, utilitats i exemples. Conèixer la eina gvSIG. Conèixer els estàndards més estesos de l'Open Geospatial Consortium (OGC) i en especial del Web Processing Services. Analitzar, dissenyar i desenvolupar un client capaç de consumir serveis wps.

Diseño y Desarrollo de un cliente Web Processing Service (WPS) para gvSIG

Estudi dels estàndards definits per l'Open Geospatial Consortium, i més concretament en l'estàndard Web Processing Service (wps). Així mateix, ha tingut una component pràctica que ha consistit en el disseny i desenvolupament d'un client capaç de consumir serveis Web creats segons wps i integrat a la plataforma gvSIG.

Desenvolupament d'un Videojoc en 3D basat en OPENGL

L'objectiu d'aquest treball ha estat desenvolupar un videojoc en un entorn de tres dimensions utilitzant les llibreries gràfiques d'OpenGL. Aquesta aplicació s'ha desenvolupat en Java, cosa que dóna més independència perquè aquesta és precisament la filosofia d'aquest llenguatge de programació.