Thesis (Ph.D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2002. / Includes bibliographical references (leaves 142-154). / Poly-l-lysine and hexadimethrine bromide (polybrene) are cationic polymers which are frequently used to enhance the transduction efficiency of recombinant retroviruses in gene therapy experiments. Conversely, chondroitin sulfate proteoglycan is an anionic polymer endogenously present in retrovirus stocks which inhibits transduction efficiency. An experimental study was performed to determine the mechanisms of retrovirus transduction modulation by these charged polymers, and it was found that they were capable of increasing or decreasing the flux of virus particles onto the cell surface. These effects, and adsorption in general, were independent of the cellular receptor-virus envelope interaction which was believed to provide the driving force for initial virus attachment. In order to consider the feasibility of alternative driving forces for virus attachment, a mathematical model of adsorption was constructed taking into account the electrostatic properties of the system. The model predicted that either cationic polymer-mediated virus aggregation or membrane charge shielding could yield adsorption phenomenon consistent with the previous observations. An experimental study was undertaken to distinguish between these two potential mechanisms, and it was found that both were at work depending on the physicochemical characteristics of the cationic polymer. All cationic polymers were capable of charge shielding, however, only high molecular weight polymers (> 15 kD) could aggregate the virus. Anionic polymers, conversely, were found to inhibit transduction and adsorption via preventing cationic polymers from performing these functions. / by Howard E. Davis, Jr. / Ph.D.

Thesis: Ph. D. in Medical Engineering and Medical Physics, Harvard-MIT Program in Health Sciences and Technology, 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 94-103). / Invasive electrical brain stimulation has been increasingly used to treat an ever wide range of neuropsychiatric disorders from Parkinson's disease to epilepsy and depression. In addition, single pulse electrical stimulation (SPES) is increasingly used to map connections between cortical areas using cortico-cortical evoked potentials (CCEPs). However, the properties and mechanisms underlying brain stimulation remain mostly unknown, hindering the application of stimulation to new neurological disorders and the development of adaptive stimulation technologies that could improve clinical outcome. To improve understanding of SPES, we systematically explored the effects of cortical electrical stimulation in human epilepsy patients. These patients have intracranial electrodes implanted for intractable epilepsy as part of their clinical course, creating a unique opportunity to simultaneously stimulate and record the human brain in multiple locations. Single pulses of electrical current were delivered across pairs of electrodes in the human cortex, and the neurophysiological responses are recorded. Examining some fundamental properties of CCEPs, we show that the brain's response to less than a millisecond pulse of stimulation can be detected up to one second post-stimulus. This response has two peaks with distinct properties; compared to the second peak, the first is less variable, and its timing is less delayed by distance, while its magnitude is more diminished by distance. Looking at the spatial distribution of CCEPs, we show that stimulation-derived networks are more closely related to structural connectivity than functional connectivity. However, correcting for distance eliminates this difference. Monitoring CCEPs across different brain states, we show that the second peak of the CCEP is significantly diminished during anesthesia. Taken together, these results provide important insight into the basic neurophysiological properties of CCEPs, their spatial distribution, and how they are modulated by the state of the brain itself. These characteristics can inform experimental design, provide input parameters for modeling studies, and be applied towards the development of adaptive closed-loop stimulation paradigms. / by Britni Crocker. / Ph. D. in Medical Engineering and Medical Physics

Thesis (Ph. D.)--Harvard-MIT Program in Health Sciences and Technology, 2012. / 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 (p. 165-[181]). / Humans live in association with trillions of microbes and yet we know remarkably little about their symbiotic relationship. The role these microorganisms have in humans has been characterized only in the case of few bacteria and much less is understood about the dynamic of this relationship. Lately, the mass sequencing efforts accompanying the Human Microbiome Project have begun to uncover the composition of these different microbial niches, and shed light on some the effects they have on their host. The immune system largely determines the composition of bacterial populations living in association with humans. It lights off pathogens while allowing specific bacteria to colonize the body. However, immune system and microbiota appear even more intimately connected than previously imagined. Recent evidence shows that interaction with the associated microbiota is necessary for the proper development of the immune response throughout life. The interface with commensal microbes is notoriously difficult to probe experimentally, due to the diversity of its composition, which makes differentiating the individual ramifications of each associated microbe a much harder task. To understand the complex relationship between the human immune system and microbiome, we need methodologies that can simultaneously probe both in a high throughput fashion, as well as analysis tools to cope with the large amount of resulting data. Herein I present the development of immune mass screening tools capable of comprehensively profiling the antibody-mediated and cell-mediated immune response to microbes. I employ microfluidics techniques to describe the response of single immune cells at high-resolution and in a physiologically relevant environment. I also present the application of machine learning to gut microbiome data and demonstrate how it can be used to differentiate between diseased and healthy individuals in an IBD patient cohort and to allows to deal with the complexity of microbial community data. Moving forward, the goal is to combine these approaches to map how changes in the immune response affects microbiome composition and vice versa. In turn, characterizing this interplay will contribute to our understanding of how bacteria shape our homeostasis and health, facilitating the prediction of which imbalances may lead to disease. / by Eliseo Papa. / Ph.D.

Thesis (Ph. D. in Biomedical Engineering)--Harvard-MIT Program in Health Sciences and Technology, 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 108-126). / Chemical exchange saturation transfer (CEST) is a relatively new magnetic resonance imaging (MRI) acquisition technique that generates contrast dependent on tissue microenvironment, such as protein concentration and intracellular pH. CEST imaging has the potential to become an important biomarker in a wide range of disorders. As an indicator of tissue pH, CEST imaging may allow the identification of the ischemic penumbra in stroke, and predict chemo- and radiation therapy outcomes in cancer. As a marker of protein concentration, CEST may be able to delineate tumor margins without contrast enhancement, identify disease onset in Alzheimer's disease, and monitor cartilage repair therapies. Despite several promising pilot studies, CEST imaging has had limited clinical application due to two main technical challenges. First, CEST imaging is extremely sensitive to magnetic field inhomogeneity. Images suffer from large susceptibility artifacts unless specialized BO inhomogeneity correction methods are employed that tremendously increase scan time. Second, the CEST contrast cannot be separated from the intrinsic macromolecular magnetization transfer (MT) asymmetry and brain images reflect the MT properties of white and gray matter rather than the desired protein and pH contrast. We have developed a novel CEST imaging acquisition scheme, dubbed saturation with frequency alternating RF irradiation (SAFARI), designed to be insensitive to Bo inhomogeneity and MT asymmetry. Studies in healthy volunteers demonstrate that SAFARI is robust in the presence of BO inhomogeneity and eliminates the need for specialized BO correction, thereby reducing scan time. In addition, results show that SAFARI removes the confounding MT asymmetry. We applied SAFARI imaging towards the study of the saturation transfer contrast in patients with high grade glioma. Results show that the contrast in brain tumors, which was previously attributed to an increase in the CEST signal from amide protons due to an elevated protein concentration, is instead the result of the loss of MT asymmetry found in the normal brain. Therefore, our work has lead to a new understanding of the different sources of signal in saturation transfer images of the brain with important implications for the design and analysis of future CEST studies of brain tumors. / by Rachel Nora Scheidegger. / Ph.D.in Biomedical Engineering

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.