Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2004. / Includes bibliographical references (p. 65). / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Drug development in the United States is a lengthy and expensive endeavor. It is estimated that average development times range from eleven to fifteen years and exceed costs of one billion dollars. The development pathway includes basic scientific discovery, pre-clinical testing in animals, clinical development in humans, and an application process. The Food and Drug Administration is responsible for the oversight and approval of drugs going through this process. Numerous financial and economic studies have been conducted that show the benefits to accelerating the drug development process. In 1992, the United States Congress enacted the Prescription Drug User Fee Act I, which mandated faster response times from the FDA in return for user fee payments to the FDA by the drug developing companies. Data on approval times for new drugs indicate that this process was indeed shortened. In contrast, the average drug development process prior to the filing of an application has been increasing in cost and time. The first purpose of this research is to quantify the benefits of accelerated new drug application review time under the Prescription Drug User Fee Acts I and II. The second purpose of the research is to investigate what industry and the FDA can do together to reduce the development process time between the IND and NDA without compromising patient safety and welfare, specifically the Phase II, Phase III, and NDA components. The research indicates that PDUFA has improved approval times in a statistically significant way. Furthermore, the financial and social benefits as measured using net present value have far exceeded the PDUFA costs. Quantitative and qualitative surveys of fifty individuals in large pharmaceutical and biotech companies / (cont.) resulted in the identification of several significant opportunities and useful suggestions for reducing development times in Phase II, Phase III, and the NDA. Specifically, company interviewees indicated that they were willing to pay additional monies for increased interaction and communication with the FDA from Phase II through the NDA in hopes of reducing information asymmetry and increasing information transparency. Other recommendations included a mandatory audit and review of a sample of NDAs post approval to identify best practices, implementation of metrics and performance tracking during clinical phases, and implementation of consistent project management and communication standards across therapeutic divisions. / by Adrian Hedley Benjamin Gottschalk. / S.M.

Thesis (Ph.D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 1998. / Includes bibliographical references (leaves 214-229). / by Stephen Allen Boppart. / Ph.D.

Thesis (M. Eng.)--Harvard-MIT Division of Health Sciences and Technology, 2005. / Includes bibliographical references (leaves 48-49). / Hepatocytes are widely used in the pharmaceutical and medical fields for drug metabolism studies, bioartificial liver devices, and repopulation of damaged livers as an alternative to transplantation. However, these cells are scarce and difficult to maintain in culture for prolonged periods of time. Banks of cryopreserved liver cells would significantly alleviate issues of hepatocyte availability, and efforts are being made to improve the viability and functionality of frozen hepatocytes. Previously, most work on improving post-thaw viability has hinged on limiting the physical damage of freezing by adding cryoprotective agents and optimizing cooling rates. Membrane-permeable cryoprotectants, such as dimethyl sulfoxide, though widely used, can be extremely toxic to the cell. More natural, non-membrane-permeable cryoprotectants, inspired by freeze-tolerant animals have also been used. A non-metabolizable glucose analog, 3-0-methyl- glucose (30MG), has shown promise with hepatocytes and was used in this study. Kinetics of the rGLUT2 cellular transporter used for 30MG uptake were quantified; Km and Vmax were determined to be 27.6 mM and 1.38 mM/s, respectively, by Lineweaver-Burk analysis and 70.0 mM and 1.82 mM/s, respectively, by Eadie-Hofstee analysis. This study also aimed to investigate the role of mitochondria in cell death induced by freezing. In particular, mitochondrial membrane potential (MMP) was investigated as a predictor of a cell's likelihood to avoid apoptosis from freeze-induced stress. Cells were sorted into high and low MMP subpopulations, frozen, thawed, and cultured for 24 hours. / (cont.) Cell cultures were analyzed for attachment yield, viability of attached cells and overall viability, which were 87%, 68% and 59%, respectively for the high MMP subpopulation, and 68%, 53% and 35%, respectively for the low MMP subpopulation. Morphological differences such as extent of membrane blebbing were observed as well, verifying that cells with a high MMP are more likely to survive the cryopreservation process. These results demonstrated that MMP is a determinant of both frozen hepatocyte adherence efficiency and viability; a high MMP yields a significant advantage in both. Our understanding of the role of MMP in freeze-thaw death and of the characteristics of the rGLUT2 transporter will lead to the development of more successful cryopreservation protocols. / by Margaux E. Daly. / M.Eng.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / Includes bibliographical references (p. 157-168). / Spectrally encoded confocal microscopy (SECM) is a technique that facilitates the incorporation of confocal microscopy into small, portable clinical instruments. This would allow in vivo evaluation of cellular and sub-cellular features in a non-destructive, minimally invasive manner. Prior studies have demonstrated the potential of the techniques as well as highlighted the need for faster acquisition rates and higher sensitivity. In this thesis, new laser sources, optical fiber arrangements and probe designs are explored to ultimately evaluate SECM's relevance as a clinical tool. Clinical imaging at cellular scales requires imaging rates on the order of tens of frames per second to reduce motion artifacts from unavoidable patient movements. Rapid SECM imaging was achieved through the development of a novel wavelength swept laser which simultaneously provided high output power (> 10mrW), narrow linewidth (10GHz), broad wavelength tuning (80 nm centered at 1310 nm) and fast repetition rates (up to 16,000 Hz), while being compact and environmentally stable. Imaging with a wavelength swept SECM system was characterized by coupling the laser to a tabletop imaging arm comprising a high density holographic grating, a galvanometer mounted mirror and a 0.9 NA water immersion microscope objective. / (cont.) Rapid SECM imaging is performed at a transverse resolution of 1.4 microns, axial resolution of 6 microns over a field of view of 440x440 microns and allows subcellular imaging ex vivo (excised specimens) and in vivo (human skin). A study on 40 excised head and neck specimens showed that SECM has the potential to perform tissue identification, but also revealed the presence of speckle noise due to the coherent nature of the illumination and collection schemes through a single mode optical fiber. A partially coherent system based on single mode fiber for illumination and multimode fiber for detection was simulated, implemented and tested to find adequate balance between attenuation of speckle noise and conservation of resolution. A coupling of 20 modes was found to reduce speckle by a factor 4.5 with a minimal sectioning penalty of 0.25, while allowing a signal increase of 8dB. This improvement in sensitivity allowed SECM table top system to be used for investigations in developmental biology where Dual clad fibers (DCF) were previously shown to allow partially coherent endoscopic imaging, using the single mode core for illumination and inner clad for multimodal collection. / (cont.) Commercially available DCF's which propagate thousands of modes are ill suited for confocal endoscopes as collecting such a number of modes would destroy the axial resolution. Based on results from the previous section and through modal analysis, a DCF was designed, drawn - via a collaboration with Boston University Photonics Center -, and tested for use with SECM. The prototype DCF yielded promising results (3 fold speckle attenuation, optical sectioning degradation of 0.85), and showed the need for implementation of better coupling mechanisms to take advantage of increased signal collection. Finally, a portable SECM system was built for in vivo evaluation of pediatric vocal fold. A preliminary study on porcine and cadaveric tissue showed that SECM can distinguish between epithelium, superior and intermediate layers of the lamina propria, which could help elucidate the development mechanism of the voice apparatus if performed in vivo. The handheld instrument comprises a custom grating scanner imaging the scanning pivot onto the back pupil of a high NA microscope objective. The imaging tube can easily be interchanged to accommodate geometrical constraints imposed by different age groups. / (cont.) The probe, currently under review by the biomedical engineering committee, revealed cellular and sub cellular details of human skin in vivo at depth and acquisition rates sufficient to capture blood cells flowing through capillaries. Through major improvements in acquisition speeds, sensitivity, and speckle appearance, this work established SECM as a potent clinical and biological imaging tool. Ultimate confirmation will be revealed through in vivo studies to come, but limitations are likely to be of engineering nature rather than from physical considerations. Future work should explore the possibility to combine SECM with other contrast mechanisms to provide imaging with increased specificity. / by Caroline Boudoux. / Ph.D.

Thesis (Sc. D.)--Harvard University--Massachusetts Institute of Technology Division of Health Sciences and Technology, Program in Medical Engineering and Medical Physics, 1990. / Includes bibliographical references (leaves 233-249). / by Robert Lie-Yuan Sah. / Sc.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 53-56). / In recent years, significant advances have been made in the realm of in vitro diagnostics with the development of novel tests which are able to meaningfully impact the course of a patients' disease management. This transformation has strained the traditional in vitro diagnostic business model and raised questions as to whether the economics support the commercial development of these tests. The goal of this study is to evaluate the economics of in vitro diagnostics from development to commercialization, with a focus on a specific a class of novel and complex tests called In Vitro Diagnostic Multivariate Index Assays (IVDMIA). My hypothesis is that the current dynamics of the market can only sustain a small number of such novel tests. To evaluate this hypothesis, I construct an economic model of the development of a hypothetical new in vitro diagnostics which focuses on both the cost of development and commercialization together with market potential and adoption. The analysis reviews specific break-even scenarios to determine the parameters which would allow for an economically viable complex in vitro diagnostic. The conclusion I reach based on this analysis is that only a very small number of medical conditions could economically support the development of a novel in vitro diagnostic. The medical conditions which could support the development of a novel test are governed by complexity, severity and prevalence of the disease. Given the dramatic impact these new tests may have on disease management, incentives may be required to offset the risks associated with expanding novel diagnostics into smaller but medically significant disease areas. / by Adrian A. Bignami. / S.M.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / Includes bibliographical references (p. 201-207). / In the past decade, biology has been revolutionized by an explosion in the availability of data. Translating this new wealth of information into meaningful biological insights and clinical breakthroughs will require a complete overhaul both in the questions being asked, and the methodologies used to answer them. One of the largest challenges in organizing and understanding the data coming from genome sequencing, microarray experiments, and other high-throughput measurements, will be the ability to find large-scale structure in biological systems. Ideally, this would lead to a simplified representation, wherein the thousands of genes in an organism can be viewed as a much smaller number of dynamic modules working in concert to accomplish cellular functions. Toward demonstrating the importance of higher-level, modular structure in biological systems, we have performed the following analyses: 1. Using computational techniques and pre-existing protein-protein interaction (PPI) data, we have developed general tools to find and validate modular structure. We have applied these approaches to the PPI networks of yeast, fly, worm, and human. / (cont.) 2. Utilizing a modular scaffold, we have generated predictions that attempt to explain existing system-wide experiments as well as predict the function of otherwise uncharacterized proteins. 3. Following the example of comparative genomics, we have aligned biological networks at the modular level to elucidate principles of how modules evolve. We show that conserved modular structure can further aid in functional annotation across the proteome. In addition to the detection and use of modular structure for computational analyses, experimental techniques must be adapted to support top-down strategies, and the targeting of entire modules with combinations of small-molecules. With this in mind, we have designed experimental strategies to find sets of small-molecules capable of perturbing fimctional modules through a variety of distinct, but related, mechanisms. As a first test, we have looked for classes of small-molecules targeting growth signaling through the phosphatidyl-inositol-3-kinase (PI3K) pathway. This provides a platform for developing new screening techniques in the setting of biology relevant to diabetes and cancer. In combination, these investigations provide an extensible computational approach to finding and utilizing modular structure in biological networks, and experimental approaches to bring them toward clinical endpoints. / by Gopal Ramachandran. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / 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. 145-147). / Nasal codas in English and Standard Chinese (SC) are compared to distinguish between the acoustic correlates of language-universal distinctive features and language-specific enhancing attributes. The distinctive feature theory and the theory of enhancement provide a framework for quantifying the acoustic and articulatory patterns observed in the two languages. An acoustic model of nasalization is first presented, in which the area of the velopharyngeal port and the place of oral constriction are varied, in order to observe the behavior of the acoustic correlates for the feature [nasal] and to establish a quantal relation between the continuous displacement of the primary articulator and the acoustic consequence of this displacement. The first two experiments identify differences in the distribution of acoustic correlates of nasalization contained in the vowel transition and the murmur regions in vowel-nasal environments in English and SC. Results for the low vowel /a/ show a mapping based on vowel rather than coda similarity. Acoustic analysis shows that the SC vowel /a/ shifts in the frequency of the second formant (F2) depending on the nasal coda, while the English vowel does not. / (cont.) The SC mid vowel /e/ shifts in F2 while the SC high vowel /i/ does not. Furthermore, analysis of syllable-initial nasals in Chinese and English shows that the SC nasals behave like the English nasals. The third experiment is a perceptual study in which subjects are asked to make judgments of the place of articulation based on limited portions of stimuli that can be either nasal or non-nasal and contain one of the three vowels. The nasal place of articulation was identified best when the nasal was preceded by the mid vowel /e/, was identified less when followed by the low vowel /a/, and was identified the worst when the nasal was preceded by the high vowel /i/. Together, the results of these experiments suggest that language-specific constraints play an important role in determining the enhancing attributes that occur alongside languageuniversal features. The interactions of the distinctive features and the enhancing gestures may lead to differences in the acoustic manifestation of the same feature in different languages. / by Xiaomin Mou. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, February 2011. / "February 2011." Cataloged from PDF version of thesis. / Includes bibliographical references. / Biological membranes form transient, conductive pores in response to elevated transmembrane voltage, a phenomenon termed electroporation. These pores facilitate electrical and molecular transport across cell membranes that are normally impermeable. By applying pulsed electric fields to cells, electroporation can be used to deliver nucleic acids, drugs, and other molecules into cells, making it a powerful research tool. Because of its widely demonstrated utility for in vitro applications, researchers are increasingly investigating related in vivo clinical applications of electroporation, such as gene delivery, drug delivery, and tissue ablation. In this thesis, we describe a quantitative, mechanistic model of electroporation and concomitant molecular transport that can be used for guiding and interpreting electroporation experiments and applications. The model comprises coupled mathematical descriptions of electrical transport, electrodiffusive molecular transport, and pore dynamics. Where possible, each of these components is independently validated against experimental results in the literature. We determine the response of a discretized cell system to an applied electric pulse by assembling the discretized transport relations into a large system of nonlinear differential equations that is efficiently solved and analyzed with MATLAB. We validate the model by replicating in silico two sets of experiments in the literature that measure electroporation-mediated transport of fluorescent probes. The model predictions of molecular uptake are in excellent agreement with these experimental measurements, for which the applied electric pulses collectively span nearly three orders of magnitude in pulse duration (50 ts -20 ms) and an order of magnitude in pulse magnitude (0.3 -3 kV/cm). The advantages of our theoretical approach are the ability to (1) analyze in silico the same quantities that are measured by experimental studies in vitro, (2) simulate electroporation dynamics that are difficult to assess experimentally, and (3) quickly screen a wide array of electric pulse waveforms for particular applications. We believe that our approach will contribute to a greater understanding of the mechanisms of electroporation and provide an in silico platform for guiding new experiments and applications. / by Kyle Christopher Smith. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / "June 2009." Cataloged from PDF version of thesis. / Includes bibliographical references (p. 49-52). / It is widely believed that healthcare information technology (health IT) can improve care and lower costs. However, the pattern and uptake of beneficial features of health IT is poorly understood, and is an important part of realizing the full benefits of health IT. This thesis examines the factors relating to adoption and use of reporting features within an outpatient practice management system. A retrospective observational study was performed utilizing web log data from a practice management and electronic health record system vendor. Two years of data were analyzed on the use of features within the system in two different scenarios: the use of a newly released custom reporting feature among existing clients, and the use of a physician-level monthly report among new clients. Among these two different populations and features, the first use and subsequent utilization exhibited similar patterns. Using the Bass model of technology diffusion to quantify the adoption of these features, it was found that adoption had a low social component (coefficient of imitation) and a high personal component (coefficient of innovation). One physician's use of a feature in his practice did not appear to influence whether a new physician joining the same practice would use the feature. In addition, the earliest users of a feature tended to utilize that feature more often. Practices and providers that used these features performed better across three of four operational and financial metrics. The purchase and installation of a health IT system by an organization does not ensure that individuals within it will fully utilize the system and realize all the benefits. / (cont.) Incentives for health IT should focus on the advantages gained from these systems, and not merely on their purchase. Health IT vendors should be cognizant of the way they introduce new functionality to their clients in order to ensure maximal use. / by Adam Weinstein. / S.M.