Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Vita. / Includes bibliographical references (leaves 149-150). / The overall goal of this dissertation was to study the auditory component of feedback control in speech production. The first study investigated auditory sensorimotor adaptation (SA) as it relates to speech production: the process by which speakers alter their speech production in order to compensate for perturbations of normal auditory feedback. Specifically, the first formant frequency (F1) was shifted in the auditory feedback heard by naive adult subjects as they produced vowels in single syllable words. These results indicated that subjects demonstrate compensatory formant shifts in their speech. This compensation was maintained when auditory feedback was masked by noise. The second study investigated perceptual discrimination of vowel stimuli differing in F frequency, using the same subjects as in the SA studies. This study showed that the extent of adaptation was positively correlated with subject auditory acuity. The last study consisted of a series of simulations of SA experiments using a model which describes the motor planning and control of human speech by the brain; these simulations showed that the model can account for several properties of adaptation as measured from the human subjects. / (cont.) The findings in this dissertation support the idea that phonemic speech movements are planned as goal regions in an auditory space, and that mappings between this auditory space and the speech motor plan are adaptable. Moreover, the size of these goal regions-as reflected in speaker auditory acuity-influences the degree to which speakers adapt to errors in auditory feedback. / by Virgilio Mangubat Villacorta. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 87-99). / Synaptic ribbons are electron-dense structures surrounded by vesicles and anchored to the presynaptic membrane of photoreceptors, retinal bipolar cells and hair cells. Ribbon synapses are characterized by sustained exocytosis that is graded with stimulus intensity and can achieve high release rates. Leading hypotheses implicate the ribbon in maintenance of a large readily releasable pool (RRP) of presynaptic vesicles which enables rapid and precisely-timed exocytosis that supports instantaneous discharge rates of well over 1000 spikes per second. To gain insight into the function of this specialized presynaptic molecular machinery, we characterized the response properties of single auditory nerve (AN) fibers in a mouse with targeted deletion of a presynaptic scaffolding gene, bassoon, in which ribbons are no longer anchored to the active zone. Since each mammalian AN fiber usually receives input from a single inner hair cell active zone to which a single ribbon is typically anchored, single-fiber recordings from bassoon mutants and control mice offer a sensitive functional metric of the contribution of individual ribbons to neural function. Response properties of mutant AN fibers were similar, in many respects, to wild-type. Spike intervals remained irregular, thresholds were unaffected, dynamic range was unchanged, spike synchronization to / (cont.) stimulus phase was unimpaired, the time course of post-onset adaptation and recovery from adaptation were normal, and the ability to sustain discharge throughout a long-duration stimulus was unaffected. These data indicate that the presynaptic mechanisms which regulate precise timing of exocytosis, graded release rates and sustained neurotransmitter release were not impaired by loss of the ribbon. However, reductions were seen in spontaneous and sound-evoked AN fiber discharge rates, coinciding with an increased variance of first spike timing to stimulus onset. Unlike fibers from wild-type mice, mutants failed to show increased peak rate as stimulus onset became more abrupt. The reduction of peak rates and increased first spike variance likely result from degraded reliability of discharge to stimulus onset via a mechanism such as reduced RRP size. Thus, the ribbon appears to support a large RRP that enables the rapid onset rates necessary for the auditory system to resolve stimulus features key for many perceptual tasks. / by Bradley N. Buran. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 192-204). / Recovery from central nervous system (CNS) injuries is hindered by a lack of spontaneous regeneration. In injuries such as stroke and traumatic brain injury, loss of viable tissue can lead to cavitation as necrotic debris is cleared. Using a rat model of penetrating brain injury, this thesis investigated the use of collagen biomaterials to fill a cavitary brain defect and deliver therapeutic agents. Characterization of the untreated injury revealed lesion volume expansion of 29% between weeks 1 and 5 post-injury. The cavity occupied parts of the striatum and cortex in the left hemisphere, and was surrounded by glial scarring. Implantation of a collagen scaffold one week after injury resulted in a modest cellular infiltrate four weeks later consisting of macrophages, astrocytes, and endothelial cells. The scaffold was able to fill the cavity and provide a substrate for cellular migration into the defect. Incorporation of a Nogo receptor molecule aimed at binding inhibitory myelin proteins did not appear to promote axonal regeneration, but resulted in increased infiltration of macrophages and endothelial cells. The increased vascularization observed within the scaffolds represents a modified environment that might be more suitable for regenerative therapies. A scaffold was also used to investigate the delivery of neural progenitor cells one week after injury. After four weeks, viable implanted cells were found to have differentiated into astrocytes, oligodendrocytes, endothelial cells, neurons, and possibly macrophages/microglia. These results demonstrate the potential utility of combinatorial therapies involving collagen biomaterials, myelin protein antagonists, and neural progenitors for treatment of CNS injuries. / by Paul Ziad Elias. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references (leaves 33-35). / Location tracking systems in healthcare produce a wealth of data applicable across many aspects of care and management. However, since dedicated location tracking systems, such as the oft mentioned RFID tracking system, are still sparsely deployed, a number of other data sources may be utilized to serve as a proxy for physical location, such as barcodes and manual timestamp entry, and may be better suited to indicate progress through clinical workflows. INCOMING!, a web-based platform that monitors and tracks patient progress from the operating room to the post-anesthesia care unit (PACU), is one such system that utilizes manual timestamps routinely entered as standard process of care in the operating room in order to track a patient's progress through the post-operative period. This integrated real time system facilitates patient flow between the PACU and the surgical ward and eases PACU workload by reducing the effort of discharging patients. / (cont.) We have also developed a larger-scale integrated system for perioperative processes that integrates perioperative data from anesthesia and surgical devices and operating room (OR) / hospital information systems, and projects the real-time integrated data as a single, unified, easy to visualize display. The need to optimize perioperative throughput creates a demand for integration of the datastreams and for timely data presentation. The system provides improved context-sensitive information display, improved real-time monitoring of physiological data, real-time access to readiness information, and improved workflow management. These systems provide improved data access and utilization, providing context-aware applications in healthcare that are aware of a user's location, environment, needs, and goals. / by Mark A. Meyer. / S.M.

Thesis: Ph. D. in Medical Engineering and Medical Physics, Harvard-MIT Program in Health Sciences and Technology, 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 151-167). / Atherosclerosis is the leading causes of mortality and morbidity in the world. While there are a plethora of methods for treating clinical atherosclerosis, the primary cause of mortality is acute coronary syndrome (ACS) following rupture of an atheroma, an event that is poorly predicted and remains the most common first indicator of cardiovascular disease. Current tools for determining atherosclerotic burden rely assessing a patient's risk factors, clinical symptoms, and biochemical profile, followed by angiographic imaging. However, patients with subclinical atherosclerotic disease can also be at high risk for ACS. In fact, nearly half of the patients suffer from sudden cardiac death without any prior indication of atherosclerotic disease. For these patients, proper characterization of the plaque burden has been shown to have a strong diagnostic value in guiding preventative treatments. Current noninvasive medical imaging methods lack the combination of resolution and contrast required to characterize atherosclerotic plaque. Recently, a new mode of medical imaging known as X-ray phase contrast imaging (XPCI) has been shown to produce exceptional contrast in soft tissues, and has the potential to noninvasively characterize atherosclerotic disease. This thesis develops a new experimental XPCI system, as well as novel algorithms for reconstructing the amplitude and phase of X-rays for the purpose of noninvasive imaging of atherosclerotic disease. Our methods extend the transport of intensity equation, which enables the retrieval of phase and amplitude from multi-dimensional intensity distributions. We present a compressive tomographic reconstruction framework for 3-dimensional phase distributions, including algorithms for both single-shot and multi-shot phase retrieval. We introduce a method for compressive phase tomography based on the phase attenuation duality. We further propose a novel regularization scheme for projection imaging called the structural similarity regularizer, which exploits the sparsity of phase edges according to an absorption prior. Finally, we present an algorithm known as simultaneous attenuation phase retrieval, which is capable of combining absorption and phase information to improve reconstruction results. For each algorithm, we present simulation and experimental results from test phantoms and biological specimens. The results of this thesis show that X-ray phase imaging can successfully characterize atherosclerotic plaques, and lays the groundwork for the use of XPCI as a diagnostic tool for atherosclerosis. / by Adam Pan. / Ph. D. in Medical Engineering and Medical Physics

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references. / Endothelial cells and basement membrane interact as a biochemical and mechanical co-regulatory unit. The wide spectrum of manifestations of diabetic vascular disease could be related to altered kinetics of vasoactive compounds within this regulatory unit. We hypothesized that hyperglycemic stress mediates storage, release, and function of fibroblast growth factor-2 (FGF-2) through changes in interaction between endothelial cells and basement membrane. We discovered that basement membrane associated FGF-2 increased linearly with culture glucose concentration. Using novel assays, we demonstrated that FGF-2 binding kinetics were surprisingly unchanged over a range of basement membrane culture glucose. Instead, the combination of increased endothelial cell apoptosis-associated FGF-2 release and enhanced endothelial cell permeability allowed more FGF-2 to bind into the basement membrane. Such high levels of basement membrane FGF-2 abrogated the effects of hyperglycemia on proliferation but not apoptosis. An FGF-2 stimulus returned endothelial cell proliferation close to euglycemic levels, but increased apoptosis was still evident as FGF-2 signaling down an intracellular survival pathway was inhibited by glucose. / (cont.) These same findings were confirmed in vivo where FGF-2 levels were elevated in the aortic subendothelial space of diabetic animals. This thesis suggests a new paradigm for active cellular control of basement membrane and indicates the complexities of growth factor signaling in endothelial cells. Characterization of the interaction between endothelial cells and basement membrane in health and disease may advance our understanding of diabetic vascular disease and lead to development of novel biomimetic materials for therapeutic intervention. / by Alisa Sharon Morss. / Ph.D.

Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 91-105). / Atoh1, the proneural basic-helix-loop-helix transcription factor, is critical for the differentiation of inner ear hair cells. Hair cells do not develop in mice that lack Atoh1, and overexpression of the transcription factor in embryonic ears induces differentiation of extra hair cells. The level of Atoh1 expression is under the control of a Wnt and Notch transcriptional regulatory network to keep the level of mRNA within a narrow range. Once the protein is made, it activates its own expression through an interaction with the Atoh1 enhancer, such that Atoh1 transcription is self-perpetuating. Because of this autoregulatory loop, halting transcription of the gene to maintain Atoh1 at an appropriate level would require that the amount of protein be decreased. Since the ubiquitin-proteasome pathway regulates catabolism of key regulatory proteins, we assessed its role in the degradation of Atoh1. E3 ubiquitin ligases confer substrate specificity to degradation of proteins by transferring a ubiquitin tag to a specific protein substrate. Using an immunoprecipitation/mass spectrometry screening approach, we identified Huwe1, a HECT domain E3 ubiquitin ligase, as an Atoh1 binding partner. We validated the binding between Atoh1 and Huwe1 through reciprocal co-immunoprecipitation and mass spectrometry. We found that Huwe1 promoted polyubiquitylation of Atoh1 through a lysine 48-linked polyubiquitin chain. Mutation at a catalytic cysteine within the HECT domain of Huwe1 reduced the polyubiquitylation. We also defined a motif in the C-terminus of Atoh1 responsible for interaction with Huwe1. Inhibition of proteasomal activity, as well as Huwe1 depletion, stabilized Atoh1 in the cochlea and resulted in generation of new hair cells in the newborn cochlea. / by Yen-Fu Cheng. / Ph. D.

Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 111-115). / Granger causality methods analyze the flow of information between time series. The Geweke measure of Granger causality (GG-causality) has been widely applied in neuroscience because its frequency-domain and conditional forms appear well-suited to highly-multivariate oscillatory data. In this work, I analyze the statistical and structural properties of GG-causality in the context of neuroscience data analysis. 1. I analyze simulated examples and derive analytical expressions to demonstrate how computational problems arise in current methods of estimating conditional GG-causality. I show that the use of separate full and reduced models in the computation leads to either large biases or large uncertainties in the causality estimates, and high sensitivity to uncertainties in model parameter estimates, producing spurious peaks, valleys, and even negative values in the frequency domain. 2. I formulate a method of correctly computing GG-causality that resolves the above computational problems. 3. I analyze how generative system properties and frequency structure map into GG-causality to demonstrate deeper conceptual pitfalls: (a) I use simulated examples and derive analytical expressions to show that GG-causality is independent of the receiver dynamics, particularly the magnitude of response, which is counter-intuitive to physical notions of causality. (b) Overall, GG-causality combines transmitter and channel dynamics in a way that cannot be disentangled without evaluating the component dynamics of the full model estimate. 4. I discuss relevant concepts from causality analyses in other fields to better place causality analysis in a modeling and system identification framework. The computational uncertainties in GG-causality estimates make the interpretation of frequency-domain structure highly problematic. Even if these computational issues are overcome, correct interpretation of the GG-causality values is still challenging and could be easily misinterpreted without careful consideration of the component dynamics of the full model estimate. Through this work, I provide conceptual clarification of GG-causality and place it in the broader framework of modeling and system analysis, which may enable investigators to better assess the utility and interpretation of such methods. / by Patrick A. Stokes. / Ph. D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 137-154). / Because there is little knowledge in the areas of stereocilia development, maintenance, and function in the hearing system, I decided to pursue a proteomics-based approach to discover proteins that play a role in stereocilia function. I employed a modified "twist-off" technique to isolate hair bundle proteins, and I developed a method to purify proteins and to process them for analysis using multi-dimensional protein identification technology (MudPIT). The MudPIT analysis yielded a substantial list of proteins. I verified the presence of 21 out of 34 (62%) existing proteins known to be present in stereocilia. This provided strong evidence that my proteomics approach was efficient in identifying hair bundle proteins. Next, I selected three proteins and localized them to murine cochlear stereocilia. StarD10, a putative phospholipid binding protein, was detectable along the shaft of stereocilia. Nebulin, a putative F-actin regulator, was located toward the base of stereocilia. Finally, twinfilin 2, a putative modulator of actin polymerization, was found at the tips of stereocilia. In order to determine the function of twinfilin 2, I localized the protein predominately to the tips of shorter stereocilia where it is up-regulated during the final phase of elongation. When overexpressed, I found that twinfilin 2 causes a shortening of microvilli in LLC-PK1/CL4 cells and in native cochlear stereocilia. The main result of this thesis was determining the sub-cellular localization of three interesting proteins and functionally characterizing one protein. My thesis also confirmed the proteomics screen I developed as an efficient method for identifying proteins in stereocilia. / by Anthony Wei Peng. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / Includes bibliographical references. / Drug-eluting stents (DES) virtually eradicate the clinical phenomena of vessel restenosis; yet, they also increase the short and long term risks for stent thrombosis. To improve their safety and efficacy, it is critical to examine factors that alter local biologic outcome. The central hypothesis of this thesis is that local efficacy and toxicity are in part determined by the duration of drug exposure and local arterial drug concentrations. This thesis investigates how factors both intrinsic and extrinsic to the device impact local intravascular drug delivery. Computational models of local fluid mechanics and drug transport were formulated to study how arterial drug uptake is modulated by local blood flow, stent placement, administered drug dose and release kinetics, and the evolving local vascular response to the device. Lumenally flowing blood around stent struts was capable of transporting drug to the arterial wall in the presence of both single and multiple configurations of drug eluting stent struts. The extent of blood flow mediated arterial drug delivery depended upon the rate of drug release and administered dose. Slow drug release led to sustained, low magnitude drug uptake; exceedingly fast release resulted in transient and minimal tissue absorption due to rapid drug depletion. / (cont.) Drug release over several minutes maximized peak arterial drug concentrations, though arterial drug levels were not sustained. Mural thrombus did not alter the rate of drug release from a stent; however, clots increased local drug availability and reduced the extent of drug washout. Subsequently, variability in mural thrombi formation caused fluctuations in arterial drug levels. Computational modeling revealed that free diffusion of hydrophobic drugs was slower than experimental arterial drug absorption. Subsequently, a novel mechanism for arterial drug transport has been proposed in which drug diffuses faster through the arterial wall due to its association with carrier proteins. Within this thesis, we have elucidated that device, patient, and physician-dependent device implantation are among the factors governing arterial drug deposition; these subsequently dictate local efficacy and toxicity. Thus, rational design of improved local therapeutics requires consideration of how multiple interrelated factors intrinsic and extrinsic to the device determine local efficacy and toxicity. / by Brinda Balakrishnan. / Ph.D.