Thesis (Ph.D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 1999. / Includes bibliographical references (leaves 115-122). / by Paula M. Ragan. / Ph.D.

Thesis: Ph. D. in Biomedical Engineering, Harvard-MIT Program in Health Sciences and Technology, 2018. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references (pages 181-208). / MYC is one of the most commonly dysregulated genes across all cancers. As a master transcription factor with greater than 10,000 binding sites throughout the genome, the MYC oncoprotein coordinates a transcriptional regulatory network consisting of approximately 15% of all genes, controlling cancer hallmark expression programs responsible for cellular proliferation, growth, metabolism, and evasion from apoptosis. MYC dysregulation occurs genetically, epigenetically, and post-transcriptionally through a wide variety of mechanisms. Despite its well-characterized properties as a proto-oncogene, direct potent and selective inhibition of MYC remains a significant challenge. Models of systemic MYC inhibition utilizing inducible genetic constructs in mice have revealed that inhibition of MYC activity leads to potent tumor regression with an evident therapeutic window, suggesting that pharmacologic MYC inhibition may be a viable cancer therapeutic strategy. Small molecule inhibitors designed to block MYC protein activity exhibit low potency, display poor selectivity, and lack antitumor efficacy, which has led MYC to be historically classified as 'undruggable.' Efforts aimed at indirectly targeting MYC transcription often lead to development of resistance characterized by reinforced expression of MYC. Clearly, alternate strategies are needed to achieve selective and potent inhibition of MYC. The goals of this research were to develop antisense oligonucleotides specifically targeted against the MYC mRNA to achieve potent inhibition of MYC translation, and to characterize the activity of these molecules as specific modulators of MYC expression and as prototypical MYC-directed therapeutics. We designed and synthesized a library of MYC-targeting antisense oligonucleotides (MYCASOs) containing several chemical synthetic features to increase target affinity and stability. Treatment of MYC-expressing cancer cells with MYCASOs leads to RNase H-mediated cleavage of MYC mRNA and a potent decrease in MYC protein levels. MYC knockdown is accompanied by significant effects on cellular viability and inhibition of cellular proliferation. Furthermore, MYCASO treatment specifically perturbs MYC-driven gene expression signatures. In a MYC-induced murine model of hepatocellular carcinoma, MYCASO treatment leads to cleavage of the MYC transcript, decreased MYC protein levels within tumors, and reduced tumor burden. MYCASOs represent a new chemical tool for in vitro and in vivo modulation of MYC activity, and promising therapeutic agents for MYC-addicted tumors. / by Taylor Elizabeth Gill. / Ph. D. in Biomedical Engineering

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2008. / Includes bibliographical references (p. 98-101). / Coronary heart disease (CHD) is a major health concern for Americans and people worldwide. Arteriogenesis, an adaptive remodeling process in which pre-existing collateral arterioles remodel to form large diameter conductance arteries, has received recent attention for its therapeutic potential in treating CHD, but the mechanisms regulating the process remain incompletely understood. In particular, little is known about how collateral flow, and the resulting effect of shear stress acting along the collateral vessel wall, regulates coronary collateralization. This Thesis combines a series of experimental systems to define the responses evoked in endothelial cells exposed to hemodynamic waveforms characteristic of coronary collateral vessels and the subsequent paracrine effects on smooth muscle cells. Initially, a lumped parameter model of the human coronary collateral circulation was used to simulate normal (NCC) and adaptive remodeling (ACC) coronary collateral shear stress waveforms. These waveforms were then applied to cultured human endothelial cells (EC) and the resulting differences in EC gene expression were assessed by genome-wide transcriptional profiling, identifying genes distinctly regulated by collateral flow, including genes important for endothelial-smooth muscle interactions. In particular, the transcription factor KLF2 was upregulated by the ACC waveform and several of its downstream targets displayed the expected modulation, including the downregulation of Connective tissue growth factor (CTGF). Moreover, delivery of endothelial conditioned medium generated throughout the collateral flow experiments to culture smooth muscle cells (SMC) resulted in the modulation of SMC genes related to vessel maturation and stabilization. In the second part of this Thesis, the effect of endothelial KLF2 expression on SMC migration was characterized using a 3D microfluidic assay capable of monitoring SMC migration in co-culture with EC. Using this 3D system, it was found that KLF2-expressing EC co-cultured with SMC significantly reduce SMC migration compared to control EC and that this reduction can be rescued by delivery of soluble CTGF. / (cont.) Collectively, these results demonstrate that the shear stress generated by collateral flow evokes distinct EC gene expression profiles and functional phenotypes that subsequently influence vascular events important for adaptive remodeling and provides experimental evidence supporting efforts directed at investigating endothelial KLF2 as a molecular target for therapeutic arteriogenesis. / by Pater J. Mack. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / "September 2009." Cataloged from PDF version of thesis. / Includes bibliographical references (p. 120-126). / An Electrolarynx (EL) is a battery-powered device that produces a sound that can be used to acoustically excite the vocal tract as a substitute for laryngeal voice production. ELs provide laryngectomy patients with the basic capability to communicate, but current EL devices produce a mechanical speech quality which has been largely attributed to the lack of natural fundamental frequency (F0) variation. In order to improve the quality of EL speech, the present study aimed to develop and evaluate an automatic F0 control scheme, in which F0 was modulated based on variations in the root-mean-squared (RMS) amplitude of the EL speech signal. Recordings of declarative sentences produced by two male subjects before and after total laryngectomy were used to develop procedures for calculating F0 contours for EL speech, and perceptual experiments and acoustic analyses were conducted to examine the impact of F0 modulation on the quality and prosodic function of the EL speech. The results of perceptual experiments showed that modulating the F0 of EL speech using a linear relationship between amplitude and frequency made it significantly more natural sounding than EL speech with constant F0, but also revealed some limitations in terms of communicating linguistic contrasts (distinction between question vs. statement and location of contrastive stress). Results are interpreted in relation to the acoustic characteristics of F0 modified EL speech and discussed in terms of their clinical implications and suggestion for improved algorithms of F0 control in EL speech. / by Yoko Saikachi. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2008. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / Optical Coherence Tomography (OCT) is a developing medical imaging technology that generates micron resolution cross-sectional images of subsurface internal tissue structure in situ and in real time, without the need to remove and process specimens. Previous studies have suggested that OCT holds great potential for use in laparoscopic and endoscopic applications to detect early stage neoplastic pathologies. A minimally invasive imaging modality capable of identifying pre-malignant tissues in vivo could be used to guide conventional excisional biopsy and histology, thereby reducing sampling error and enabling earlier detection and treatment. One limitation of prior endoscopic OCT imaging methods is the inability to visualize cellular features characteristic of early disease states such as neoplasia. This thesis seeks to demonstrate that advances in OCT resolution and in miniaturized imaging devices will lead to enhanced visualization of pathologic changes in vivo at both the tissue architectural and cellular levels. Toward this goal, three technological advances are made. First, compact and portable laser light sources for clinical ultrahigh resolution OCT are demonstrated based on supercontinuum generation in highly nonlinear optical fibers. Second, an extension of OCT called optical coherence microscopy (OCM) is developed for in vivo cellular imaging. High speed OCM system designs are demonstrated and characterization of OCM imaging parameters is performed. Importantly, this work demonstrates that OCM can make use of broadband laser sources to image cellular features with reduced numerical aperture compared to confocal microscopy, thereby facilitating the development of small diameter endoscopic probes. / (cont.) Third, two-axis scanning catheters based on micromirror technology are designed and demonstrated for ultrahigh resolution three-dimensional and en face OCT imaging. To demonstrate feasibility of these advances in future clinical applications, ex vivo imaging studies of endoscopically accessible human gastrointestinal tissues including key pathologies are performed. Results demonstrate that three-dimensional and cellular resolution optical coherence imaging can significantly improve performance over conventional OCT methods for gastrointestinal endoscopy. Finally, this thesis also explores a new application for optical coherence tomography in neuroscience. Optical methods are currently being used to study the neurovascular response to functional activation, but most existing techniques lack depth resolution. Through correlation with video microscopy, OCT is shown to enable depth-resolved cross-sectional imaging of functional activation in the important rat somatosensory cortex model system. With further development, OCT may offer a new tool for basic and applied neuroscience research. / by Aaron Dominic Aguirre. / Ph.D.

Thesis: Ph. D. in Medical Engineering and Medical Physics, Harvard-MIT Program in Health Sciences and Technology, 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 299-330). / More than one million joint replacements are performed in the USA annually. However, around 10 % of patients require revision surgery within 10 years with prosthetic joint infections (PJI) as a common reason. PJI has a recurrence rate of 16 %, a mortality rate of 2.5 %, and end-stage treatments involving arthrodesis and amputation. Most drug eluting polymers that were in development to address this problem failed due to toxic degradation products, insufficient drug release, and insufficient mechanical strength. The gold standard of treatment uses antibiotic eluting bone cement which has a mechanical failure rate of 26-60 % within 49-54 months if used under load bearing conditions. Therefore, despite advances in orthopedic materials, development of drug-eluting devices with effective, sustained delivery with the necessary mechanical strength for a fully load bearing joint implant has been elusive. Here, we report the synthesis and application of a drug eluting, fully load bearing, and articulating joint prosthesis that has superior mechanical strength and drug elution profile compared to the clinical gold standard, antibiotic eluting bone cement. We modified the eccentricity of drug clusters and percolation threshold in the polymeric matrix of Ultra-High Molecular Weight Polyethylene (UHMWPE), which resulted in maximized drug elution and mechanical strength retention. The optimized antibiotic eluting UHMWPE elutes antibiotic at a higher concentration for a longer period of time than antibiotic eluting bone cement while retaining the mechanical and wear properties of clinically used UHMWPE joint prosthesis. After drug elution, the empty drug clusters in the polymer were filled with biological lubricants during articulation, which through a combination of weeping and elastohydrodynamic lubrication, reduced the overall wear rate of the UHMWPE. Treatment of Staphylococcus aureus infected lapine knee with the antibiotic eluting UHMWPE showed complete bacterial eradication without any detectable systemic side effect. Taken together, our study showed that the drug-eluting UHMWPE joint implants in this study are promising candidates for further clinical trial and as the next generation prosthetic joints. / by Vincentius Jeremy Suhardi. / Ph. D. in Medical Engineering and Medical Physics

Thesis (M. Eng.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / MIT Institute Archives copy: Pages 101-130 bound in reverse order. / Includes bibliographical references (p. 123-130). / Cardiac arrhythmias are characterized by a disruption or abnormal conduction of electrical signals within the heart. Treatment of arrhythmias has dramatically evolved over the past half-century, and today, minimally-invasive catheter-based therapy is the preferred method of eliminating arrhythmias. Using an electroanatomical (EA) mapping system, which precisely tracks the position of catheters inside the patient's body, it is possible to construct three-dimensional maps of the ventricular and atrial chambers of the heart. Each point of these maps is annotated based on bioelectrical signals recorded from the electrodes located at the tip of the catheter. These maps are then used to guide catheter ablation within the heart. However, the electroanatomical mapping procedure results in relatively sparse sampling of the heart and a significant amount of time and skill are require to generate these maps. In this thesis, we present our software system for the integration of pre-operative, patient-specific magnetic resonance (MR) or computed tomography (CT) imaging data with real-time electroanatomical mapping (EAM) information. / (cont.) Following registration between the EAM and imaging data, the system allows for real-time catheter navigation within patient-specific anatomy. We then evaluate candidate registration strategies to rapidly and accurately align the pre-operative imaging data with the intra-operative mapping data using simulated electroanatomical mapping data using the great cardiac vessels including the aorta, superior vena cava, and coronary sinus. Based on these in vitro results, we focus on a registration strategy which is constrained by the ascending and descending aorta. In vivo prospective evaluation of the resulting image integration was then performed (n>200) in both experimental and clinical electrophysiology procedure. To compensate for residual error following registration or patient movement during a procedure, we present and evaluate warping strategies for deforming the pre-operative imaging data into agreement with the intra-operative mapping information. / by Zachary John Malchano. / M.Eng.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references (leaf [39]). / Introduction: In the medical device space, a large proportion of the breakthrough inventions are developed by small firms that use private equity to bring their technologies from concept to varying stages of development. Medical Device companies spend a large proportion (11.4 % in 2002) of their sales on R&D, second only to Pharmaceutical companies. Smaller companies, in the meanwhile, spent 343 % of their sales in the same year'. [The Lewin Group (AdvaMed), 2004]. Private Equity financing is a critical factor that enables small start-ups to develop new technologies without a viable revenue stream to support the necessary R&D expenditure. In the medical device space, it has been noted that Venture Capital firms (VC's) use high risk capital to invest in early stage companies, and look for "exits" through either an Initial Public Offering (IPO) or through the sale of the start-up to an established firm. Corporations are also involved in varying degrees in early venture investments, through what is sometimes called Corporate Venture Capital (CVC), mainly for strategic reasons. Through CVC investments, some corporations hope, that as an insider, they would be able to judge better whether a particular company is a good target for acquisition. In this paper I review the exits through acquisition, from the perspective of venture backed start-ups, and hypothesize that factors related to the nature of investors, the type of investment, the impact of capital markets and the Intellectual Property of the company are associated with a higher exit valuation. / Ganesh R. Nair. / S.M.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / "June 2007." / Includes bibliographical references (leaves 153-157). / A classic finding in asthma is a change in the structural organization of the airway epithelium. This complex process known as airway remodeling is not fully understood, and we believe that the forces accompanying airway constriction activate the epithelium and contribute to airway remodeling. To better understand this mechanotransduction mechanism we used an in vitro system of cultured normal human bronchial epithelial cells that could simulate compressive stresses experienced by the epithelium during bronchoconstriction. The application of a transcellular pressure gradient (10-50cmH20) for 10 minutes resulted in transient activation of the epidermal growth factor receptor (EGFR) - MAP kinase (ERK) signaling pathway. Furthermore, specialized real-time high-speed imaging revealed an exponential decrease in the volume of the compliant lateral intercellular space (LIS) separating neighboring cells. The measured LIS volume collapse curves were directly inputted into 2-D and 3-D numerical finite element models, whose output was EGFR-ligand concentration dynamics in the LIS. / (cont.) During the first three minutes under pressure, the calculated increase in ligand concentration (specifically HB-EGF, which is made by the cells and shed into the LIS, thereby constituting an autocrine loop with the EGFR) matched the measured phosphorylated EGFR (pEGFR) dynamics. The model thus provided crucial insight into how an observed change in LIS geometry esulted in activation of the EGFR signaling pathway. This insight, coupled to EGFR signaling models, could one day be applied to the design of novel pharmacogenetic therapeutics aimed at preventing airway over-activation and potentially hindering airway remodeling progression in asthmatic patients. / by Nikola Kojić. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 51-54). / Background: If we are to successfully treat cancer, we must understand the biologic underpinnings in conjunction with early diagnosis. Genome-wide expression studies have advanced the research of many cancers. Nevertheless, understanding which genes are expressed in a tumor is not equivalent to knowing which proteins are being produced. Proteomics hold great promise for careful examination of the proteins in complex biologic fluids and tissues, and it may be possible to detect disease from a patient's serum, long before it would otherwise be clinically evident. Although there have been steady advances in all the steps of a proteomic analysis, much remains to be standardized. Because of some high-profile problems with the initial analysis of ovarian cancer proteomic data, early exuberance has now been tempered and replaced by a more methodical approach to these studies. Hypothesis: My hypothesis in this thesis is that proteomics is a valuable tool in the diagnosis and study of cancer, as will be demonstrated in several steps. Methods: First, I describe the current field of proteomics, specifically as it applies to early detection of cancer and biomarker discovery. / (cont.) I lay out the current state-of-the-art technologies for preparing samples and enumerating the proteins in complex fluids and tissues, giving special treatment to the main threats to validity-chance and bias. I also describe the bioinformatic tools necessary for analyzing the large amounts of data produced. Through the example of a mouse model of colorectal carcinoma, I demonstrate the steps involved in a proteomic study, from procuring samples to peptide and protein determination to bioinformatic analysis. Finally, I discuss these findings in light of the proteomic considerations discussed earlier. Results: From this work, I discovered that proteomic profiling can describe the proteins in serum from mice both with and without colon cancer. Furthermore, I developed a naive Bayes classifier that could distinguish between the serum of mice with colorectal carcinoma and their normal litter-mates. Contributions: Through this work, I have contributed the following. I described the field of proteomics with special emphasis on cancer biomarker discovery and early detection. I enumerated the challenges and pitfalls to developing early detection schemes for cancer based on high-dimensional proteomic analyses. / (cont.) I described a set of experiments on mice harboring a gene mutation that predisposes them to colorectal carcinoma. I detailed the bioinformatic analysis of this data, including the development of a naive Bayes classifier to differentiate the cancerous state from the normal state. Finally, I discussed the caveats of the current work, in reference to the initial discussion on the challenges and pitfalls of early detection schemes and cancer biomarker discovery. / by Samuel Louis Volchenboum. / S.M.