Probing Tissue Microstructure Using Susceptibility Contrast Magnetic Resonance Imaging

Magnetic resonance imaging is a research and clinical tool that has been applied in a wide variety of sciences. One area of magnetic resonance imaging that has exhibited terrific promise and growth in the past decade is magnetic susceptibility imaging. Imaging tissue susceptibility provides insight into the microstructural organization and chemical properties of biological tissues, but this image contrast is not well understood. The purpose of this work is to develop effective approaches to image, assess, and model the mechanisms that generate both isotropic and anisotropic magnetic susceptibility contrast in biological tissues, including myocardium and central nervous system white matter.

This document contains the first report of MRI-measured susceptibility anisotropy in myocardium. Intact mouse heart specimens were scanned using MRI at 9.4 T to ascertain both the magnetic susceptibility and myofiber orientation of the tissue. The susceptibility anisotropy of myocardium was observed and measured by relating the apparent tissue susceptibility as a function of the myofiber angle with respect to the applied magnetic field. A multi-filament model of myocardial tissue revealed that the diamagnetically anisotropy α-helix peptide bonds in myofilament proteins are capable of producing bulk susceptibility anisotropy on a scale measurable by MRI, and are potentially the chief sources of the experimentally observed anisotropy.

The growing use of paramagnetic contrast agents in magnetic susceptibility imaging motivated a series of investigations regarding the effect of these exogenous agents on susceptibility imaging in the brain, heart, and kidney. In each of these organs, gadolinium increases susceptibility contrast and anisotropy, though the enhancements depend on the tissue type, compartmentalization of contrast agent, and complex multi-pool relaxation. In the brain, the introduction of paramagnetic contrast agents actually makes white matter tissue regions appear more diamagnetic relative to the reference susceptibility. Gadolinium-enhanced MRI yields tensor-valued susceptibility images with eigenvectors that more accurately reflect the underlying tissue orientation.

Despite the boost gadolinium provides, tensor-valued susceptibility image reconstruction is prone to image artifacts. A novel algorithm was developed to mitigate these artifacts by incorporating orientation-dependent tissue relaxation information into susceptibility tensor estimation. The technique was verified using a numerical phantom simulation, and improves susceptibility-based tractography in the brain, kidney, and heart. This work represents the first successful application of susceptibility-based tractography to a whole, intact heart.

The knowledge and tools developed throughout the course of this research were then applied to studying mouse models of Alzheimer’s disease in vivo, and studying hypertrophic human myocardium specimens ex vivo. Though a preliminary study using contrast-enhanced quantitative susceptibility mapping has revealed diamagnetic amyloid plaques associated with Alzheimer’s disease in the mouse brain ex vivo, non-contrast susceptibility imaging was unable to precisely identify these plaques in vivo. Susceptibility tensor imaging of human myocardium specimens at 9.4 T shows that susceptibility anisotropy is larger and mean susceptibility is more diamagnetic in hypertrophic tissue than in normal tissue. These findings support the hypothesis that myofilament proteins are a source of susceptibility contrast and anisotropy in myocardium. This collection of preclinical studies provides new tools and context for analyzing tissue structure, chemistry, and health in a variety of organs throughout the body.

Globalizing the Sculptural Landscapes of the Sarapis and Isis Cults in Hellenistic and Roman Greece

“Globalizing the Sculptural Landscape of Isis and Sarapis Cults in Roman Greece,” asks questions of cross-cultural exchange and viewership of sculptural assemblages set up in sanctuaries to the Egyptian gods. Focusing on cognitive dissonance, cultural imagining, and manipulations of time and space, I theorize ancient globalization as a set of loosely related processes that shifted a community's connections with place. My case studies range from the 3rd century BCE to the 2nd century CE, including sanctuaries at Rhodes, Thessaloniki, Dion, Marathon, Gortyna, and Delos. At these sites, devotees combined mainstream Greco-Roman sculptures, Egyptian imports, and locally produced imitations of Egyptian artifacts. In the last case, local sculptors represented Egyptian subjects with Greco-Roman naturalistic styles, creating an exoticized visual ideal that had both local and global resonance. My dissertation argues that the sculptural assemblages set up in Egyptian sanctuaries allowed each community to construct complex narratives about the nature of the Egyptian gods. Further, these images participated in a form of globalization that motivated local communities to adopt foreign gods and reinterpret them to suit local needs.

I begin my dissertation by examining how Isis and Sarapis were represented in Greece. My first chapter focuses on single statues of Egyptian gods, describing their iconographies and stylistic tendencies through examples from Corinth and Gortyna. By comparing Greek examples with images of Sarapis, Isis, and Harpokrates from around the Mediterranean, I demonstrate that Greek communities relied on globally available visual tropes rather than creating site or region-specific interpretations. In the next section, I examine what other sources viewers drew upon to inform their experiences of Egyptian sculpture. In Chapter 3, I survey the textual evidence for Isiac cult practice in Greece as a way to reconstruct devotees’ expectations of sculptures in sanctuary contexts. At the core of this analysis are Apuleius’ Metamorphoses and Plutarch’s De Iside et Osiride, which offer a Greek perspective on the cult’s theology. These literary works rely on a tradition of aretalogical inscriptions—long hymns produced from roughly the late 4th century B.C.E. into the 4th century C.E. that describe the expansive syncretistic powers of Isis, Sarapis, and Harpokrates. This chapter argues that the textual evidence suggests that devotees may have expected their images to be especially miraculous and likely to intervene on their behalf, particularly when involved in ritual activity inside the sanctuary.

In the final two chapters, I consider sculptural programs and ritual activity in concert with sanctuary architecture. My fourth chapter focuses on sanctuaries where large amounts of sculpture were found in underground water crypts: Thessaloniki and Rhodes. These groups of statues can be connected to a particular sanctuary space, but their precise display contexts are not known. By reading these images together, I argue that local communities used these globally available images to construct new interpretations of these gods, ones that explored the complex intersections of Egyptian, Greek, and Roman identities in a globalized Mediterranean. My final chapter explores the Egyptian sanctuary at Marathon, a site where exceptional preservation allows us to study how viewers would have experienced images in architectural space. Using the Isiac visuality established in Chapter 3, I reconstruct the viewer's experience, arguing that the patron, Herodes Atticus, intended his viewer to inform his experience with the complex theology of Middle Platonism and prevailing elite attitudes about Roman imperialism.

Throughout my dissertation, I diverge from traditional approaches to culture change that center on the concepts of Romanization and identity. In order to access local experiences of globalization, I examine viewership on a micro-scale. I argue that viewers brought their concerns about culture change into dialogue with elements of cult, social status, art, and text to create new interpretations of Roman sculpture sensitive to the challenges of a highly connected Mediterranean world. In turn, these transcultural perspectives motivated Isiac devotees to create assemblages that combined elements from multiple cultures. These expansive attitudes also inspired Isiac devotees to commission exoticized images that brought together disparate cultures and styles in an eclectic manner that mirrored the haphazard way that travel brought change to the Mediterranean world. My dissertation thus offers a more theoretically rigorous way of modeling culture change in antiquity that recognizes local communities’ agency in producing their cultural landscapes, reconciling some of the problems of scale that have plagued earlier approaches to provincial Roman art.

These case studies demonstrate that cultural anxieties played a key role in how viewers experienced artistic imagery in the Hellenistic and Roman Mediterranean. This dissertation thus offers a new component in our understanding of ancient visuality, and, in turn, a better way to analyze how local communities dealt with the rise of connectivity and globalization.

Numerical Simulations for the Design of Novel Integrated Parallel Reception, Excitation, and Shimming (iPRES) Coil Arrays

Magnetic field inhomogeneity results in image artifacts including signal loss, image blurring and distortions, leading to decreased diagnostic accuracy. Conventional multi-coil (MC) shimming method employs both RF coils and shimming coils, whose mutual interference induces a tradeoff between RF signal-to-noise (SNR) ratio and shimming performance. To address this issue, RF coils were integrated with direct-current (DC) shim coils to shim field inhomogeneity while concurrently emitting and receiving RF signal without being blocked by the shim coils. The currents applied to the new coils, termed iPRES (integrated parallel reception, excitation and shimming), were optimized in the numerical simulation to improve the shimming performance. The objectives of this work is to offer a guideline for designing the optimal iPRES coil arrays to shim the abdomen.

In this thesis work, the main field () inhomogeneity was evaluated by root mean square error (RMSE). To investigate the shimming abilities of iPRES coil arrays, a set of the human abdomen MRI data was collected for the numerical simulations. Thereafter, different simplified iPRES(N) coil arrays were numerically modeled, including a 1-channel iPRES coil and 8-channel iPRES coil arrays. For 8-channel iPRES coil arrays, each RF coil was split into smaller DC loops in the x, y and z direction to provide extra shimming freedom. Additionally, the number of DC loops in a RF coil was increased from 1 to 5 to find the optimal divisions in z direction. Furthermore, switches were numerically implemented into iPRES coils to reduce the number of power supplies while still providing similar shimming performance with equivalent iPRES coil arrays.

The optimizations demonstrate that the shimming ability of an iPRES coil array increases with number of DC loops per RF coil. Furthermore, the z direction divisions tend to be more effective in reducing field inhomogeneity than the x and y divisions. Moreover, the shimming performance of an iPRES coil array gradually reach to a saturation level when the number of DC loops per RF coil is large enough. Finally, when switches were numerically implemented in the iPRES(4) coil array, the number of power supplies can be reduced from 32 to 8 while keeping the shimming performance similar to iPRES(3) and better than iPRES(1). This thesis work offers a guidance for the designs of iPRES coil arrays.

Utilisation de la tomodensitométrie à deux énergies pour le calcul de dose en curiethérapie à bas débit

Dans la pratique actuelle de la curiethérapie à bas débit, l'évaluation de la dose dans la prostate est régie par le protocole défini dans le groupe de travail 43 (TG-43) de l'American Association of Physicists in Medicine. Ce groupe de travail suppose un patient homogène à base d'eau de même densité et néglige les changements dans l'atténuation des photons par les sources de curiethérapie. En considérant ces simplifications, les calculs de dose se font facilement à l'aide d'une équation, indiquée dans le protocole. Bien que ce groupe de travail ait contribué à l'uniformisation des traitements en curiethérapie entre les hôpitaux, il ne décrit pas adéquatement la distribution réelle de la dose dans le patient. La publication actuelle du TG-186 donne des recommandations pour étudier des distributions de dose plus réalistes. Le but de ce mémoire est d'appliquer ces recommandations à partir du TG-186 pour obtenir une description plus réaliste de la dose dans la prostate. Pour ce faire, deux ensembles d'images du patient sont acquis simultanément avec un tomodensitomètre à double énergie (DECT). Les artéfacts métalliques présents dans ces images, causés par les sources d’iode, sont corrigés à l'aide d’un algorithme de réduction d'artefacts métalliques pour DECT qui a été développé dans ce travail. Ensuite, une étude Monte Carlo peut être effectuée correctement lorsque l'image est segmentée selon les différents tissus humains. Cette segmentation est effectuée en évaluant le numéro atomique effectif et la densité électronique de chaque voxel, par étalonnage stoechiométrique propre au DECT, et en y associant le tissu ayant des paramètres physiques similaires. Les résultats montrent des différences dans la distribution de la dose lorsqu'on compare la dose du protocole TG-43 avec celle retrouvée avec les recommandations du TG-186.

A Generic Model of Execution for Synthesizing Domain-Specific Models

Software engineering researchers are challenged to provide increasingly more pow- erful levels of abstractions to address the rising complexity inherent in software solu- tions. One new development paradigm that places models as abstraction at the fore- front of the development process is Model-Driven Software Development (MDSD). MDSD considers models as first class artifacts, extending the capability for engineers to use concepts from the problem domain of discourse to specify apropos solutions. A key component in MDSD is domain-specific modeling languages (DSMLs) which are languages with focused expressiveness, targeting a specific taxonomy of problems. The de facto approach used is to first transform DSML models to an intermediate artifact in a HLL e.g., Java or C++, then execute that resulting code. Our research group has developed a class of DSMLs, referred to as interpreted DSMLs (i-DSMLs), where models are directly interpreted by a specialized execution engine with semantics based on model changes at runtime. This execution engine uses a layered architecture and is referred to as a domain-specific virtual machine (DSVM). As the domain-specific model being executed descends the layers of the DSVM the semantic gap between the user-defined model and the services being provided by the underlying infrastructure is closed. The focus of this research is the synthesis engine, the layer in the DSVM which transforms i-DSML models into executable scripts for the next lower layer to process. The appeal of an i-DSML is constrained as it possesses unique semantics contained within the DSVM. Existing DSVMs for i-DSMLs exhibit tight coupling between the implicit model of execution and the semantics of the domain, making it difficult to develop DSVMs for new i-DSMLs without a significant investment in resources. At the onset of this research only one i-DSML had been created for the user- centric communication domain using the aforementioned approach. This i-DSML is the Communication Modeling Language (CML) and its DSVM is the Communication Virtual machine (CVM). A major problem with the CVM’s synthesis engine is that the domain-specific knowledge (DSK) and the model of execution (MoE) are tightly interwoven consequently subsequent DSVMs would need to be developed from inception with no reuse of expertise. This dissertation investigates how to decouple the DSK from the MoE and sub- sequently producing a generic model of execution (GMoE) from the remaining appli- cation logic. This GMoE can be reused to instantiate synthesis engines for DSVMs in other domains. The generalized approach to developing the model synthesis com- ponent of i-DSML interpreters utilizes a reusable framework loosely coupled to DSK as swappable framework extensions. This approach involves first creating an i-DSML and its DSVM for a second do- main, demand-side smartgrid, or microgrid energy management, and designing the synthesis engine so that the DSK and MoE are easily decoupled. To validate the utility of the approach, the SEs are instantiated using the GMoE and DSKs of the two aforementioned domains and an empirical study to support our claim of reduced developmental effort is performed.

Working in a Mexican Classroom: An Autoethnographic Study

This autoethnographical study seeks to develop a deeper understanding of the challenges that are faced by the researcher in adapting to a new cultural and linguistic setting as well as describing the teaching practices that the researcher encounters in a Mexican classroom; data will be collected through the process of reflective journaling as well as the collection of pictures and artifacts.

Literatura en el espacio público : Rivas y su obra: un punto de inflexión en la recuperación de la memoria histórica

Tras una revisión diacrónica del tratamiento del tema de la guerra civil en la narrativa gallega, el artículo analiza la función performativa que en ese contexto han desempeñado una serie de obras narrativas de Manuel Rivas y su eficacia como factores de legitimación y dinamización del proceso de recuperación de la memoria histórica. Como conclusión se propone considerar a Rivas como un emprendedor de la memoria (Jelin) y sus obras como 'lieux de memoire' (Nora) por su condición de artefactos culturales de integración social.

Cadmium analytical results from sediment and foraminifera shells

There has been a major contradiction between benthic foraminiferal Cd/Ca and d13C data concerning the labile nutrient chemistry of the Southern Ocean during the Last Glacial Maximum (LGM). Cd data indicates that LGM South Atlantic nutrient concentrations were as low as they are today, indicative of a persistent influx of nutrient-depleted North Atlantic Deep Water (NADW). d13C data indicates that LGM South Atlantic nutrient concentrations were much higher than at present (even higher than anywhere else in the ocean at that time), and these data have been interpreted as signifying the complete shutdown ofthe export of NADW into the global ocean. This paper examines both true geochemical differences and various confounding foraminiferal artifacts for both tracers. While many different processes and artifacts affect both tracers in the margin, we conclude the discrepancy is mainly due to the "Mackensen Effect" of low foraminiferal d13C as a result of high carbon flux to the sediments, and that LGM Atlantic Sector Southern Ocean nutrient concentrations remained similar to the levels encountered today.

Seawater carbonate chemistry and Strongylocentrotus purpuratus body length and gene expression pattern changes during experiments, 2011

Extensive use of fossil fuels is leading to increasing CO2 concentrations in the atmosphere and causes changes in the carbonate chemistry of the oceans which represents a major sink for anthropogenic CO2. As a result, the oceans' surface pH is expected to decrease by ca. 0.4 units by the year 2100, a major change with potentially negative consequences for some marine species. Because of their carbonate skeleton, sea urchins and their larval stages are regarded as likely to be one of the more sensitive taxa. In order to investigate sensitivity of pre-feeding (2 days post-fertilization) and feeding (4 and 7 days post-fertilization) pluteus larvae, we raised Strongylocentrotus purpuratus embryos in control (pH 8.1 and pCO2 41 Pa e.g. 399 µatm) and CO2 acidified seawater with pH of 7.7 (pCO2 134 Pa e.g. 1318 µatm) and investigated growth, calcification and survival. At three time points (day 2, day 4 and day 7 post-fertilization), we measured the expression of 26 representative genes important for metabolism, calcification and ion regulation using RT-qPCR. After one week of development, we observed a significant difference in growth. Maximum differences in size were detected at day 4 (ca. 10 % reduction in body length). A comparison of gene expression patterns using PCA and ANOSIM clearly distinguished between the different age groups (Two way ANOSIM: Global R = 1) while acidification effects were less pronounced (Global R = 0.518). Significant differences in gene expression patterns (ANOSIM R = 0.938, SIMPER: 4.3% difference) were also detected at day 4 leading to the hypothesis that differences between CO2 treatments could reflect patterns of expression seen in control experiments of a younger larva and thus a developmental artifact rather than a direct CO2 effect. We found an up regulation of metabolic genes (between 10 to 20% in ATP-synthase, citrate synthase, pyruvate kinase and thiolase at day 4) and down regulation of calcification related genes (between 23 and 36% in msp130, SM30B, SM50 at day 4). Ion regulation was mainly impacted by up regulation of Na+/K+-ATPase at day 4 (15%) and down regulation of NHE3 at day 4 (45%). We conclude that in studies in which a stressor induces an alteration in the speed of development, it is crucial to employ experimental designs with a high time resolution in order to correct for developmental artifacts. This helps prevent misinterpretation of stressor effects on organism physiology.

(Table 2) Location, age of accompanied sediments, chemical and Sr isotopic compositions of manganese nodules in DSDP/ODP cores

Strontium isotopic compositions of acetic acid (HOAc) leachate fractions of eight manganese oxide deposits from the modern seafloor, and of twenty-one buried manganese nodules from Cretaceous to Recent sediments in DSDP/ODP cores were measured. ratios of HOAc leachates in all modern seafloor manganese oxides of various origins are identical with present seawater. The ratios of the HOAc leachates of buried nodules from DSDP/ODP cores are significantly lower than those of nodules from the modern seafloor and are mostly identical with coeval seawater values estimated from the age of associated sediments. It is suggested that the buried nodules in DSDP/ODP cores are not artifacts transported from the present seafloor during the drilling process, but are in situ fossil deposits from the past deep-sea floor during Cretaceous to Quaternary periods. The formation of deep-sea fossil nodules prior to the formation of Antarctic Bottom Water (AABW) indicates that the circulation of oxygenated deep seawaters have activately deposited manganese oxides since the Eocene Epoch, or earlier.

(Table 2) U-channel paleomagnetic record of ODP Site 178-1098

Thick Holocene sedimentary sections (>45 m) cored in the Palmer Deep by the United States Antarctic Program (USAP) and during Ocean Drilling Program (ODP) Leg 178 provide the first opportunity to examine past geomagnetic field behavior at high southern latitudes. After removal of a low-coercivity drilling overprint the sediments display a stable, single-component remanent magnetization. Two short cores that recovered the uppermost 2.6 m of sediment have inclinations that fluctuate about the present day inclination (-57°) measured at Faraday Station, and several features with wavelengths of 10 to 20 cm appear to be correlative. However, shipboard measurements of inclination fluctuations on split-core samples from three holes drilled at ODP Site 1098 do not correlate well with each other, even though the intensity and susceptibility data correlate very well and the overall mean inclination for cores from each hole is consistent with the expected geocentric axial dipole (GAD) inclination. The correlation is improved dramatically by using inclinations measured on u-channels taken from the pristine center of a split core. Consequently, the anomalous directions and the resulting poor between-hole correlation of inclinations obtained from shipboard data can be attributed to coring-induced deformation, which is common on the outer edge of ODP piston cores, and/or measurement artifacts in the split-core data. Our preferred inclination record is thus derived from u-channel results. The upper ~25 m represents continuous sedimentation over the past 9000 yr, with an average sedimentation rate exceeding 250 cm/kyr (0.25 cm/yr). Given that remanence measurements on u-channels average over an interval <7 cm long, we obtained independent measurements of the paleo-geomagnetic field that average over only ~30 yr. This high-resolution record is characterized by an inclination that fluctuates within +/-15° of the current GAD inclination.

ThreeDimensional Epigraphic Recording at Stobi (Former Yugoslav Republic of Macedonia): Creating a Virtual Lapidarium

There is an increased need for 3D recording of archaeological sites and digital preservation of their artifacts. Digital photogrammetry with prosumer DSLR cameras is a suitable tool for recording epigraphy in particular, as it allows for the recording of inscribed surfaces with very high accuracy, often better than 2 mm and with only a short time spent in the field. When photogrammetry is fused with other computational photography techniques like panoramic tours and Reflectance Transformation Imaging, a workflow exists to rival traditional LiDAR­based methods. The difficulty however, arises in the presentation of 3D data. It requires an enormous amount of storage and end­user sophistication. The proposed solution is to use game­engine technology and high definition virtual tours to provide not only scholars, but also the general public with an uncomplicated interface to interact with the detailed 3D epigraphic data. The site of Stobi, located near Gradsko, in the Former Yugoslav Republic of Macedonia (FYROM) was used as a case study to demonstrate the effectiveness of RTI, photogrammetry and virtual tour imaging working in combination. A selection of nine sets of inscriptions from the archaeological site were chosen to demonstrate the range of application for the techniques. The chosen marble, sandstone and breccia inscriptions are representative of the varying levels of deterioration and degradation of the epigraphy at Stobi, in which both their rates of decay and resulting legibility is varied. This selection includes those which are treated and untreated stones as well as those in situ and those in storage. The selection consists of both Latin and Greek inscriptions with content ranging from temple dedication inscriptions to statue dedications. This combination of 3D modeling techniques presents a cost and time efficient solution to both increase the legibility of severely damaged stones and to digitally preserve the current state of the inscriptions.

Disability in the Digital Age: Reconfiguring Access, Inclusion and Equality

There is an abundance of research that examines disability and technology in the context of computers and the Internet, however few have examined disability and mobile devices. Also largely absent from existing literature are the voices of disabled people themselves. This dissertation draws upon science and technology studies (STS) and disability studies to address these gaps by conducting in-depth qualitative research that examines disabled people’s experiences using smartphones and tablets. At its core, this dissertation aims to provide insight on the following: 1) an understanding of how disability is perceived in the digital age and the subjective meanings of access, inclusion and equality; 2) the ways in which mobile devices impact the lived experience of disability; and 3) how perspectives in disability studies and STS can be applied to understand the relationship between the body, disability and technology. The empirical contribution of this research draws from participant diaries and interviews with disabled people, as well as from open-ended questionnaires completed by mobile app developers. The concept of ‘subjectivities of disability’ is introduced to refer to the uniquely personal and individual experience of disability. Findings reveal that mobile device use amongst disabled people redefines their subjectivities of disability through socio-technical interactions whereby disabled people use their devices in ways that are integrated into their everyday lives and positively shapes how they view themselves in relation to their experience of disability. The responses from app developers reveal that there is a place for disability in the mobile market and that disabled people play a key role in making apps accessible. The data suggests that mobile devices facilitate access, inclusion and equality by integrating the body in ways that recognize and accommodate diversity. The results furthermore make it clear that the interaction between disabled people and mobile devices takes on an embodied and social characteristic. This research concludes that both on an individual level and collectively, disabled people are engaging with digital artifacts in ways that promote agency and independence as well as reshaping how disability is experienced and perceived in the digital age.

CT Image Electron Density Quantification in Regions with Metal Implants: Implications for Radiotherapy Treatment Planning

In radiotherapy planning, computed tomography (CT) images are used to quantify the electron density of tissues and provide spatial anatomical information. Treatment planning systems use these data to calculate the expected spatial distribution of absorbed dose in a patient. CT imaging is complicated by the presence of metal implants which cause increased image noise, produce artifacts throughout the image and can exceed the available range of CT number values within the implant, perturbing electron density estimates in the image. Furthermore, current dose calculation algorithms do not accurately model radiation transport at metal-tissue interfaces. Combined, these issues adversely affect the accuracy of dose calculations in the vicinity of metal implants. As the number of patients with orthopedic and dental implants grows, so does the need to deliver safe and effective radiotherapy treatments in the presence of implants. The Medical Physics group at the Cancer Centre of Southeastern Ontario and Queen's University has developed a Cobalt-60 CT system that is relatively insensitive to metal artifacts due to the high energy, nearly monoenergetic Cobalt-60 photon beam. Kilovoltage CT (kVCT) images, including images corrected using a commercial metal artifact reduction tool, were compared to Cobalt-60 CT images throughout the treatment planning process, from initial imaging through to dose calculation. An effective metal artifact reduction algorithm was also implemented for the Cobalt-60 CT system. Electron density maps derived from the same kVCT and Cobalt-60 CT images indicated the impact of image artifacts on estimates of photon attenuation for treatment planning applications. Measurements showed that truncation of CT number data in kVCT images produced significant mischaracterization of the electron density of metals. Dose measurements downstream of metal inserts in a water phantom were compared to dose data calculated using CT images from kVCT and Cobalt-60 systems with and without artifact correction. The superior accuracy of electron density data derived from Cobalt-60 images compared to kVCT images produced calculated dose with far better agreement with measured results. These results indicated that dose calculation errors from metal image artifacts are primarily due to misrepresentation of electron density within metals rather than artifacts surrounding the implants.

DNA from historical and trophy samples provides insights into white shark population origins and genetic diversity

Characterizing genetic variation by retrospective genotyping of trophy or historical artifacts from endangered species is an important conservation tool. Loss of genetic diversity in top predators such as the white shark Carcharodon carcharias remains an issue, exacerbated in this species by declining, sometimes isolated philopatric populations. We successfully sequenced mitochondrial DNA (mtDNA) D-loop from osteodentine of contemporary South African white shark teeth (from 3 jaws), and from 34 to 129 yr old dried cartilage and skin samples from 1 Pacific Ocean and 5 Mediterranean sharks. Osteodentine-derived sequences from South African fish matched those derived from an individual’s finclips, but were generally of poorer quality than those from skin and cartilage of historical samples. Three haplotypes were identified from historical Mediterranean samples (n = 5); 2 individuals had unique sequences and 3 shared the contemporary Mediterranean haplotype. Placement of previously undescribed mtDNA haplotypes from historical material within both the Mediterranean and Pacific clades fits with the accepted intra-specific phylogeny derived from contemporary material, verifying our approaches. The utility of our methodology is in its provision of additional genetic resources from osteodentine (for species lacking tooth pulp) and cartilage of rare and endangered species held in often uncurated, contemporary and historical dry collections. Such material can usefully supplement estimates of connectivity, population history, and stock viability. We confirm the depauperate haplotype diversity of historical Mediterranean sharks, consistent with founding by a small number of Pacific colonizers. The consequent lack of diversity suggests serious challenges for the maintenance of this top predator and the Mediterranean ecosystem.