XML is a widely used data exchange format. The verbose nature of XML leads to the requirement to efficiently store and process this type of data using compression. Various general-purpose transforms and compression techniques exist that can be used to transform and compress XML data. More compact alternatives to XML data have been developed, namely JSON due to the verbosity of XML data. Similarly, there is a requirement to efficiently store and process SMILES data used in Chemoinformatics. General-purpose transforms and compressors can be used to compress this type of data to a certain extent, however, these techniques are not specific to SMILES data. The primary contribution of this research is to provide developers that use XML, JSON or SMILES data, with key knowledge of the best transformation techniques to use with certain types of data, and which compression techniques would provide the best compressed output size and processing times, depending on their requirements. The main study in this thesis, investigates the extent of which using data transforms prior to data compression can further improve the compression of XML and JSON data. It provides a comparative analysis of applying a variety of data transform and data transform variations, to a number of different types of XML and JSON equivalent datasets of various sizes, and applying different general-purpose compression techniques over the transformed data. A case study is also conducted, to investigate data transforms prior to compression to improve the compression of data within a data-specific domain. / The files of software accompanying this thesis are unable to be presented online with the thesis.

En plongée, lors d’une décompression, une partie des gaz dissous dans l’organisme est éliminée sous formede bulles qui peuvent être à l’origine d’accidents parfois sévères. Des modèles mathématiques permettentde déterminer des procédures de décompression par paliers fiables mais ne s’appliquent que pour certainesconfigurations de plongée (profondeur, durée, gaz respirés). Une extrapolation de ces modèles à denouveaux types d’exposition comme la plongée profonde aux mélanges est actuellement hasardeuse. Onsuppose ici qu’une modélisation biophysique des mécanismes de la décompression doit apporter dessolutions préventives plus sures, même pour des expositions moins explorées combinant azote et hélium.Deux modèles ont été élaborés pour la prévention des accidents articulaires et neurologiques, formesd’accident les plus fréquentes. Ils ont été corrélés à partir de bases de données et d’analyses de risqueexistantes. Tous deux permettent de représenter l’apparition de symptômes tardifs. Pour l’accidentarticulaire, on montre 1/ l’impact de la diffusion intra-tissulaire (entre un tendon et son voisinage) de gazinerte sur la dynamique d’amplification de la phase gazeuse générée 2/ une augmentation quantifiable durisque d’accident avec le volume de gaz généré 3/ une faible efficacité des paliers 4/ une efficacité modéréede la respiration d’oxygène pur aux paliers proches de la surface. Pour les accidents neurologiques, lemodèle global proposé permet d’estimer le volume instantané des microbulles formées dans les tissus(muscles et graisses) et transférées (via le système lymphatique par ex) dans le sang veineux de retour. Lasurcharge du filtre pulmonaire par les bulles est supposée être un événement précurseur dans la genèse del’accident. La méthode de corrélation du modèle, originale, utilise notamment des campagnes d’écoutes debulles circulantes par système Doppler après plongées, dont une dédiée à cette thèse. Il ressort de cesinvestigations que I/ le risque d’accident peut être relié au volume des bulles transféré dans le sang sur unepériode donnée II/ l’introduction de paliers profonds ne diminue pas le risque III/ la respiration d’oxygènepur aux paliers est très efficace pour réduire ce risque. Un deuxième modèle neurologique dédié à laprévention des accidents médullaires se produisant rapidement après la décompression et à la déterminationdes premiers paliers requis est aussi proposé. L’ensemble de ces trois modélisations offre des perspectivesde prévention intéressantes. / During a scuba diving decompression, a part of the gas that is dissolved in the body is eliminated throughbubbles that can generate potentially severe forms of decompression sickness (DCS). Known mathematicalmodels allow the determination of safe decompression procedures by stages but can only be applied for alimited range of diving configurations (pressure, duration, breathing gas). An extrapolation of these modelsto new expositions such as deep/short dives using mixtures is currently hazardous. In the presented work itis deemed that a biophysical modeling of the decompression mechanisms can produce safer preventivesolutions even for less explored expositions combining nitrogen and helium. Two models have beendeveloped for the prevention of articular and neurological DCS, which are the most frequent forms ofinjury. Existing database and risk analyses have been used to correlate the models. Both predict potentialdelays for the occurrence of DCS symptoms after a decompression. For the articular model it is shown that1/ the intratissular diffusion of inert gases between a target tendon and its neighborhood impacts theamplification dynamics of the generated gas phase 2/ the more the generated gas volume, the bigger theDCS risk 3/ stages of short and moderate durations have a low efficiency 4/ the efficiency of pure oxygenbreathing in order to reduce the risk during the shallow stages is moderated. For neurological DCS, theproposed global model allows estimation of the instantaneous volume of microbubbles that are formed intissues (muscles and adipose tissues) and that are transferred via the lymphatic system for instance in thevenous blood. The overload of the pulmonary filter by bubbles is assumed to be a primary event in the DCSpathogenesis. The original model correlation method uses in particular the recording of circulating bubblessignals through Doppler detections campaigns. One of these campaigns is dedicated to the presented thesiswork. The analysis leads to the following conclusions: I/ the DCS risk is linked to the total bubbles volumethat is transferred into the blood over a given period II/ the introduction of deep stages does not decreasethe risk III/ the breathing of pure oxygen during the shallow stages is very efficient in reducing this risk. Asecond neurological model is proposed: it is dedicated to the prevention of spinal cord DCS forms whichoccur early after the decompression and to the determination of the first required stops. The threedeveloped models give interesting prevention perspectives.

As lesões nervosas são freqüentes nos alongamentos e correções de deformidades dos membros inferiores. As lesões por estiramento do nervo fibular podem ser tratadas pela redução da taxa de alongamento ou do ritmo de correção gradual de deformidades até melhora clínica, ou pela descompressão cirúrgica, como demonstrado em estudos clínicos. Essa cirurgia mostrou-se eficaz para o tratamento dessas lesões, assim como outras de diversas etiologias, mas a quantificação da redução da tensão no nervo, a partir de uma descompressão limitada, não é conhecida. O presente estudo objetivou a mensuração da variação da tensão no nervo fibular após a osteotomia em varo da tíbia proximal, e em seguida após a descompressão limitada desse nervo. Essa descompressão limitada é realizada em dois pontos considerados anatomicamente importantes para o aumento da tensão no nervo: as fáscias superficial e profunda do músculo fibular longo, e o septo intermuscular anterior. A tensão no nervo foi medida através de um aparelho desenvolvido para tracionar o nervo perpendicularmente a seu eixo e medir sua reação em microdeformações com um transdutor de força. O gráfico de força por deformação produzido pelo computador mostrou uma fase inicial de acomodação, e depois apresentou comportamento linear. Essa porção da linear da curva, possibilitou o cálculo da rigidez do nervo em três momentos: pré osteotomia em varo, após a osteotomia em varo, e após a descompressão do nervo fibular. Os valores obtidos em sete cadáveres (quatorze membros inferiores) foram tratados estatisticamente através de análise de variância para medidas repetidas, obtendo-se o aumento significativo da tensão (p = 0,0002) após a osteotomia e a redução da mesma (p = 0,0003) após a descompressão do nervo fibular ao nível do colo da fíbula. Foi observado também que não houve diferença significativa entre os valores observados ao início em relação aos valores obtidos após descompressão do nervo (p= 0,3666). / Nerve injuries are complications often observed in lengthening and deformity correction in lower limbs. The peroneal nerve stretch lesions can be treated by slowing the rate of distraction or deformity correction or by surgical decompression, as demonstrated by clinical studies. This surgery proved to be very efficient to treat these lesions, but the amount of reduction of the nerve tension was not quantified. This study aims to measure the variation of the tension in the peroneal nerve (after varus osteotomy in the proximal tibia and after surgical decompression). The decompression is performed in two levels considered anatomically important to the increase of the nerve tension: the superficial and deep peroneus longus muscle fasciae, and the anterior intramuscular septum. The nerve tension was measured through a device developed to apply traction in the nerve perpendiculary to its axis, and capture the nerve reaction with a force transducer. It was then possible to plot a graphic of force by deformation that showed an accomodation phase followed by a linear segment. This region of the curve allowed to obtain the rigidity values in the three situations: pre varus osteotomy, after varus osteotomy and after peroneal nerve decompression. The values obtained in seven cadavera (fourteen lower limbs) were statistically treated by the multiple variance analysis. The results showed there was a significative increase of tension (p = 0.0002) after the osteotomy and varus positioning, and an also significant decrease (p = 0.0003) after peroneal nerve decompression at the level of the fibular neck. It was also observed no significative difference between the values obtained in the beginning of the experiment (pre varus osteotomy) if compared with the values obtained after nerve decompression (p= 0.3666).

Diante da necessidade de produzir uma vedação com maior vida útil frente as condições de descompressão explosiva de CO2 incorporou-se quantidades diferentes de MWCNT (multiwalled carbono nanotubes) curtos e longos (0,25 phr e 1 phr) e com graus de funcionalidade de grupos oxigenados variando entre 0% e 7,5% em elastômeros fluorados. A incorporação foi realizada utilizando-se o processo de mistura em cilindro aberto (Copê) e as mantas de borracha obtidas foram termoprensadas e submetidas a doses de irradiação de 5, 10 e 20 kGy em ar atmosférico. Analisaram-se os nanocompósitos e os MWCNT por análises térmicas, difrações de raios-X e micrografias. A partir dos nanocompósitos também foram confeccionados corpos de prova para ensaios mecânicos, análises dinâmico-mecânicas, ensaios de dessorção. Os resultados indicaram em geral aumento dos módulos a 100% e secante a 15% nas amostras com adição de 1 phr, mas pouca mudança da temperatura de transição vítrea foi observada, indicando pouca alteração da mobilidade das cadeias. As micrografias apontaram algumas extremidades de MWCNT soltas da matriz polimérica após o processo de preparação da amostra. Os resultados apontaram melhora na dessorção dos nanocompósitos após a incorporação dos MWCNT. / Faced with the need to produce a gasket with longer useful life against the explosive decompression conditions of CO2, it was incorporated different amounts of short and long MWCNT (0.25 phr and 1 phr) and degrees of oxygenated groups functionality ranging between 0% and 7.5% in fluorinated elastomers. The incorporation was performed using the open mill with two rolls (COPE) and rubber blankets were obtained thermopressed and subjected to radiation doses of 5, 10 and 20 kGy in air atmosphere. Nanocomposites and MWCNT were analyzed by thermal analysis, X-ray diffraction and SEM micrographs. From the nanocomposites were also prepared specimens for mechanical testing, dynamic mechanical analysis, desorption tests. The results indicated, in generally, an increase of modules to 100% and secant to 15% in the samples with the addition of 1 phr, however little change in the glass transition temperature was observed, indicating little variation of mobility of the chains. The micrographs showed some free ends of MWCNT the polymer matrix after sample preparation process. The results pointed improvement on dessorpotion of nanocomposites after the incorporation of MWCNT.

"As water covers over 75% surface area of the earth, humans have an innate desire to explore the underwater environment for various aims. Physiological responses are induced in humans and animals to adapt to different stresses imposed by the hyperbaric environment. When these stresses become overwhelming, certain hazards can occur to individuals in underwater or in similar hyperbaric environments, and they may include nitrogen narcosis, oxygen toxicity and decompression sickness (DCS). There are evidences showing that the autonomic nervous system (ANS) plays an important role in diving reflex and physiological responses to diving hazards. However, the assessment of the autonomic nervous activity during SCUBA dives and diving-related hazards are mostly absent from the literature. Thus, in order to evaluate the autonomic nervous alterations that may occur during diving, especially during DCS, the following three experiments were performed in this study: the simulated dives of human subjects in a hyperbaric chamber, the SCUBA diving performed in seawater and induced decompression sickness in a swine model. A novel algorithm developed in our lab, principal dynamic mode (PDM) analysis, is applied to the above data. It has been shown that the PDM is able to accurately separate the sympathetic and parasympathetic dynamics of the ANS, and subsequently it is able to obtain a better quantification of the autonomic nervous activity than a current golden-standard approach. Through the study, dominance of the parasympathetic modulation was found in both hyperbaric chamber and SCUBA diving conditions. And more stresses were present in real dives, compared to simulated dives in chamber. In the swine DCS model, we found neurological DCS and cardiopulmonary DCS resulted in different alterations in the ANS. Furthermore, tracking dynamics of the parasympathetic modulations via the PDM method may allow discrimination between cardiopulmonary DCS and neurological DCS, and has potential use as a marker for early diagnosis of cardiopulmonary DCS. "

<p>The intent of the work discussed in this dissertation is to apply the engineering methods of theory/modeling, numerics/computation, and experimentation to a diverse assemblage of projects. Several projects are discussed: probabilistic modeling of decompression sickness, comparative hydrodynamics of cetacean flippers, optimization of CT/MRI protocols, evaluation of modified catheters, rudder cavitation, and modeling of mass transfer in amphibian cone outer segments. </p><p>The first project discussed is the probabilistic modeling of decompression sickness (DCS). This project involved developing a system for evaluating the success of decompression models in predicting DCS probability from empirical data. Model parameters were estimated using maximum likelihood techniques, and exact integrals of risk functions and tissue kinetics transition times were derived. Agreement with previously published results was excellent including maximum likelihood values within one log-likelihood unit of previous results and improvements by re-optimization, mean predicted DCS incidents within 1.4% of observed DCS, and time of DCS occurrence prediction. Alternative optimization and homogeneous parallel processing techniques yielded faster model optimization times. The next portion of this project involved investigating the nature and utility of marginal decompression sickness (DCS) events in fitting probabilistic decompression models to experimental dive trial data. Three null models were developed and compared to a known decompression model that was optimized on dive trial data containing only marginal DCS and no-DCS events. It was found that although marginal DCS events are related to exposure to decompression, empirical dive data containing marginal and full DCS outcomes are not combinable under a single DCS model; therefore, marginal DCS should be counted as no-DCS events when optimizing probabilistic DCS models with binomial likelihood functions. The final portion of this project involved the exploration of a multinomial DCS model. Two separate models based on the exponential-exponential/linear-exponential framework were developed: a trinomial model, which is able to predict the probabilities of mild, serious and no-DCS simultaneously, and a tetranomial model, which is able to predict the probabilities of mild, serious, marginal and no-DCS simultaneously. The trinomial DCS model was found to be qualitatively better than the tetranomial model, for reasons found earlier concerning the utility of marginal DCS events in DCS modeling. </p><p>The next project discussed is comparative hydrodynamics of cetacean flippers. Cetacean flippers may be viewed as being analogous to modern engineered hydrofoils, which have hydrodynamic properties such as lift coefficient, drag coefficient and associated efficiency. The hydrodynamics of cetacean flippers have not previously been rigorously examined and thus their performance properties are unknown. By conducting water tunnel testing using scale models of cetacean flippers derived via computed tomography (CT) scans, as well as computational fluid dynamic (CFD) simulations, a baseline work is presented to describe the hydrodynamic properties of several cetacean flippers. It was found that flippers of similar planform shape had similar hydrodynamic performance properties. Furthermore, one group of flippers of planform shape similar to modern swept wings was found to have lift coefficients that increased with angle of attack nonlinearly, which was caused by the onset of vortex-dominated lift. Drag coefficient versus angle of attack curves were found to be less dependent on planform shape. Larger cetacean flippers were found to have degraded performance at a Re of 250,000 compared to flippers of smaller odontocetes, while performance of larger and smaller cetacean flippers was similar at a swim speed of 2 m/s. Idealization of the planforms of cetacean flippers was found to capture the relevant hydrodynamic effects of the real flippers, although unintended consequences such as the lift curve slope changing from linear to nonlinear were sometimes observed. A numerical study of an idealized model of the humpback whale flipper showed that the leading-edge tubercles delay stall compared to a baseline (no tubercle) flipper because larger portions of the flow remaining attached at higher angles of attack. </p><p>The third project discussed is optimization of CT/MRI protocols. In order to optimize contrast material administration protocols for Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), a custom-built physiologic flow phantom was constructed to model flow in the human body. This flow phantom was used to evaluate the effect of varying volumes, rates, and types of contrast material, use of a saline chase, and cardiac output on aortic enhancement characteristics. For CT, reducing the volume of contrast material decreased duration peak enhancement and reduced the maximum value of peak enhancement. Increasing the rate of contrast media administration increased peak enhancement and decreased duration of peak enhancement. Use of a saline chase resulted in an increase in peak enhancement. Peak aortic enhancement increased when reduced cardiac output was simulated. For MRI, when the same volume of contrast material was injected at the same rate, the type of contrast material used has a significant effect on the greatest peak signal intensity and duration peak signal intensity. A higher injection rate of saline chaser is more advantageous than a larger volume of saline chaser to increase the peak aortic signal intensity using low contrast material doses. Furthermore, for higher volumes of contrast material, the effect of increasing the volume of saline chaser makes almost no difference while increasing the rate of injection makes a significant difference. When a saline chaser with a high injection rate is used, the dose of the contrast material may be reduced by 25-50% and more than 86% of the non-reduced dose peak aortic enhancement will be attained.</p><p>The next project discussed is evaluation of modified angiocatheters. In this study, a standard peripheral end hole angiocatheter was compared to those modified with side holes or side slits by using experimental techniques to qualitatively compare the contrast material exit jets, and by using numeric techniques to provide flow visualization and quantitative comparisons. A Schlieren imaging system was used to visualize the angiocatheter exit jet fluid dynamics at two different flow rates, and a commercial computational fluid dynamics (CFD) package was used to calculate numeric results for various catheter orientations and vessel diameters. Experimental images showed that modifying standard peripheral intravenous angiocatheters with side holes or side slits qualitatively changed the overall flow field and caused the exiting jet to become less well-defined. Numeric calculations showed that the addition of side holes or slits resulted in a 9-30% reduction of the velocity of contrast material exiting the end hole of the angiocatheter. With the catheter tip directed obliquely to the wall, the maximum wall shear stress was always highest for the unmodified catheter and always lowest for the 4 side slit catheter. Modified angiocatheters may have the potential to reduce extravasation events in patients by reducing vessel wall shear stress. </p><p>The next project discussed involves studying the effect of leading-edge tubercles on cavitation characteristics for marine rudders. Three different rudders were constructed and tested in a water tunnel: baseline, 3-tubercle leading edge, and 5-tubercle leading edge. In the linear (non-stall) regime, tubercled rudders performed equally to the smooth rudder. Hydrodynamic stall occurred at smaller angles of attack for the tubercled rudders than for the smooth rudder. When stall did occur, it was more gradual for the tubercled rudders, whereas the smooth rudder demonstrated a more dramatic loss of lift. At lower Re, the tubercled rudders also maintained a higher value of lift post-stall than the smooth rudder. Cavitation onset for the tubercled rudders occurred at lower angles of attack and higher values of cavitation number than for the smooth rudder, but cavities on the tubercled rudders were localized in the slots as opposed to the smooth rudder where the cavity spread across the entire leading edge. </p><p>In the final project discussed, modeling of mass transfer in amphibian cone outer segments, a detailed derivation of a simplified (continuum, one-dimensional) mathematical model for the radio-labeled opsin density profile in the amphibian cone outer segment is presented. This model relies on only one free parameter, which was the mass transfer coefficient between the plasmalemma and disc region. The descriptive equations were nondimensionalized, and scale analysis showed that advective effects could be neglected as a first approximation for early times so that a simplified system could be obtained. Through numeric computation the solution behavior was found to have three distinct stages. The first stage was marked by diffusion in the plasmalemma and no mass transfer in the disc region. The second stage first involved the plasmalemma reaching a metastable state whereas the disc region density increased, then involved both the plasmalemma and disc regions increasing in density with their distributions being qualitatively the same. The final stage involved a slow relaxation to the steady-state solution.</p> / Dissertation

Chest compressions in cardiopulmonary resuscitation are of utmost importance although not without a risk. Many injuries are described but the incidence of these is hard to define due to methodological differences. It is strenuous to perform chest compressions and therefore mechanical chest compressions have been looked upon with interest. This thesis presents new insights on the panorama and incidence of injuries in modern CPR and a comparison of safety and efficacy between manual chest compressions and mechanical chest compressions with the LUCAS™ device. We also evaluated if computed tomography could be an aid in the detection of these injuries. Two pilot trials were conducted and one presented no difference in early survival with 26% and 31% having return of spontaneous circulation when comparing manual chest compressions with the LUCAS device in out-of-hospital cardiac arrest. The other revealed no difference in autopsy-detected injuries. A third multicentre autopsy trial revealed that in patients treated with manual chest compressions 78.3% had at least one injury and 63.9% had at least one rib fracture. The corresponding numbers for patients treated with the LUCAS device was 92.8% (p = 0.002) and 77.7% (p=0.022). Sternal fractures occurred in 54.2% and in 58.3% of the cases treated with manual chest compressions and the LUCAS device respectively (p = 0.556). The median number of rib fractures was 7 in the group receiving manual chest compressions and 6 in the group receiving chest compressions with the LUCAS device. In 31 cases a computed tomography was conducted prior to autopsy and we found a very strong correlation in the discrimination of patients with or without rib fractures (kappa=0.83). Mean difference between the two methods in detecting rib fractures was 0.16. The detection of other injuries did not have a strong correlation. In conclusion there is no difference in early survival between the two methods and mechanical chest compressions adds 14-15% more patients with rib fractures but the amount of rib fractures, sternal fractures and other injuries is equal. CT can aid but not replace autopsies in the detection of these injuries.