Developing a distributed electronic health-record store for India

The DIGHT project is addressing the problem of building a scalable and highly available information store for the Electronic Health Records (EHRs) of the over one billion citizens of India

A requirement-driven approach for modelling software architectures

Throughout the software development lifecycle (SDLC) there are many pitfalls which software engineers have to face. Regardless of the methodology adopted, classic methodologies such as waterfall or more modern ones such as agile or scrum, defects can be injected in any phase of the SDLC. The main avenue to detect and remove defects is through Quality Assurance (QA) activities. The planned activities to detect, fix and remove defects occur later on and there is less effort spent in the initial phases of the SDLC to either detect, remove or prevent the injection of defects. In fact, the cost of detecting and fixing a defect in the later phases of the SDLC such as development, deployment, maintenance and support is much higher than detecting and fixing defects in the initial phases of the SDLC. The software architecture of the application also has an incidence on defect injection whereby the software architecture can be regarded asthe fundamental structures of a software system. The impact of detecting and fixing defects later on is exacerbated for software architecture which are distributed, such as service-oriented architectures or microservices. Thus, the aim of this research is to develop a semi-automated framework to translate requirements into design with the aim of reducing the introduction of defects from the early phases of the SDLC. Part of the objectives of this work is to conceptualize a design for architectural paradigms such as object-oriented and service-oriented programming. The proposed framework uses a series of techniques from Natural Language Processing (NLP) and a blend of techniques from intelligent learning systems such as ontologies and neural networks to partially automate the translation of requirements into a design. The novelty focuses on moulding the design into an architecture which is better adapted for distributed systems. The framework is evaluated with a case study where the design and architecture from the framework is compared to a design and architecture which was drawn by a software architect. In addition, the evaluation using a case study aims to demonstrate the use of the framework and how each individual design and architecture artefacts fair

The Ro/SSA Complex in Systemic Lupus Erythematosus Patients

In this work the involved mechanisms between Ro/SSA complex, composed also by the tripartite motif 21 (TRIM21alpha) and trove domain 2 (TROVE2) proteins, with respect to systemic lupus erythematosus (SLE) autoantibodies is studied. The work is divided in three chapters: I- In vitro and in silico analysis of the molecular recognition between lupus autoantibodies and TRIM21alpha Fc Receptor ; II- In vitro evidence of bipolar-bridged immune TROVE2 complexes in the pathogenesis of systemic lupus erythematosus and III- Label-free piezoelectric biosensor for prognosis and diagnosis of Systemic Lupus Erythematosus. Samples of lupic patients and health subjects were kindly provided by La Fe hospital, accordingly the required protocols. After its extraction and purification, the immunoglobulin samples were obtained to study in vitro protein interactions and the involved mechanism by using a quartz crystal microbalance with dissipation factor attributions, and dual polarization interferometry. Techniques such, polarization modulation infrared interferometry, x-ray photoelectron interferometry and contact angle measurement were used in order to characterize surfaces. Pre-steady-state analysis revealed an antibody bipolar bridging involved in both TRIM21alpha and TROVE2 proteins. Identification of the main immunodominant human linear epitope for TRIM21alpha was finely mapped using a series of overlapping synthetic polypeptides with a size of 21 amino acids. The epitopes recognised by autoantibodies for this protein spanned the linear sequence from the aminoacid 151 to 183, and a conformational epitope for SLE patients and healthy subjects, respectively. Autoantibodies from lupic patients targeted protein epitopes, allowing health subjects to be discriminated. Major Histocompatibility Complex Class-II binding peptide prediction results corroborated the sequence as the immunodominant linear epitope, mostly coded as the HLA DRB1*1304 allele for SLE patients, and HLA DRB1*0806 for controls. The subdominant epitope corresponded to the PRY-SPRY domain, recently known as mammalian Fc receptor. Finally, the TRIM21alpha protein structure was modeled by a new homology modeling, never before presented. From the TROVE2 protein, the major linear epitope recognized by autoantibodies correspond to the sequence from the aminoacid 160 to 210 for healthy subjects. However, the major epitope in SLE serum is undiscovered. We suggest that the difference between epitopes could correspond to a majority necrosis-induced specificity in SLE patients, and an apoptotic via in healthy subjects. TROVE2 showed the ability to bind to Fcs, depending on alkaline earth cations in solution. The results suggest that the TROVE2-TRIM21alpha binding is a calcium-dependent protein interaction linked through the MIDAS-like motif in the vWFA-like domain. Finally, a pratical consequence of all study was the development of label-free biosensing method, based in microbalance technology, for in vitro diagnostics of systemic lupus erythematosus patients, allowing the premature sensing of autoantibodies against TRIM21alpha and TROVE2 protein, in advance of the clinical illness symptoms appear.En este trabajo se ha estudiado el mecanismo involucrado entre el complejo Ro/SSA, compuesto también por las proteínas tripartite motif 21 alpha(TRIM21alpha;) y trove domain 2 (TROVE2) con respecto a autoanticuerpos de pacientes que tienen lupus eritematoso sistémico, en comparación con autoanticuerpos de personas sanas. El estudio comprende tres capítulos: I- Análisis in vitro e in silico del reconocimiento molecular entre autoanticuerpos de lupus y receptor TRIM21alpha; Fc; II- Evidencias in vitro de complejos inmunes TROVE2 bipolares con puentes en la patogénesis del lupus eritematoso sistémico y III- Biosensor piezoeléctrico libre de marcaje para el pronóstico y el diagnóstico del lupus eritematoso sistémico. Las muestras de pacientes lúpicos y personas sanas fueron proporcionadas por el hospital La Fe de acuerdo con los protocolos establecidos. Tras una etapa de extracción y purificación de las inmunoglobulinas fueron estudiadas la interacción de proteínas in vitro utilizando una microbalanza de cristal de cuarzo con atribución de factor de disipación e interferometria de polarización dual. Técnicas de caracterización como espectroscopía infrarroja de reflexión-absorción por modulación de la polarización, espectroscopía fotoelectrónica de rayos-x y análisis de ángulo de contacto fueron utilizadas con la finalidad de caracterizar superficies. El análisis del estado pre estacionario ha revelado un mecanismo de puente bipolar para las dos proteínas, TRIM21alpha; y TROVE2. Tras su identificación, el epítopo linear inmunodominante fue mapeado para TRIM21alpha;, utilizando una serie de polipéptidos sintéticos superpuestos de 21 aminoácidos. Los epitopos reconocidos por autoanticuerpos para esta proteína abarca la secuencia lineal a partir del aminoácido 151 hasta el 183 para epitopos de pacientes lúpicos y sujetos sanos, respectivamente. Autoanticuerpos de pacientes lúpicos reconocieron epítopos de proteínas, permitiendo la discriminación de pacientes sanos. Los resultados de la unión del Complejo Mayor de Histocompatibilidad clase II con el péptido de unión corroboraron la secuencia cómo el epítopo lineal inmunodominante, codificado como el alelo HLA DRB1 * 1304 para pacientes con LES y HLA DRB1 * 0806 para los controles. El epitopo subdominante corresponde al dominio PRY-SPRY, recientemente conocido receptor Fc de mamífero. Finalmente, la estructura de la proteína TRIM21alpha; fue determinada utilizando un nuevo modelo de homología no presentado antes. De la proteína TROVE2, el epitopo lineal immunodominante reconocido por los autoanticuerpos corresponde a la secuencia que pudiera corresponder del aminoácido 160 hasta 210 para sujetos sanos. Sin embargo, el epitopo mayoritario en sueros lúpicos no fue determinado. Se sugiere que la diferencia entre los epitopos se corresponde mayoritariamente a una necrosis-inducida en pacientes lúpicos, y a una vía apoptótica en pacientes sanos. TROVE2 presentó la habilidad de unirse a Fcs dependiendo de los cationes alcalinos presentes en la disolución. Los resultados sugieren que la unión TROVE2-TRIM21alpha; es dependiente de la interacción con calcio vinculada a través del motivo MIDAS en el dominio vWFA. Finalmente, una consecuencia práctica de todo el estudio fue el desarrollo de un biosensor libre de marcaje para diagnóstico in vitro de lupus eritematoso sistémico, permitiendo la detección prematura de autoanticuerpos anti TRIM21alpha; y anti TROVE2, varios años antes de la aparición de los síntomas clínicos de la enfermedad.En aquest treball s'ha estudiat el mecanisme involucrat en el complex Ro/SSA, compost per les proteïnes tripartite motif 21 (TRIM21alpha;) i trove domain 2 (TROVE2) respecte a autoanticossos de pacients que tenen lupus eritematós sistèmic, en comparació amb autoanticossos de persones sanes. L'estudi es divideix en tres capítols: : I- Anàlisi in vitro i in silico del reconeixement molecular entre autoanticossos de lupus i receptor TRIM21alpha; Fc; II- Evidències in vitro de complexos immunes TROVE2 bipolars amb ponts en la patogènesi del lupus eritematós sistèmic i III-Biosensor piezoelèctric lliure de marcatge per al pronòstic i el diagnòstic del lupus eritematós sistèmic. Les mostres de pacients lúpics y persones sanes van ser amablement proporcionades per l'hospital La Fe d'acord amb els protocols establerts. Després d'una etapa de purificació adequada, el pool de mostres de immunoglobulines va ser estudiat les interaccions in vitro de les proteïnes utilitzant una microbalança de cristall de quars amb atribució de factor de dissipació i interferometria de polarització dual. Tècniques de caracterització, como ara espectroscòpia de infraroja de reflexió-absorció per modulació de la polarització, espectroscòpia fotoelèctrica de rajos X i anàlisi d'angle de contacte van ser emprades amb per tal de caracteritzar les superfícies. L¿anàlisi de l`estat preestacionari ha revelat un mecanisme de pont bipolar que involucra les dos proteïnes, TRIM21alpha; i TROVE2. Una vegada identificat, va ser mapat l'epítop immunodominant lineal per a TRIM21alpha; emprant una sèrie de polipèptids sintètics superposats de 21 aminoàcids. Els epítops reconeguts per autoanticossos per a aquesta proteïna engloben la seqüència lineal a partir de l'aminoàcid 151 fins al 183 per a epítops de pacients lúpics y subjectes sans, respectivament. Autoanticossos de pacients lúpicos van reconèixer epítops de proteïnes, fet que va permetre la discriminació de pacients sans. Els resultats de la unió del Complexe Major de Histocompatibilitat classe II amb el pèptid de unió van corroborar la seqüència com l'epítop lineal immunodominant, codificat com l'al·lel HLA DRB1 * 1304 per a pacients amb LES i HLA DRB1 * 0806 per als controls. L'epítop subdominant correspon al domini PRY-SPRY, recentment conegut receptor Fc de mamífer. Finalment, l'estructura de la proteïna TRIM21alpha; va ser determinada utilitzant un nou model d'homologia no presentat abans. De la proteïna TROVE2, l'epítop lineal immunodominant reconegut pels autoanticossos correspon a la seqüència que pogués correspondre l'aminoàcid 160 fins al 210 per a subjectes sans. No obstant això, l'epítop majoritari en sèrums lúpics no va ser determinat. Es suggereix que la diferència entre els epítops es correspon majoritàriament a una necrosis induïda en pacients lúpics i a una via apoptòtica en pacients sans. TROVE2 va mostrar l'habilitat de unir-se a Fcs en funció dels cations alcalins presents en la dissolució. Els resultats suggereixen que la unió TROVE2-TRIM21alpha; depèn de la interacció amb calci vinculada a través del motiu MIDAS en el domini vWFA. Finalment, la conseqüència pràctica de tot l'estudi va ser el desenvolupament d'un biosensor sense marcatge per al diagnòstic in vitro de lupus eritematós sistèmic, el qual permet la detecció prematura d'autoanticossos cap a les proteïnes TRIM21alpha; i TROVE2 anys abans de l'aparició dels símptomes clínics de la malaltia.Do Nascimento, NM. (2017). The Ro/SSA Complex in Systemic Lupus Erythematosus Patients [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/80534TESI

Sedimentology and geochemistry of gas hydrate rich sediments from the Oregon margin (Ocean Drilling Program Leg 204)

Gas hydrates have been recently recognized as a key factor affecting a number of global processes such as the climatic change, sea floor stability, etc. In this thesis we present the multidisciplinary study of gas hydrate rich sediments recovered during ODP Leg 204. The main objective of this thesis is to study how the textural characteristics of marine sediments can affect the main pathways and intensity of fluid flow and how fluid flow determines the distribution of gas hydrates in the continental margins, as well as the main geochemical processes that occur during early diagenesis.To reach these objectives, a complete sedimentary and geochemical study of 581 sediment samples from southern Hydrate Ridge was carried out. The methods and techniques that were applied include: complete textural analyses, mineralogy, physical properties and geochemistry.The southern Hydrate Ridge sediments are mainly made up of four lithofacies defined as: hemipelagites, turbidites, ash layers and debrites. Mass&#8208;transport deposits such as turbidites and debrites are more abundant in Lithostratigraphic Unit III and II, as well as in Lithostratigraphic Unit IA in the slope basin of southern Hydrate Ridge. Some increasing trends with depth can be observed in the smectite content in the clay mineral assemblages. These features suggest that the transport in suspension of fine sediments through the California Current was more effective during the Pliocene and early Pleistocene period. Bedload transport of coarse material from local and distal areas was more effective during the middle Pleistocene and Holocene due to the tectonic reactivation of the southern Hydrate Ridge uplift. During the Pleistocene and owing to the pervasive fluctuation of sealevel, gas hydrate dissociation together with the seismic movements in the Oregon margin seems a plausible triggering mechanism for mass&#8208;movements.The results presented here confirm that the sedimentation patterns in the Hydrate Ridge region are controlled by climate and tectonic parameters such as the regional intensity of the California Current or the local tectonic movements that lead to the uplift of the Ridge. These parameters mainly control the clay mineral distribution as well as the sedimentary facies that were produced.The sedimentary fabric of gas hydrate&#8208;rich intervals is disturbed during core recovery due to gas hydrate dissociation. The two main disturbance fabrics generated through this process are mousselike and soupy. The gas hydrate&#8208;rich sediments analyzed for this thesis are coarser grained in respect to the hemipelagite sediments. The coarse&#8208;grained layers such as turbidites and ash layers could act as conduits for fluids in the southern Hydrate Ridge region because of their higher porosity and permeability. In this context, methane&#8208;rich fluids migrate through these layers from deep in the sedimentary sequence and into the gas hydrate stability zone. A number of barium fronts have been identified in southern Hydrate Ridge sediments and interstitial waters. Barite fronts were formed as a result of the barite recycling process during early diagenesis, which is controlled by the availability of methane&#8208;rich fluids, in situ decomposition of organic matter and the sulphate gradient. Modelling of these data shows that these processes were active at southern Hydrate Ridge for a period of up to one thousand years.A number of geochemical and sedimentological processes are proposed in this thesis as plausible mechanisms to allow the survival of the barite fronts during diagenesis. The sedimentary texture plays an important role in controlling the major fluid flow pathways in the continental margins. The temporal evolution of the fluid flow can be studied in a given area through the distribution of the mineral phases that form during early diagenesis, as well as the interstitial water composition.EXTRACTE DE TESI:Aquesta tesi integra els resultats de l'anàlisi sedimentológica i geoquímica de sediment marins rics en hidrats de gas, recuperats durant la campanya "Ocean Drilling Program" Leg 204 en el marge d'Oregon (USA). L'objectiu principal d'aquest estudi és conèixer les característiques sedimentàries que afecten el fluxe de fluids i gasos a través del sediment i com els fluids afecten la distribució d'hidrats de gas en aquesta àrea, així com alguns processos geoquímics que operen durant la diagènesi inicial. Els mètodes i tècniques aplicats inclouen l'anàlisi de sedimentològia, mineralogia, susceptibilitat magnètica i geoquímica.Els sediments de southern Hydrate Ridge estan formats per 4 litofàcies: hemipelagita, turbidita, cendra volcànica i debrita. La sedimentació està controlada per factors climàtics i tectònics com ara la intensitat del corrent oceànic Californià o moviments tectònics locals. Aquests paràmetres exerceixen un control fonamental en la distribució dels minerals d'argila i de les fàcies sedimentàries en el marge continental. La seva evolució des del Pliocè és discutida en aquesta tesi.Els sediments analitzats rics en hidrats de gas són més grollers que els sediments hemipelàgics. Els sediments més grollers actuen com a conductes preferents per a la circulació de fluids degut a la seva porositat i permeabilitat. En aquest context, fluids rics en metà migren des dels sediments profunds cap a la zona d'estabilitat dels hidrats de gas, on possibiliten la seva formació.Diversos fronts de barita han estat identificats en els sediments de southern Hydrate Ridge. Es formen com a resultat del reciclatge de barita durant la diagènesi inicial, controlada per la presència de fluids rics en metà, la degradació de matèria orgànica i la presència de sulfat. La modelització de les dades obtinguda mostra que aquest procés va ser actiu durant un període de >1000 anys. En aquesta tesi, es discuteixen els possibles processos geoquímics i sedimentaris que permetrien la supervivència de la barita durant la diagènesis.La textura sedimentària juga un paper molt important en el flux de fluids als marges continentals. La seva evolució temporal en una àrea determinada pot ser deduïda estudiant les fases minerals que es formen durant la diagènesi.</i

A comparison of the CAR and DAGAR spatial random effects models with an application to diabetics rate estimation in Belgium

When hierarchically modelling an epidemiological phenomenon on a finite collection of sites in space, one must always take a latent spatial effect into account in order to capture the correlation structure that links the phenomenon to the territory. In this work, we compare two autoregressive spatial models that can be used for this purpose: the classical CAR model and the more recent DAGAR model. Differently from the former, the latter has a desirable property: its ρ parameter can be naturally interpreted as the average neighbor pair correlation and, in addition, this parameter can be directly estimated when the effect is modelled using a DAGAR rather than a CAR structure. As an application, we model the diabetics rate in Belgium in 2014 and show the adequacy of these models in predicting the response variable when no covariates are available

A Statistical Approach to the Alignment of fMRI Data

Multi-subject functional Magnetic Resonance Image studies are critical. The anatomical and functional structure varies across subjects, so the image alignment is necessary. We define a probabilistic model to describe functional alignment. Imposing a prior distribution, as the matrix Fisher Von Mises distribution, of the orthogonal transformation parameter, the anatomical information is embedded in the estimation of the parameters, i.e., penalizing the combination of spatially distant voxels. Real applications show an improvement in the classification and interpretability of the results compared to various functional alignment methods

A Textbook of Advanced Oral and Maxillofacial Surgery

The scope of OMF surgery has expanded; encompassing treatment of diseases, disorders, defects and injuries of the head, face, jaws and oral cavity. This internationally-recognized specialty is evolving with advancements in technology and instrumentation. Specialists of this discipline treat patients with impacted teeth, facial pain, misaligned jaws, facial trauma, oral cancer, cysts and tumors; they also perform facial cosmetic surgery and place dental implants. The contents of this volume essentially complements the volume 1; with chapters that cover both basic and advanced concepts on complex topics in oral and maxillofacial surgery