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. / Vita. / Includes bibliographical references (p. 289-300). / Metabolic diseases are an increasing health concern in the developed world. Type 2 Diabetes, (T2D) affects over 100 million people worldwide and significantly contributes to chronic diseases such as atherosclerosis and kidney failure. This condition is characterized by deregulation of glucose homeostasis through the development of insulin resistance, manifested as increased glucose production in the liver. Hepatic gluconeogenesis provides de novo formation of glucose from three carbon precursors such as glycerol, lactate, pyruvate and alanine. The upregulation of this pathway underlies the persistent hyperglycemia observed in diabetic patients. We have developed stable isotope tracer methods to reconstruct hepatic glucose production fluxes by infusion of [13C, 2H]-glycerol and mass spectrometry analysis of plasma metabolites. Using this methodology we observe physiologic changes in liver cell lines and primary hepatocyte cultures in the presence of hormones insulin/glucagon and in response to gluconeogenic precursor availability. We put forth the hypothesis that in the presence of glycerol as a gluconeogenic substrate, glucose-6-phosphatase has an important role in modulating metabolic flux through upper gluconeogenesis. Infusion of simultaneous tracer combinations in vivo including a novel [U-13C,2H5]-glycerol allow detailed net flux and reversibility reconstruction of upper gluconeogenesis to an unprecedented degree in a single experiment. We deployed the developed methods to probe glucose overproduction in the liver insulin receptor knockout (LIRKO) transgenic model of Type 2 Diabetes, and found unexpected similarities in the metabolic flux profile not observed by genomic, protein or metabolite measurements. / (cont.) Our results underscore the importance of flux measurement as a physiologic parameter akin to gene and protein expression in revealing the metabolic phenotype of cells, tissues and organisms. These methods have the potential to contribute as clinical assays to characterize excess glucose production as well as in drug development for new targets to control hepatic glucose production. / by José O. Alemán. / Ph.D.

Thesis (Ph. D. in Speech and Hearing Bioscience and Technology)--Harvard-MIT Program in Health Sciences and Technology, 2012. / Cataloged from PDF version of thesis. Vita. / Includes bibliographical references (p. 78-85). / While evidence from clinical and functional neuroimaging domains converges on a notion that auditory-motor networks can be remodeled functionally and structurally in response to experiences, studies that seek to evaluate these hypotheses by combining behavioral, functional, and structural measures are rare. Given relatively recent advances in neuroimaging, e.g. diffusion-tensor imaging (DTI) and functional neuroimaging methods (fMRI), it is now possible to structurally and functionally analyze these networks, as well as make inferences about them in situations where the networks are either functionally compromised by an auditory-motor feedback disorder, or structurally enhanced by an intense long-term auditory-motor training regimen. To this end, a three-fold course of study has been undertaken: (1) a between-group comparison of the structural aspects of the arcuate fasciculus (a prominent white-matter fiber tract that reciprocally connects the temporal and inferior frontal lobes and is thought to be important for auditory-motor interactions) of singers and those of matched nonsinging musicians, in order to evaluate the hypothesis that singers will exhibit structural differences specifically for aspects of vocal output that require rapid temporal processing and precise sound-motor matching. (2) a within-subject fMRI comparison of responses of young adults (non-musicians) to auditory feedback that is either unperturbed or shifted in pitch while they perform a pitch-matching task, to ascertain a functional network related to perceiving and perhaps compensating for mismatched auditory feedback. (3) a within-subject pilot study of the network ascertained in (2), now in a smaller group of young adults with an auditory-motor disorder/disconnection syndrome commonly referred to as tonedeafness (TD) or congential amusia (a conditioned marked by a high pitch discrimination threshold as well as readily apparent difficulty in matching pitches), in order to provide insight into how this network might behave in a state of long-term disorder. While this work corroborates previous work in clinical, behavioral, and neuroimaging domains, and sheds light on the organization of these auditory-motor networks (structurally and functionally) in the normal population, it also aids in understanding how these networks may be remodeled and optimized (structurally) in response to intense long-term training, how they adapt to an acutely compromised state (i.e. when input to the network is compromised or perturbed), as well as how they may adapt functionally in a chronically compromised state (i.e. tonedeafness). Taken together, these observations help to explain the functioning of the auditory-motor network in normal individuals and those with communication disorders, as well as well as shedding light on possible mechanisms of recovery as they participate in an intensive long-term auditory-motor therapy program. / by Gus F. Halwani. / Ph.D.in Speech and Hearing Bioscience and Technology

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / Includes bibliographical references (leaves 110-114). / My first hypothesis in this thesis is that there is significant value vested in traditional Chinese medicine that can be captured by converting them into ethical drugs through scientific analysis, screening and validation. Further, holistic treatment is a key difference between traditional Chinese medicine and western-type chemical drugs, which makes Chinese medicine a very valuable category of knowledge. Using mixed formula is a primary method of treatment in Chinese medicine. It is the application of distinctive medical philosophies of Chinese herbal medicines in practices, reflecting the uniqueness and advantages of Chinese medicine. For example, there are 96,592 mixed formula recorded by "Dictionary of Chinese Medicine Mixed Formula" published in 1997. My second hypothesis in this thesis is that value can be created and captured, under the globalization context, from mixed herbal formulas for the mainstream world market with the aid of fingerprint technologies. To enter western markets as officially approved drugs through critical pathways, both scientific and regulatory, Chinese herb drugs must demonstrate sound evidence for safety and efficacy. I address in this thesis one of the central concerns of the pharmaceutical companies and FDA, that is, how quality control and material consistency is assured and how toxicity and drug kinetics of Chinese herbal medicines, either in its raw form, its purified form, its composite extract form or its mixed formula form, may be measured with reasonable scientific certainty and what would be the likely trajectory of further research. / (cont.) My thesis research involves the following aspects: firstly, I characterize, by and through historical review and analysis, the formation of unique Chinese holistic medical philosophy to apply herbal medicines, particularly mixed herbal formulas, to systematically modulate the human body to prevent illnesses, to combat health problems and to restore balanced health; secondly, I performed a comparative study on the regulatory systems between Chinese SFDA and US FDA to provide insights on the trend of harmonic convergence of laws and regulations and challenges going forward, including collection and extrapolation of relevant statistical data; thirdly, I researched emerging fingerprint technologies to address the central issues of standardization, quality control, material consistency, safety and efficacy measurements of Chinese herbal medicines; fourthly, I performed data collection on major Chinese sources of published literatures and patent applications/grants for public and private medicinal knowledge formation, which may be viewed as a surrogate indicator for embedded economic value in the system, to compare trend and gaps between China and developed countries; and lastly, I presented three case studies of development of an-diabetic drugs from herbal sources, to illustrate how value may be created and captured through using modern technologies to tap into the accumulative knowledge base in herbal medicine. The thesis concludes that there are significant values to be captured, by and through cross-border collaborations under the globalization context, from Chinese herbal medicine. Both ethical single molecular entity (singleton) herb-derived drugs and mixed formula herb-derived drugs may be created going forward. / by Lizhe Sun. / S.M.

Thesis (Ph. D. in Medical and Electrical Engineering)--Harvard-MIT Program in Health Sciences and Technology, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 108-114). / Adhesion-based cell capture on surfaces in microfluidic devices forms the basis of numerous biomedical diagnostics and in vitro assays. Solid surface microfluidic platforms have been widely explored for biomedical diagnostics since samples can be precisely and reproducibly manipulated under well-defined physicochemical conditions. However, at these small length scales, the fluid dynamics are dominated by the high surface-to-volume ratio and interfacial phenomena limiting device performance at high flow rates. In contrast, cell homing to porous vasculature is highly effective in vivo during inflammation; stem cell trafficking and cancer metastasis. In this work, we demonstrate that fluid-permeable surface functionalized with cell-specific antibodies can promote efficient and selective cell capture in vitro. This architecture might be advantageous due to enhanced transport due to fluid field modification leading to diverted streamlines towards the surface. Moreover, specific cell-surface interactions can be promoted due to reduced shear, allowing gentle cell rolling and arrest. Together, these synergistic effects enable highly effective target cell capture at flow rates over an order of magnitude larger than existing devices with solid surfaces. Additionally, in this study, we overcome a major limitation relevant to porous surfaces due to formation of stagnant layers of cells from non-target background population. These stagnant layers are detrimental to device performance as they act to reduce interaction of the cells with the reactive surface thereby reducing capture efficiency. We theoretically and experimentally understand the mechanisms for formation of the stagnant bioparticle layer in microfluidic devices and define a parameter space for optimal operation of the device over long periods of time. Key insights from these studies, collectively allow us to design a spatially modified microfluidic devices that allow us to isolate cancer lines as low as 5 cells/mL spiked into buffy coat. / by Sukant Mittal. / Ph.D.in Medical and Electrical Engineering

Thesis (Ph. D. in Medical Engineering)--Harvard-MIT Program in Health Sciences and Technology, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 125-129). / Metastasis, the spread and growth of tumor cells from the primary site to distant organs, is arguably the most devastating and deadly attribute of cancer, and is ultimately responsible for 90% of cancer-related deaths. Circulating tumor cells (CTCs) are exceedingly rare cells found in the whole blood of cancer patients which have the potential to serve as a 'blood biopsy'. The intricate characterization of these cells could result in an entire new class of therapies directly targeting metastasis. Present technologies enable only a susbset of potential analyses to be conducted, principally due to sub-optimal cell isolation sensitivity, purity, throughput, or handling method. Here, we present two novel technologies to address the challenge of CTC isolation. First, we build on affinity-based microfluidic cell capture platforms by developing sacrificial hydrogel coatings to enable the innocuous release of captured cells; we demonstrate that model CTCs captured from whole blood remain viable and proliferative following release and are compatible with downstream immunostaining and FISH analysis. Second, we present a novel cell sorting system that interrogates over 10 million individual events each second, resulting in a high throughput, ultra-efficient rare cell sorter that delivers enriched cells in a vial, readily compatible with virtually any downstream assay. This is the first system combining the high sensitivity and single cell resolution that is characteristic of FACS with the practicality of MACS at a throughput and specificity afforded by inertial focusing, enabling operation in both 'positive selection' and 'negative depletion' modes. We find greater than 90% cell isolation efficiencies with over 2.5 log depletion of contaminating WBCs. Furthermore, the system is applied to clinical patient samples, and proof-of-concept is demonstrated in a cohort of breast, lung and prostate patients. Working in a negative depletion mode to isolate target cells in an unbiased fashion, we used the system to assess single putative CTCs isolated from an endogenous pancreatic mouse model for gene expression of tumor markers. Initial data confirms CTC heterogeneity at the single cell level, and positions us to move forward with single cell transcriptome sequencing, which may reveal a broad array of CTC phenotypes including metastatic precursors. / by Ajay Mukesh Shah. / Ph.D.in Medical Engineering

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 99-102). / The Massachusetts Pharmaceutical and Medical Device Manufacturer Code of Conduct (PCOC) or 105 CMR 970.000 was enacted by the Massachusetts state legislature and adopted by the Department of Public Health (DPH) in July 2009 under Chapter 305 of the Acts of 2008, An Act To Promote Cost Containment, Transparency and Efficiency in the Delivery of Quality Health Care. The state law requires pharmaceutical and medical device manufacturers to comply with a marketing code of conduct, obey specific compliance activities, and disclose payments to Massachusetts-licensed healthcare providers with a value of $50 or more in connection with sales and marketing activities. This thesis qualitatively assessed the impact of 105 CMR 970.000 on physician-industry collaboration related to technology development and physician education in the Massachusetts medical device industry, as depicted by academic physicians and representatives of medical device companies during the first quarter of calendar year 2010. A pilot study comprising interviews and surveys of stakeholders in the Massachusetts medical device industry was conducted to summarize the initial impressions of the impact of 105 CMR 970.000 on medical device physician-industry collaboration, with the intention of creating a roadmap for future analysis. Informal interviews (36) included individuals at medical device manufacturers, distributors, academic medical centers, venture capital firms, law firms, consulting firms, MassMedic, and the DPH. Formal surveys (40) included academic physicians and medical device company representatives selling to Massachusetts licensed physicians. The hypothesis was confirmed that 105 CMR 970.000 has impaired medical device physician-industry collaboration related to technology development and physician education in Massachusetts. Our results may have state and federal regulatory implications for the medical device industry and can serve as a guide for future analysis. / by Daniel W. Wolf. / S.M.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2004. / Includes bibliographical references (leaves 138-145). / (cont.) parametric effect, which can be considered an imaging artifact. Additionally, it may be possible to use the nonlinear interaction of scattered waves to form images that rely on the presence of small scatterers; a technique that may be enhanced with the use of contrast agents containing small scattering micro-bubbles in vivo. / This thesis explores the nature of the ultrasound-stimulated vibro-acoustography (USVA) imaging method introduced by Fatemi and Greenleaf in 1998. The USVA method relies upon the generation of a difference frequency signal from the interaction of two pressure fields with a target. A thorough understanding of USVA will be necessary to further advance this dual-frequency method. Prior studies demonstrate a correlation between difference frequency signal response and tissue temperature, and difference frequency signal response and tissue coagulation, suggesting that USVA may be well suited for monitoring focused ultrasound surgery. This thesis explores three possible sources of the difference frequency signal: 1) the parametric effect, 2) linear reflection of the local difference frequency field, and 3) nonlinear interaction of linearly scattered waves. The research compares the relative significance of these three possible sources using mathematical analysis, computer simulations, and experimental results. The results set forth in this thesis suggest that the parametric effect may be the most significant source of difference frequency signal, reaching pressures of 1-10 Pa and significantly overshadowing the other two enumerated effects. The second effect, the linear reflection of the local evanescent difference frequency field, is undetectable experimentally. Finally, the third effect, the nonlinear interaction of linearly scattered waves for a single bubble, contributes to the difference frequency signal only slightly, albeit detectably, reaching levels of .1-1 Pa. These results have a number of implications for future implementations of USVA. In order to utilize USVA as a successful imaging tool, one must take measures to avoid the signal from the / by Jonathan S. Thierman. / Ph.D.

Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Even prior to the elucidation of the structure of DNA, the theoretical foundations of population genetics had been well developed. Advances made by Sewall Wright, John B.S. Haldane, and Ronald A. Fisher form the basis with which we understand the statistical dynamics of evolution and inheritance. Using this foundation, recent advances in DNA profiling technologies have enabled genome-wide analysis of thousands of individuals from a diverse array of human populations. These new analyses can answer fundamental questions about human population differences, natural selection, and admixture. However, with this deluge of newly available data, confusion about statistical methods may lead to misleading conclusions about human population history and natural selection. We view it as imperative to put analyses of population differences on sound statistical footing. In the course of this thesis, we have developed methods and reanalyzed existing results in two related areas: the detection of natural selection and estimation of genetic distance. Throughout our work, we have strived for statistical rigor, attempting to understand variation in previously reported results and provide a resource for other researchers in our field. Where necessary, we have made simplifying assumptions about evolutionary processes but have attempted to state these clearly and validate their reasonableness using simulations. Our efforts have culminated in three projects that will be described in the subsequent chapters: (1) A model based approach to detect natural selection in 3 populations (2) A protocol to generate consistent estimates of FST and, (3) Reanalysis of previously reports of selection in African Americans since the arrival of their ancestors in the Americas. We note that our work is just part of a rich literature on population and evolutionary genetics. We have attempted to cite this literature in detail and have published our own methods to enable others to utilize and improve upon them. / by Gaurav Bhatia. / Ph. D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2004. / Includes bibliographical references (p. 67-70). / Patients and their family members are increasingly turning to the Internet for health information. However, the search strategies consumers are using to obtain information are often unsuccessful. Since some patients are using the information they obtain to influence health decisions, it is increasingly important to identify strategies that aid consumer access to quality information to address their needs. Three different strategies to improve consumer health information retrieval are explored in this thesis, and suggestions for the application of these tactics and incorporation into healthcare delivery are discussed. Consumers have the option to choose between medically specific web sites and generic search engines with the whole Internet as their search space. For this project, a rigorous comparison of Internet searches in these two scopes was conducted to determine which search scope provides better returns. No statistical difference was found between the two different scopes, but several pros and cons of each were identified. Queries generated by consumers to initiate a free-text Internet search are often too short or too general to be effective. Additionally, consumers often employ vocabulary that does not match the terminology of health content. For this research, reformulation of original consumer queries using professional terminology was explored. A trend was noted towards increased search precision when substitutions were provided for lay terms, abbreviations, and acronyms, though performance often worsened when reformulated queries contained ill-fitted or arcane terminology. It is essential to study information needs to devise strategies to support consumer health information retrieval. The specific needs of asthma patients / (cont.) and the extent they can be met by Internet resources are the focus of the final chapter of this thesis. To ascertain their information needs, asthma patients were interviewed before and after a clinical visit. The answers to these needs were then sought in a website limited to quality asthma content. Though many of the questions are answered during a clinical visit, a large proportion of patients leave the clinic with unanswered questions. Half of the needs expressed by patients were answered by the website. / by Robert M. Plovnick. / S.M.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references. / In title on title page, the word "Mitochondrial" is spelled "Mitochondial." / Mitochondria are cellular compartments that perform essential roles in energy metabolism, ion homeostasis, and apoptosis. Mitochondrial dysfunction causes disease in 1 in 5,000 live births and also has been associated with aging, neurodegeneration, cancer, and diabetes. To systematically explore the function of mitochondria in health and in disease, it is necessary to identify all of the proteins resident in this organelle and to understand how they integrate into pathways. However, traditional molecular and biochemistry methods have identified only half of the estimated 1200 mitochondrial proteins, including the 13 encoded by the tiny mitochondrial genome. Now, newly available genomic technologies make it possible to identify the remainder and explore their roles in cellular pathways and disease. Toward this goal, we performed mass spectrometry, GFP tagging, and machine learning on multiple genomic datasets to create a mitochondrial compendium of 1098 genes and their protein expression across 14 mouse tissues. We linked poorly characterized proteins in this inventory to known mitochondrial pathways by virtue of shared evolutionary history. We additionally used our matched mRNA and protein measurements to demonstrate a widespread role of upstream open reading frames (uORFs) in blunting translation of mitochondrial and other cellular proteins. Next we used the mitochondrial protein inventory to identify genes underlying inherited diseases of mitochondrial dysfunction. In collaboration with clinicians, we identified causal mutations in five genes underlying diseases including hepatocerebral mtDNA depletion syndrome, autosomal dominant mitochondrial myopathy, and several forms of inherited complex I deficiency. These discoveries have enabled the development of diagnostic tests now widely available. More broadly, the mitochondrial compendium provides a foundation for systematically exploring the organelle's contribution to both basic cellular biology and human disease. / by Sarah E. Calvo. / Ph.D.