Optoacoustic (OA) imaging is an emerging low-cost hybrid imaging investigation/technique currently in clinical feasibility studies for breast cancer diagnosis and staging. The technique applies pulsed light to the tissue of interest where molecules absorb the light photons and generate acoustic pressure waves. The resulting acoustic responses are detected using ultrasound transducers and converted into images. Image contrast within a pixel is dependent on the relative concentration and absorption characteristics (i.e. spectrum) of the chromophores within the illuminated tissue. Thus, tissue responses from illumination using multiple wavelengths, chosen to reflect the differential absorption of oxy-/deoxy- and total haemoglobin, can be measured. In turn, these signals can be regarded as surrogate measures of tissue hypoxia and neoangiogenesis, hallmarks of cancer associated with adverse outcomes. The aim of this PhD was to translate optoacoustic imaging into the breast clinic to try and fulfil some of the unmet clinical needs in breast cancer imaging using the imaging biomarker roadmap by O'Connor et al. Translation of this new technology to the clinical environment required extensive preparatory work, including the procurement and installation of a scanner prototype, liaison with UK regulatory bodies to secure ethical and MHRA approval, as well as several technical developments (performed during the course of the PhD) to make the technology suitable for breast cancer imaging. The first chapter of the thesis reviews the unmet needs of breast cancer imaging, being followed by a summary of recent techniques and technologies that may potentially fulfil gaps in knowledge and address some of the specific diagnostic challenges in breast cancer imaging. The capabilities of optoacoustic imaging are then discussed in the context of this evolving landscape of new imaging techniques and technologies with a particular focus on the tumour biology (neoangiogenesis and hypoxia) that can be measured in humans using multimodality and multi parametric imaging. Chapter 2 reviews of the current state of clinical translation of optoacoustic imaging, highlighting the particular areas in which clinical translation has advanced the most (breast cancer, melanoma and inflammatory bowel disease). Chapter 3 discusses the logistical, regulatory and technical challenges and solutions involved in translating optoacoustic imaging to the clinic and setting up a clinical service. Chapter 4 presents a series of validation experiments of oxygen saturation aimed at establishing the relationship between the optoacoustic signal and invasive pO2 measurements with an OxyLite probe in a porcine kidney model. This work was conducted in close collaboration with leading clinicians from the local transplant team. The following chapter describes the results of the first stage of our clinical work in the breast, namely the healthy volunteer study. This part had several aims: to perform qualitative assessment of the optoacoustic features of the normal breast under physiological conditions; to establish a robust scanning technique and identify technical and image interpretation pitfalls; and to perform qualitative evaluation of the hormonal changes that occur during the menstrual cycle and menopause, which, in turn, were used to validate surrogate measures of oxy-, deoxy and total haemoglobin. Chapter 6 then focuses on the qualitative assessment of benign and malignant breast lesions and their appearances on optoacoustic imaging. The patient study was divided into three phases. Phase 1 created a feature set to differentiate benign from malignant lesions, while Phase 2 was a transition between the prototype scanner and the installation of the first-generation clinical scanner. In Phase 3 the feature set created in Phase 1 was validated in a reader study. The sensitivity and specificity of optoacoustic imaging for lesion detection and differentiation of benign from malignant lesions was compared with mammography and ultrasound. Chapter 7 then deals with the quantitative analysis of the Phase 1 and Phase 3 data acquired in Chapter 6, assessing the relationships between the use of single wavelengths, spectral unmixing, vascularity versus receptor status, heterogeneity of signal intensity in relation to tumour stage and grade. This chapter also discusses the potential and limitations of quantifying the optoacoustic signal and leads to the final chapter, a discussion of future directions in optoacoustic imaging in breast cancer. At the end of this thesis, chapter 8 briefly discusses the potential future directions for the use of optoacoustic imaging as a clinical and scientific tool.

Cardiovascular disease is the leading cause of death in the United States, accounting for approximately 25% of total deaths. Myocardial infarction (MI) is an extreme case of cardiovascular disease where ischemia leads to irreversible tissue necrosis. As the heart lacks the capacity to endogenously regenerate, the infarcted region is negatively remodeled, reducing cardiac function. Current therapies are not able to regenerate cardiac function post-MI, requiring novel approaches such as tissue engineering. However, there are three major pitfalls that are currently limiting the clinical translation of a tissue engineered cardiac patch: lack of proper vascularization within the tissues; biocompatible material; and lack of electrical integration between engineered tissue and host. The research within this dissertation aimed to engineer solutions to overcome these three pitfalls. Plants and animals exploit fundamentally different approaches to transporting fluids, yet there are surprising structural similarities. To take advantage of these similarities, we looked across different kingdoms and investigated whether plants and their innate vasculature could serve as perfusable scaffolds for tissue engineering. Standard perfusion decellularization techniques were adapted and applied to spinach leaves, which were found to be fully devoid of DNA following processing. Leaf vasculature remained patent post-decellularization and supported transport of various sized microparticles. Human cells successfully seeded onto and inside the plant scaffolds. Decellularized leaves were found to be nearly void of any cytotoxic affects. Leaf biocompatibility was then investigated in vivo through subcutaneous implantation in a rat model. Leaf scaffolds were found to be biocompatible after 4 weeks of implantation. Furthermore, leaves that were pre-functionalized with an RGD-dopamine peptide were fully integrated into the host tissue within one week. This shows the leaf scaffold’s potential to be an immuno-modulatory material, depending upon the intended application. Electrically conducting biofibers were engineered through the combination of fibrin microthreads and engineered conductive HEK293 cells. Biofibers could act as a modular platform to allow for electrical integration between the host tissue and any engineered cardiac patch. Biofibers directionally carried electrical current and were found capable of bridging electrical signal between two separate clusters of cardiomyocytes. In vivo investigation bridging a biofiber from the left atria to the left ventricle was accomplished in a rat model. Electrical maps demonstrated a visible accessory pathway that created a feedback electrical signal from the ventricle to the atria through the implanted biofiber. These results demonstrate electrical integration in vivo between host myocardium and the engineered biofiber.

T1rho MRI, spin-lattice relaxation in the rotating frame, is postulated to be sensitive to early biochemical changes within articular cartilage that may lead to osteoarthritis. This means that it has potential as a non-invasive, early biomarker for disease progression. However, T1rho has been primarily studied in a research setting. Therefore, the main question posed in this work is: Can T1rho MRI be used in an at-risk population (ACL-rupture patients) and translated to a clinical setting? To answer this question, two tools (Relaxometry program, Line Profile Analysis) were created and validated for measuring T1rho within living subjects. These tools were used to answer the following sub-questions: 1) Is there a quantifiable difference between healthy (normal subject)and injured cartilage (ACL-rupture patient) in living subjects? 2) Is there some measure which can be tracked over time and used as a meaningful pre-screening procedure for post-traumatic osteoarthritis development at 3.0T MRI? 3) Is it possible to obtain the same or similar quality data from 1.5T T1rho (predominant MRI field strength found in clinics) as found from 3.0T T1rho images? These questions were answered affirmatively, and the author concludes that T1rho could be translated and applied into a clinical setting across the nation.

Translational Biomedical Informatics (TBMI) is an emerging discipline expanding beyond traditional bioinformatics, with a focus on developing computational technologies for real-world biomedical practice. The goal of my Ph.D. research is to address a few key challenges in TBI, including: (1) the high quality and reproducibility required by medical applications when processing high throughput data, (2) the need for knowledge management solutions that allow molecular data to be handled and evaluated by researchers, regulators, and doctors collectively, (3) the need for near real-time, efficient access to decision-oriented visualizations of integrated data and data processing results, and (4) the need for an integrated solution that can evolve as medical consensus evolves, without requiring retraining, overhaul or replacement. This dissertation resulted in the development and adoption of concrete web-based application deliverables in regular use by bioinformaticians, clinicians, biologists and nanotechnologists. These include: the Chip Artifact Correction (caCORRECT) web site and grid services, the ArrayWiki community microarray repository, and the SimpleVisGrid visualization grid services (including eGOMiner, nanoDRIVE, PathwayVis and SphingoVisGrid).

Translational biomedical informatics is the application of computational methods to facilitate the translation of basic biomedical science to clinical relevance. An example of this is the multi-step process in which large-scale microarray-based discovery experiments are refined into reliable clinical tests. Unfortunately, the quality of microarray data is a major issue that must be addressed before microarrays can reach their full potential as a clinical molecular profiling tool for personalized and predictive medicine. A new methodology, titled caCORRECT, has been developed to replace or augment existing microarray processing technologies, in order to improve the translation of microarray data to clinical relevance. Results of validation studies show that caCORRECT is able to improve the mean accuracy of microarray gene expression by as much as 60%, depending on the magnitude and size of artifacts on the array surface. As part of a case study to demonstrate the widespread usefulness of caCORRECT, the entire pipeline of biomarker discovery has been executed for the clinical problem of classifying Renal Cell Carcinoma (RCC) specimens into appropriate subtypes. As a result, we have discovered and validated a novel two-gene RT-PCR assay, which has the ability to diagnose between the Clear Cell and Oncocytoma RCC subtypes with near perfect accuracy. As an extension to this work, progress has been made towards a quantitative quantum dot immunohistochemical assay, which is expected to be more clinically viable than a PCR-based test.

Irreversible electroporation is a minimally invasive technique for the non-thermal destruction of cells in a targeted volume of tissue, using brief electric pulses, (~100 µs long) delivered through electrodes placed into or around the targeted region. These electric pulses destabilize the integrity of the cell membrane, resulting in the creation of nanoscale defects that increase a cell’s permeability to exchange with its environment. When the energy of the pulses is high enough, the cell cannot recover from these effects and dies in a non-thermal manner that does not damage neighboring structures, including the extracellular matrix. IRE has been shown to spare the major vasculature, myelin sheaths, and other supporting tissues, permitting its use in proximity to these vital structures. This technique has been proposed to be harnessed as an advantageous non-thermal focal ablation technique for diseased tissues, including tumors. IRE electric pulses may be delivered through small (ø ≈ 1 mm) needle electrodes, making treatments minimally invasive and easy to apply. There is sub-millimeter demarcation between treated and unaffected cells, which may be correlated with the electric field to which the tissue is exposed, enabling numerical predictions to facilitate treatment planning. Immediate changes in the cellular and tissue structure allow real-time monitoring of affected volumes with imaging techniques such as computed tomography, magnetic resonance imaging, electrical impedance tomography, or ultrasound. The ability to kill tumor cells has been shown to be independent of a functioning immune system, though an immune response seems to be promoted by the ablation. Treatments are unaltered by blood flow and the electric pulses may be administered quickly (~ 5 min). Recently, safety and case studies using IRE for tumor therapy in animal and human patients have shown promising results. Apart from these new studies, previous work with IRE has involved studies in healthy tissues and small cutaneous experimental tumors. As a result, there remain significant differences that must be considered when translating this ablation technique towards a successful and reliable therapeutic option for patients. The dissertation work presented here is designed to develop irreversible electroporation into a robust, clinically viable treatment modality for targeted regions of diseased tissue, with an emphasis on tumors. This includes examining and creating proving the efficacy for IRE therapy when presented with the many complexities that present themselves in real-world clinical patient therapies, including heterogeneous environments, large and irregular tumor geometries, and dynamic tissue properties resulting from treatment. The impact of these factors were theoretically tested using preliminary in vitro work and numerical modeling to determine the feasibility of IRE therapy in heterogeneous systems. The feasibility of use was validated in vivo with the successful treatment of human mammary carcinomas orthotopically implanted in the mammary fat pad of mice using a simple, single needle electrode design easily translatable to clinical environments. Following preliminary theoretical and experimental work, this dissertation considers the most effective and accurate treatment planning strategies for developing optimal therapeutic outcomes. It also experimentally characterizes the dynamic changes in tissue properties that result from the effects of IRE therapy using ex vivo porcine renal cortical tissue and incorporates these into a revised treatment planning model. The ability to use the developments from this earlier work is empirically tested in the treatment of a large sarcoma in a canine patient that was surgically unresectable due to its proximity to critical arteries and the sciatic nerve. The tumor was a large and irregular shape, located in a heterogeneous environment. Treatment planning was performed and the therapy carried out, ultimately resulting in the patient being in complete remission for 14 months at the time of composing this work. The work presented in this dissertation finishes by examining potential supplements to enhance IRE therapy, including the presence of an inherent tumor-specific patient immune response and the addition of adjuvant therapeutic modalities. / Ph. D.

Yes / Vat photopolymerization has garnered interest from pharmaceutical researchers for the fabrication of personalised medicines, especially for drugs that require high precision dosing or are heat labile. However, the 3D printed structures created thus far have been insoluble, limiting printable dosage forms to sustained-release systems or drug-eluting medical devices which do not require dissolution of the printed matrix. Resins that produce water-soluble structures will enable more versatile drug release profiles and expand potential applications. To achieve this, instead of employing cross-linking chemistry to fabricate matrices, supramolecular chemistry may be used to impart dynamic interaction between polymer chains. In this study, water-soluble drug-loaded printlets (3D printed tablets) are fabricated via digital light processing (DLP) 3DP for the first time. Six formulations with varying ratios of an electrolyte acrylate …