Indiana University-Purdue University Indianapolis (IUPUI) / Radiation Therapy has been one of the most common techniques to treat various types of cancers, in particular is Head and Neck Cancer (HNC) which accounts for three percent of all cancers in the United States. During the treatment procedure, the patient is immobilized using immobilization devices such as the full head face mask, bite blocks, stereotactic frame, etc. to get accurate location of tumor. The disadvantage of these devices is that they are very uncomfortable to the patient especially people suffering from Post-Traumatic Stress Disorder (PTSD) and claustrophobia who cannot wear any confined masked system such as the full head mask or bite block during the treatment procedure. To mitigate this problem, there has been a lot of research in modifying such immobilizing devices without neglecting the accurate location of tumor. To this end, the research presented in this thesis focuses on developing a mask less system with accurately locating the position of tumor using the technique of coordinate transformation at the same time fulfilling the three important characteristics: • Comfort • Accuracy • Low price Such a system is comfortable to the patient because no confining mask system is used and we choose minimal contact points on the patient for fixing the patient. Traditionally, such type of cancer treatment is carried out in two stages: Diagnosis stage, which identifies the location of the tumor and the external markers and the Treatment stage where the tumor is treated with immobilization device being common in both the stages. In the new system, the immobilization devices vary at the two stages. The head position is monitored by using pressure sensor assembly where spring and pressure sensor setup detects the amount and direction of head deviation. We also prepare a customized 3D printed nose bridge part for extra referencing in the treatment room. Also, it is important that we use material for our immobilization devices which does not contain any metal and MRI compatible. Once the patient lies down on the treatment couch and is immobilized using the immobilization devices, then tumor location is calculated using the theory of coordinate transformation and transformation matrix in the Diagnosis and Treatment Stage. To validate the system, simulation of immobilization devices used in the new design was carried out using ANSYS Workbench 15.0 and LS-Dyna software’s Explicit Dynamics method. The simulation for the head-fixing device showed a deflection of ±0.1974 mm with respect to machine isocenter with a load of 60 N, which is lower than the customer requirement of ±3 mm with respect to machine isocenter of head deviation. The material used for the external markers for patient positioning was selected to be polyetheretherketone (PEEK) which is a radiolucent and widely used MRI compatible material. The system also takes into consideration the effect of weight loss, which is one of the drawbacks of the current systems. Although still in the development stage, this mask less system holds to be the next new variety of immobilization devices that are comfortable to the patient and less expensive to be implemented in future cancer treatment practices.

The thesis proposes a new procedure to describe bone anisotropy in the finite element model using computed tomography (CT) images. First, bone density was correlated to CT numbers using the empirical function established in previous studies; pointwise bone density gradient was then calculated from interpolation functions of bone densities. Second, principal anisotropic directions were defined using the bone density gradient. Third, the magnitude of bone density gradient was incorporated to an existing bone elasticity-density correlation established by experiments. A method was also introduced to assign the anisotropic material properties to finite element models in Abaqus. The effect on the predicted von Misses stresses and principal strains in the bone by adopting the anisotropic or isotropic material model was investigated by finite element simulations using Abaqus.

abstract: The effect of earthquake-induced liquefaction on the local void ratio distribution of cohesionless soil is evaluated using x-ray computed tomography (CT) and an advanced image processing software package. Intact, relatively undisturbed specimens of cohesionless soil were recovered before and after liquefaction by freezing and coring soil deposits created by pluviation and by sedimentation through water. Pluviated soil deposits were liquefied in the small geotechnical centrifuge at the University of California at Davis shared-use National Science Foundation (NSF)-supported Network for Earthquake Engineering Simulation (NEES) facility. A soil deposit created by sedimentation through water was liquefied on a small shake table in the Arizona State University geotechnical laboratory. Initial centrifuge tests employed Ottawa 20-30 sand but this material proved to be too coarse to liquefy in the centrifuge. Therefore, subsequent centrifuge tests employed Ottawa F60 sand. The shake table test employed Ottawa 20-30 sand. Recovered cores were stabilized by impregnation with optical grade epoxy and sent to the University of Texas at Austin NSF-supported facility at the University of Texas at Austin for high-resolution CT scanning of geologic media. The local void ratio distribution of a CT-scanned core of Ottawa 20-30 sand evaluated using Avizo® Fire, a commercially available advanced program for image analysis, was compared to the local void ratio distribution established on the same core by analysis of optical images to demonstrate that analysis of the CT scans gave similar results to optical methods. CT scans were subsequently conducted on liquefied and not-liquefied specimens of Ottawa 20-30 sand and Ottawa F60 sand. The resolution of F60 specimens was inadequate to establish the local void ratio distribution. Results of the analysis of the Ottawa 20-30 specimens recovered from the model built for the shake table test showed that liquefaction can substantially influence the variability in local void ratio, increasing the degree of non-homogeneity in the specimen. / Dissertation/Thesis / M.S. Civil and Environmental Engineering 2013

Submitted by PPG Zoologia (zoologia-pg@pucrs.br) on 2018-05-29T13:52:52Z No. of bitstreams: 1 Tese - Santos - Fid?lis.pdf: 21234236 bytes, checksum: 6b55c8c14033601ff328f8d7bed152b9 (MD5) / Approved for entry into archive by Caroline Xavier (caroline.xavier@pucrs.br) on 2018-05-29T14:16:25Z (GMT) No. of bitstreams: 1 Tese - Santos - Fid?lis.pdf: 21234236 bytes, checksum: 6b55c8c14033601ff328f8d7bed152b9 (MD5) / Made available in DSpace on 2018-05-29T14:21:21Z (GMT). No. of bitstreams: 1 Tese - Santos - Fid?lis.pdf: 21234236 bytes, checksum: 6b55c8c14033601ff328f8d7bed152b9 (MD5) Previous issue date: 2018-03-22 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / A fam?lia Anomalepididae atualmente ? constitu?da por 18 esp?cies de cobras, conhecidas como ?cobras-cegas?, fossoriais e de distribui??o geogr?fica restrita ? regi?o Neotropical. Praticamente, n?o h? informa??es a respeito da hist?ria de vida dos Anomalepididae, pois s?o animais de dif?cil coleta e a manuten??o em cativeiro para estudos com biologia ? bastante dif?cil. As informa??es dispon?veis a respeito de cobras Anomalepididae est?o concentradas em estudos anat?micos, principalmente osteologia do cr?nio, taxonomia e filogenia a n?vel de fam?lias dentro de Serpentes. Mas, desde a descri??o de Anomalepididae por Taylor em 1939, n?o houve uma revis?o taxon?mica abrangente dentro da fam?lia ou alguma infer?ncia filogen?tica com novos arranjos taxon?micos. Em rela??o ? taxonomia do grupo, a literatura ? restrita ? descri??o de novas esp?cies e revis?es taxon?micas de dois g?neros (Anomalepis e Liotyphlops). O objetivo prim?rio deste estudo foi a revis?o taxon?mica da fam?lia Anomalepididae e, para isto, foi utilizado toda a amostragem poss?vel de esp?cies e esp?cimes na aquisi??o de dados morfol?gicos, al?m do emprego da t?cnica High-Resolution X-ray Computed Tomography (HRXCT). O objetivo secund?rio foi inferir uma hip?tese filogen?tica para as esp?cies dentro de Anomalepididae com base nos caracteres anat?micos obtidos do exame de esp?cimes. Este trabalho resultou em um novo arranjo taxon?mico para Anomalepididae, com 19 esp?cies v?lidas, descri??o de duas novas esp?cies de Liotyphlops para o Brasil, sendo uma para o estado de Mato Grosso e outra para o estado de Santa Catarina e a recondu??o de Liotyphlops beui para a sinon?mia de Liotyphlops ternetzii. Al?m disto, a an?lise de parcim?nia com base em caracteres do cr?nio e da morfologia externa recuperou Anomalepididae como um t?xon monofil?tico dentro de Scolecophidia. / The family Anomalepididae currently consists of 18 species known as "blind snakes", fossorial in habit and with geographical distribution restricted to the Neotropical region. Practically, there is no information about the life history of the Anomalepididae, because they are difficult to collect and the maintenance in captivity for biology studies is quite difficult. The information available regarding Anomalepididae snakes is concentrated on anatomical studies, mainly osteology of the skull, taxonomy, and phylogeny at the level of families within Serpentes. But since the description of Anomalepididae by Taylor in 1939, there has been no comprehensive taxonomic review within the family or some phylogenetic inference with new taxonomic arrangements. In relation to the taxonomy of the group, the literature is restricted to the description of new species and taxonomic revisions of two genera (Anomalepis and Liotyphlops). The primary objective of this study was the taxonomic revision of the Anomalepididae and, for this, all possible sampling of species and specimens were used in the acquisition of morphological data, besides the use of the High-resolution X-Ray Computed Tomography (HRXCT) technique. The secondary objective was to infer a phylogenetic hypothesis for the species within Anomalepididae based on the anatomical characters obtained from the specimen examination. This work resulted in a new taxonomic arrangment for Anomalepididae, with 19 valid species, description of two new species of Liotyphlops from Brazil, being one for the state of Mato Grosso and the other for the state of Santa Catarina, and the re-conduction of Liotyphlops beui to the synonymy of Liotyphlops ternetzii. In addition, the parsimony analysis based on characters from the skull and external morphology recovered Anomalepididae as a monophyletic taxon within Scolecophidia.

No description available.

The U.S. health care system is one of the most expensive health care systems in the world, yet it is not as efficient as it is expected. Studies have shown that the use of expensive imaging procedures, such as CT scans, was significantly increasing for the past few years. However, the increased number of CT scans may not help to improve quality of care. No studies are conducted on investigate geographic variation on CT scan usage rate. This research is the first one to examine CT scan usage rate among counties and to examine variation caused by patient and hospital characteristics. We used the 2007 HCUP-SID database provided data for the research. GIS graph was used to illustrate geographic variation on CT scan usage in New York State. Contingency tables were developed to evaluate to what extent patient and hospital characteristics contribute to the variation. A logistic regression model was built to control the variation caused by patient and hospital characteristics in order to find variation contributed by other potential factors such as availability of CT scanners and radiologists. Significant geographic variation of CT scan usage rate in the county level of New York State was found. Patient demographics, insurance status and medical conditions as well as hospital bed size and teaching status were contributing factors to the variation. After controlling these factors, significant geographic variation was still found. It indicates that other potential reasons would influence the technology use. / Master of Science

La tomographie à rayons X est une technologie d’imagerie en trois dimensions. Elle se base sur la transmission de rayons X à travers l’objet d’étude. Elle est non destructive mais néanmoins irradiante. Cette technique de visualisation est utilisée principalement dans trois domaines : le diagnostic médical, le contrôle non destructif (détection de défauts dans des pièces industrielles de haute performance) et la sécurité (contrôles aéroportuaires des bagages). Les récentes avancées technologiques dans le domaine des détecteurs spectrométriques de rayons X ouvrent des perspectives d’amélioration de cette technique d’imagerie dans ses divers domaines d’application. Nous avons développé une nouvelle méthode reconstruction statistique appelée MLTR-ONE-STEP qui permet de reconstruire la variabilité énergétique du coefficient linéaire d’atténuation de l’objet étudié. Cette approche est dite « one-step » car elle reconstruit directement le volume final à partir des mesures brutes issues de détecteurs spectrométriques.Les phénomènes physiques au sein du détecteur provoquent une distorsion énergétique du spectre d’atténuation qui a été prise en compte lors de la reconstruction. La méthode utilisée s’inscrit dans le cadre bayésien et maximise la log-vraisemblance du modèle tout en prenant en compte de l’a priori spatial sur le volume reconstruit. L’objectif de la méthode est l’amélioration de la qualité de l’image finale (réduction des artefacts et niveau de bruit) et la quantification des matériaux présents. Nous avons étudié dans le cadre de données simulées l’influence des paramètres de régularisation sur la reconstruction. En pratique, le détecteur de rayon X étudié classe les photons incidents en 64 canaux. Ils sont ensuite regroupés en un nombre de canaux plus faible (2 à 25) et l’influence de ce regroupement a été étudiée. La reconstruction MLTR-ONE-STEP a ensuite été testée sur des données expérimentales regroupées en 12 canaux. / X-ray spectral tomography is a 3D visualization technique. It is based on the transmission of X-rays through object matter. It is a non-destructive technology but which irradiates the studied object/patient. X-ray tomography is mainly used in three areas: medical diagnosis, non-destructive testing (detection of defects in industry devices) and airport security (luggage screening). New technological breakthroughs in X-ray photon-counting detectors provide new perspective for improving this technique in each application field. We have developed a new reconstruction method named MLTR-ONE-STEP which enables the obtention of energetic variability of the scanned object linear attenuation coefficient. This approach belongs to the “One-Step” class because it directly reconstructs the final images from raw photon-counting detector data.Physical effects inside the detector are causing spectral distortion of the energetic spectrum. This distortion is taken into account in our reconstruction through a Detector Response Matrix. The developed reconstruction method maximizes the poissonian likelihood of the measurements with a spatial regularization Tukey term. The objectives of spectral tomography are the improvement of the image quality compared to standard tomography and the quantification of materials inside the object. We have studied the influence of regularization parameters on the final result. In practice, photon-counting detector measurements are in practice sorted in 64 energy bins. Bins are then merged in a smaller number (from 2 to 25). The influence of this binning was studied on simulated data. The MLTR-ONE-STEP was then tested on real experimental data in order to prove the feasibility of such a “One-Step” reconstruction method.

Les propriétés physiques macroscopiques des matériaux granulaires découlent directement de leurs micro-structures. L'étude de tels matériaux nécessite la segmentation de leur structures 3D à partir d'images acquises par CT-scans. Cependant, ces images sont parfois difficiles à analyser, car de nombreux défauts et artefactes de reconstruction peuvent apparaître. Obtenir des structures 3D proches des données réelles nécessite un filtrage adapté, qui ne peut être obtenu que par une analyse approfondie du matériaux.Un filtrage adapté améliore la perception de chacun des grains et la structure 3D peut être alors obtenue par segmentation. La complexité de ces structures rend la tâche difficile : les grains qui la représentent prennent des formes irrégulières, allongées et pas nécessairement convexes. Ces grains sont généralement fortement agglomérés et difficiles à séparer. De plus, des phénomènes de fracturation sont fréquemment observés. Les grains sont éclatés en petits fragments pouvant s'éloigner de la position d'origine du grain.Dans le cadre de cette thèse, une chaîne complète de segmentation est présentée. Les données brutes d'acquisition sont tout d'abord filtrés et pré-traités pour en extraire un certain nombre de mesures statistiques , telles que le nombre de phase, le nombre de grains de chaque phase, la distribution des tailles de grains et l'identification spectral de chaque phase. Une première segmentation grossière est effectuée en utilisant la transformation de ligne de partage des eaux. Une hiérarchie des contours obtenus permet d'éliminer la sur-segmentation. Enfin, une méthode permettant d'évaluer la similitude entre deux bords adjacents est présenté, et nous permettera de réassembler les grains fragmentés, dont les fragments ont été dispersés.Les acquitions par CT-scan sont conséquentes et leur étude nécessite une utilisation efficace des architectures récentes de calcul. Le choix de la chaîne de traitement est basé sur l'étude de l'état de l'art et son application aux données 3D, avec comme objectif d'équilibrer les coûts de traitement et la qualité de la segmentation. Une nouvelle méthode de segmentation nous permet d'atteindre de meilleurs performances en améliorant également la qualité des résultats. Enfin, deux nouveaux algorithmes sont proposés pour la détection de composantes connexes et la transformation de ligne de partage des eaux. / The physical properties of granular materials on a macroscopic scale derive from their microstructures. The segmentation of CT-images of this type of material is the first step towards simulation and modeling but it is not a trivial task. However, the quality of those images is often affected by the presence of noise and reconstruction artefacts. Obtaining 3D structures that fit the reality requires an adapted filter, which can only be obtained by a complete analysis of the material.This adapted filter enhances each grain and the full structure of the material is obtained by segmentation. However, non-spherical, elongated or non-convex objects fail to be separated with classical methods. Moreover, grains are commonly fragmented due to external conditions. Grains are ground into multiple fragments of different shape and volume; those fragments drift from one another in the binder phase.In this thesis, a complete process chain is proposed to segment complex structures that can be acquired by CT-scan. The raw data is first filtered and processed, and statistical features are extracted such as the number of phases, the number of grains of each phase, the size distribution and spectral identification of the phases. A primary segmentation is performed to identify every connection between touching grains and is based on the watershed transform. A hierarchy is built on the obtained contours to eliminate over-segmentation. Reconstruction of grains from fragments is achieved using affinities that match the local thickness and the regularity of the interface.Typical CT-images are voluminous, and the study of granular materials requires efficient use of modern computing architectures. Studying the state-of-the-art and its application to 3D data has oriented our choice has allowed us to balance the quality of segmentation and the computing cost. A novel segmentation method allows for higher performances while improving the quality of the result. Finally, two new algorithms are proposed for the labeling of connected components and for the watershed transformation.

Grip stiffness is an important property of carton board packaging. The structure of the packaging needs to withstand the handling of one or many consumers. A carton board packaging that feels stiff when handled conveys a sense of luxury to the consumer, one example of this is the packages containing new flagship smart phones. If a package is more or less stiff is at this moment subjectively interpreted by test panels. An objective method of measuring grip stiffness is sought after for repeat ability and speed. This master thesis investigates the influence of geometry and material parameters on the grip stiffness of a carton board packages. The purpose is to determine how the measured point loads differ between different geometries for one particular material.  Measurements are conducted using a tensile tester and a sensory device, Syntouch Biotac. Only two of the 19 sensors are analyzed in this thesis. Ther data analyzed in this thesis comes from experiments conducted by the author and experiments conducted during a bachelors thesis at Örebro University. The same equipment was used for both experiments. The authors experiments were aimed at finding how a rotation of the packaging would affect the results whereas no rotations were made during experiments not conducted by the author. The authors own experiments were also made using an actual human finger, but only on packages that were not rotated. A finite element study was performed to validate the results from the Syntouch Biotac. X-ray computed tomography was used to investigate if the damage done to the carton board material by a human finger was similar to the damage done to the carton board material by the Syntouch Biotac.  Results from the Syntouch Biotac show that it is possible to tell where along and how close to the edge of the packaging the Syntouch Biotac is touching the packaging and that it is possible to discern between materials if the surface weights are different enough. The X-ray computed tomography show that damages done to the carton material cone by either the Syntouch Biotac or a human finger, are not possible to tell apart with the method of analysis used in this thesis. / Greppstyvhet är en viktig egenskap hos kartongförpackningar. Strukturen behöver kunna motstå hantering av en eller flera kunder. En kartongförpackning som upplevs som styv när den hanteras ger kunden ett intryck av lyx, ett exempel är förpackningar för nya smarttelefoner. Om en kartongförpackning är mer eller mindre greppstyv avgörs just nu subjektivt av en testpaneler. En objektiv och upprepningsbar metod för att mäta greppstyvhet snabbare behövs. I den här masteruppsatsen undersökts geometri- och materialparametrars påverkan på kartongförpackningars greppstyvhet. Syftet var att avgöra hur de olika punktlasterna skiljer sig åt mellan olika geometrier för ett givet material.  Mätningar gjordes med en dragprovare och en sensorisk mätenhet, Syntouch Biotac. Endast två av 19 sensorer analyseras i det här arbetet. Datan som analyseras i det här arbetet kommer från experiment utförda av författaren samt experiment gjorda i samarbete med en kandidatuppsats vid Örebro Universitet. Samma utrustning användes för båda experiment. Författarens experiment gjordes för att undersöka hur rotation av kartongförpackningarna påverkade resultaten. Ingen rotation utfördes under experimenten som gjordes i samband med kandidatuppsatsen på Örebro Universitet. Experiment utförda av författaren innehåller även kompression av förpackningar gjorda med ett mänskligt finger, detta gjordes endast på förpackningar som inte roterades. En FEM-studie utfördes för att validera resultaten från Syntouch Biotac. Datortomografi användes för att undersöka om skador som uppkommit på kartongmaterialet av mänskligt finger var lika de som uppkommit från Syntouch Biotac. Resultaten från Syntouch Biotac visar att det är möjligt att se var längs med eller hur nära kanten på förpackningen som Syntouch Biotac trycker på förpackningen, samt att det är möjligt att skilja mellan material om deras ytvikter skiljer sig tillräckligt mycket. Datortomografin visar att skador som uppkommit på kartong materialet av mänskligt finger eller Syntouch Biotac inte går att särskilja med den analysmetod som använts i det här arbetet.

The three approaches followed herein aim to improve our understanding of the paleobiodiversity andevolution of Silurian radiolarians. The first approach provides an exhaustive taxonomic description ofan entirely new radiolarian fauna recovered from two sections of the Cape Phillips Formation in theCanadian Arctic which accumulated in two different paleoenvironmental settings. The samples are datedby graptolites of the Gorstian Lobograptus progenitor Zone. The obtained radiolarian fauna includes 28species, of which 3 are new, and exhibits some of the best preserved Silurian radiolarians known so far.The stratigraphic range of several species was also extended. Then, in a second approach, a CT-Scan3D reconstruction of a specimen of Gyrosphaera cavea was conducted in order to resolve significantinternal structure taxonomic issues. Higher level radiolarian classification is based on internal structures,and classical methods of observing these features repeatedly failed to uncover them. The 3D imagingrevealed a «double» coiling of the specimen that has proved useful in understanding how it grew.Eventually, the third approach is a completion of published taxonomic works in the Silurian with theaim of providing diversity trends through analyses of these radiolarian occurrences. A biotic crisis canbe observed in the Homerian, exhibiting both high extinction and low origination rates, and may belinked with enhanced marine productivity. / De tre projekten som utvecklas här har som mål att fokusera på trender inom evolutionen ochmångfalden av en grupp planktoniska mikroorganismer från Silur (från -443 till -419 Ma). I ett förstaprojekt beskrivs en helt ny fauna radiolarier som hittats i två lokaliteter på de kanadensiska arktiskaöarna, och som har deponerats i olika miljöförhållanden under Silur. Detta material daterades med hjälpav graptoliter, en grupp utdöda svalgsträngsdjur som är mycket användbara för paleozoiska dateringar,till en ålder överensstämmande med Gorstian (-427 till -425 Ma). Denna kanadensisk-arktiska fauna avradiolarier består av 28 arter (varav 3 är nya) och uppvisar några av de bäst bevarade fossilerna frånSilur överhuvudtaget. Den stratigrafiska bredden, vilket är livstiden, av flera arter har också förlängts.Därefter, i ett andra projekt, skapades en 3D-rekonstruktion av ett exemplar av Gyrosphaera cavea medhjälp av mikrotomografi för att observera och beskriva komplexa interna strukturer. Faktum är attklassificeringen av Radiolaria består till stor del av analysen och beskrivningen av dessa internastrukturer och många klassiska metoder som har använts för att observera dem, såsom med hjälp avsvepelektronmikroskop, har misslyckats konsekvent. 3D-avbildningen visade en komplex dubbelrullandeav strukturen i exemplaret, som har visat sig vara användbart i sökandet för att förstå dennesutveckling. Det tredje projektet är slutförandet av en samling av samtliga publicerade arbeten röranderadiolarier från Silur med syfte att klargöra trender inom diversitet för hela perioden genom analyser avförekomsten av dessa radiolarier. Ett utdöende kan observeras under Homerian (-430 till -427 Ma), somtroligen orsakades av frekventa utdöenden och en låg artbildningshastighet.