Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references. / The degree of irregularity apparent in the discharge patterns of electrically stimulated auditory-nerve fibers depends upon the stimulation rate. Whereas fibers fire regularly at low stimulation rates, the same fibers fire irregularly at high rates. The irregularity observed at high stimulation rates has been attributed to noise caused by the random open and closing of voltage-gated ion channels. This explanation however is incomplete: an additional mechanism must be operating to account for the different effects of noise at the two stimulation rates. We have identified such an additional rate-dependent mechanism. Specifically, we show in the Fitzhugh-Nagumo (FN) model that the stability to perturbations such as noise depends upon the stimulation rate. At sufficiently high rates a dynamical instability arises that accounts for the main statistical features of the irregular discharge pattern, even in the absence of ongoing physiological noise. In addition, we show that this instability accounts for both the statistical independence exhibited by different fibers in the stimulated population and their sensitivity to amplitude modulations applied to an ongoing stimulus. / (cont.) In cochlear implants, amplitude modulations are used to encode acoustic information such as speech. Psychophysically, sensitivity to small modulations correlates strongly with speech perception, suggesting a critical role for dynamical stability/instability in speech perception. We show that rate-dependent stability/instability occurs in the classical Hodgkin-Huxley model, as well as in biophysical models of the mammalian node of Ranvier. / by David E. O'Gorman. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 155-171). / We routinely produce movements under different mechanical contexts. All interactions with the physical environment, such as swinging a hammer or lifting a carton of milk, alter the forces experienced during movement. With repeated experience, sensorimotor maps are adapted to maintain a high level of movement performance regardless of the mechanical environment. This dissertation explored the contribution of the precentral cortex to this process of motor adaptation. In the first experiment, we recorded precentral neural activity in rhesus monkeys that were trained to perform visually-cued reaching movements while holding on to a robotic manipulandum capable of changing the forces experienced during the task. Preparation and control of the reaching movements were correlated with single cell activity throughout the precentral cortex, including the primary motor cortex and five different premotor areas. Precentral field potential activity was also modulated during the reaching behavior, particularly in the beta and high gamma frequency bands. When novel forces were introduced, single cell activity changed in a manner that specifically compensated for the applied forces and mirrored the time course of behavioral adaptation. / (cont.) Force-related changes were present in the field potential activity as well. Some of these changes were maintained following removal of the forces. Control data and simulations revealed that these residual changes were well described by a model of noisy adaptation in a redundant cortical network. In the second experiment, human subjects performed the same reaching paradigm after receiving transcranial magnetic stimulation to transiently inhibit cortical activity. Initial learning of the novel force environment was normal but recall of the field 24 hours later was impaired relative to controls. Taken together, the results suggest that distributed areas within the precentral cortex are involved in recalibrating sensorimotor maps to fit the present mechanical context and in initiating a memory trace of newly-experienced environments. / by Andrew Garmory Richardson. / Ph.D.

Thesis (Sc. D.)--Harvard-MIT Division of Health Sciences and Technology, 2004. / Includes bibliographical references (leaves 138-160). / Peroxisome proliferator-activated receptors (PPARs) belong to a nuclear receptor superfamily; two major isoforms, PPARα and PPAR[gamma], are primarily involved in lipid and glucose homeostasis. However, evidence also suggests roles for PPARs in regulating inflammation and atherosclerosis, and prompted investigation into the efficacy of PPAR agonists in parenchymal rejection (PR) and transplantation-associated arteriosclerosis (TxAA). Four different PPAR agonists (fenofibrate and Wy14643 for PPARα; BRL69453 and 15-deoxy-[delta]¹⁴̓¹⁶ Prostaglandin-J₂ for PPAR[gamma]) in an in vitro model of the alloresponse all demonstrated a robust and substantial attenuation of IFN[gamma], a cytokine that critically affects both rejection and TxAA. This occurred in a dose-dependent manner, independent of known IFN[gamma]-inducing cytokines. At the same times, PPAR activation increased the overall expression of chemokines but substantially decreased expression of two relevant chemokine receptors. Of the four agonists tested, fenofibrate, a largely PPARα-specific agonist, had the best profile of IFN[gamma] production to chemokine and chemokine receptor expression. At early time points after cardiac transplantation, fenofibrate administration showed findings consistent with those seen in vitro, including a tendency to reduce IFN[gamma]. However, long-term fenofibrate treatment significantly increased graft IFN[gamma] expression and inflammatory cell infiltration, thereby augmenting PR without ameliorating TxAA. Congenital deficiency of PPARα confirmed that the receptor plays a regulatory role in IFN[gamma] expression but is not necessary for graft infiltration by inflammatory cells. The findings constitute the first examination of the efficacy of PPAR agonists in / (cont.) solid-organ transplantation and suggest that in order to fully realize the beneficial anti-inflammatory effects of fenofibrate, additional strategies must be employed to inhibit graft inflammatory cell infiltration. Finally, a novel immunologic research tool based on the boron neutron capture reaction is proposed. / by Emanuela Binello. / Sc.D.

Thesis (Sc.D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2000. / Includes bibliographical references. / In the past decade, biodegradable polymers have become the materials of choice for a variety of biomaterials applications. In particular, poly(lactic-co-glycolic acid) (PLGA) microspheres have been extensively studied for controlled-release protein delivery. However, significant issues arise in formulating such delivery systems since few proteins have been successfully encapsulated and released from these microspheres. Here, methods are developed to determine the causes of protein instability and solutions are provided for overcoming these problems. A commonly used technique for protein encapsulation in PLGA microspheres is the double-emulsion method. The harsh processing associated with this method can cause denaturation of the encapsulated protein. Herein, we have used Fourier transform infrared (FTIR) spectroscopy to determine the secondary structures of two model proteins, bovine serum albumin (BSA) and chicken egg-white lysozyme, within PLGA microspheres. This is a novel technique for in situ evaluation of proteins within microspheres and potentially a powerful and quick method for assessment of formulations. Results for both proteins indicate changes in structure upon entrapment within the microspheres. However, addition of the stabilizing excipient trehalose prevents the denaturing effects incurred during processing. In addition, BSA released from microspheres is improved by incorporation of trehalose. With microspheres made by double emulsion, there is often a large, initial burst of drug release upon injection. This results in inefficient use of therapy. To prevent this loss, a modified spontaneous emulsification method was explored. / (cont.) With this procedure both protein and polymer are soluble in a single solvent system thus avoiding creation of a water/solvent interface. The process was optimized for microsphere size and protein loading. Addition of a charged surfactant served to improve protein solubility and thus increase protein loading. In vitro and in vivo release kinetics showed a minimal burst, lower than that found with double emulsion microspheres, followed by sustained release. Upon injection of the microspheres in vivo, the PLGA microspheres begin to degrade. Degradation of the polymer generates acidic monomers, and acidification of the inner polymer environment is a central issue in the development of these devices for drug delivery. To quantitatively determine the intraparticle acidity, pH-sensitive fluorescent dyes were entrapped within the microspheres and imaged with confocal fluorescence microscopy. The technique allows visualization of the spatial and temporal distribution of pH within the degrading microspheres. The data indicate the formation of a very acidic environment within the particles with the minimum pH as low as 1.5. The images show a pH gradient, with the most acidic environment at the center of the spheres and higher pH near the edges, which is characteristic of diffusion-controlled release of the acidic degradation products. Strategies to avoid the accumulation of acidic monomers involve decreasing the diffusion distance of the degradation products by either decreasing the overall diameter of the microspheres or creating porous particles. / by Karen Fu. / Sc.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references (p. 127-138). / With the discovery of hearing disorders caused by mutations in proteins expressed in the tectorial membrane (TM), the importance of the TM in cochlear mechanics has never been clearer. However, the exact role of the TM in cochlear mechanics remains a mystery. In this thesis, I have investigated material properties of two mouse models of genetic hearing disorders that affect proteins found in the TM, a-tectorin and type XI collagen. The Tecta mutants had a missense mutation in ac-tectorin, a protein found exclusively in the TM in the organ of Corti. The effect of the mutation was to decrease the fixed charge concentration, which was found to be the primary determinant of the bulk modulus. However, the shear modulus was not affected. Collla2 is one of the genes that encodes for type XI collagen. Mutation in this gene causes no significant change in fixed charge concentration and, therefore, bulk modulus. However, the radial shear impedance is lowered. These measurements suggest that TM shear impedance is dominated by radially oriented collagen fibers and plays a key role in driving outer hair cell (OHC) bundle deflection. At the same time, the TM bulk modulus is dominated by the presence of fixed charge and may play a key role in coupling energy from outer to inner hair cells. / by Kinuko Masaki. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 173-174). / Since the FDA Modernization Act of 1997, recent legislation has sought to establish performance goals and consistency in the regulatory review and clearance of new medical devices. Despite these goals, regulatory review times have varied dramatically for devices seeking clearance through the 510(k) pathway; devices that are by definition "substantially equivalent" to other devices previously cleared by the FDA and currently on the market. The goal of this thesis is to investigate the factors that impact the ability for a company to obtain a 510(k) clearance in a predictable timeframe and assess the most important factors that influence time to clearance. The Medical Device industry is a dynamic and rapidly evolving sector that presents complex challenges to regulatory oversight. The 510(k) program and larger device regulatory process has endured the test of time and is well structured to address these challenges. This research focuses on the 7,481 510(k) "substantially equivalent" clearances during the period from October 1, 2007 through June 30, 2010 (FY08 - Q3FY10) in order to analyze the variables that impact clearance times. By testing various hypotheses about the most important factors I aim to provide the device community with the data and suggestions for improving confidence around a particular 510(k) submission's likely approval time. I performed subset analyses on the dataset, segmenting clearances by the type of 510(k) (traditional, abbreviated, and special), clinical category, fiscal year of clearance, use of 3rd party review, submission volume, and product diversity according to clinical category. The results show a distinct increase in clearance time from FY08 to FY10 and suggest that recent scrutiny of the FDA premarket review process may be affecting the efficiency of the Agency FDA review process for medical devices. Further, the 3rd party review program is under-utilized with only 14%, on average, of eligible devices gaining clearance through this process. Through a discussion of two specific critiques of the 510(k) process, namely a recent Government Accountability Office study and an article by the Public Citizen (a public advocacy group), the potential implications of regulatory reform is explored from both a policy and industry perspective. / by Andrew J Koert. / S.M.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2003. / Includes bibliographical references. / Cardiovascular disease is the primary cause of mortality in developed nations. Current diagnostic techniques are not able to provide the information that is related to the majority of associated complications. Raman spectroscopy, which is capable of providing a detailed chemical analysis of biological tissue, has previously been shown to be a useful method for diagnosing atherosclerosis. However, widespread clinical implementation has been prohibited by the lack of optical fiber probes which can provide remote access to small diameter vessels. To this end, we have developed a new spectroscopic model and a novel Raman probe. The model interprets Raman spectra of intact tissue in terms of its morphology. The spectrally identifiable morphological structures include collagen and elastin fibers, cholesterol crystals, calcium mineralizations, adipocytes, crystals containing 3-carotene, foam cells, necrotic core, and smooth muscle cells. This model prospectively classifies atherosclerotic tissue into three categories: non-atherosclerotic, non-calcified plaque, and calcified plaque, with >94% accuracy. Furthermore, this model has the potential ability to identify the vulnerable atherosclerotic plaques whose rupture accounts for the majority of myocardial infarctions. By studying the distribution of Raman light in tissue, we have designed, constructed, and tested small diameter, high throughput optical fiber Raman probes which employ a modular micro-optical filter configuration to remove the intense background generated in the fibers. The probes have been extensively tested during peripheral vascular surgery, providing real-time disease diagnosis for the first time. These in vivo investigations demonstrate the clinical applicability of Raman spectroscopy and have also provided the first identification of vulnerable plaques with this technique. / (cont.) We have shown that plaque vulnerability is spectrally identified by determining the collagen, foam cell/necrotic core, calcification, cholesterol, and hemoglobin content of the lesion. This type of analysis may eventually lead to a diagnostic technique capable of staging atherosclerotic lesions, thereby providing a method to optimize therapeutic measures. In addition, the small diameter Raman probes have applicability for studying other diseases such as breast, oral, and gastrointestinal cancer. / by Jason Taylor Motz. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, February 2004. / Includes bibliographical references. / This thesis integrates hardware development, data analysis, and mathematical modeling to facilitate our understanding of brain cognition. Exploration of these brain mechanisms requires both structural and functional knowledge to (i) reconstruct the spatial distribution of the activity, (ii) to estimate when these areas are activated and what is the temporal sequence of activations, and (iii)to determine how the information flows in the large-scale neural network during the execution of cognitive and/or behavioral tasks. Advanced noninvasive medical imaging modalities are able to locate brain activities at high spatial and temporal resolutions. Quantitative modeling of these data is needed to understand how large-scale distributed neuronal interactions underlying perceptual, cognitive, and behavioral functions emerge and change over time. This thesis explores hardware enhancement and novel analytical approaches to improve the spatiotemporal resolution of single (MRI) or combined (MRI/fMRI and MEG/EEG) imaging modalities. In addition, mathematical approaches for identifying large-scale neural networks and their correlation to behavioral measurements are investigated. Part I of the thesis investigates parallel MRI. New hardware and image reconstruction techniques are introduced to improve spatiotemporal resolution and to reduce image distortion in structural and functional MRI. Part II discusses the localization of MEG/EEG signals on the cortical surface using anatomical information from AMTRI, and takes advantage of the high temporal resolution of MEG/EEG measurements to study cortical oscillations in the human auditory system. Part III introduces a multivariate modeling technique to identify "nodes" and "connectivity" in a / (cont.) large-scale neural network and its correlation to behavior measurements in the human motor system. / by Fa-Hsuan Lin. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 123-139). / Cells face a core tension between studiously preventing change in certain properties from extrinsic perturbations while allowing other properties to be tuned. One way cells have resolved this tension is to utilize systems that are both robust and tunable. Systems can achieve this through network design, which can contain submodules that are themselves either robust or tunable, or through network components that are robust over only a defined set of parameter ranges. This work examines these two categories with two specific examples described below. To explore how a simple network can be both robust and tunable, we make use of the osmosensing pathway in the budding yeast Saccharomyces cerevisiae. The pathway consists of two modules: a phosphorelay module that senses the osmotic shock signal that feeds into a mitogen-activated protein kinase (MAPK) module. Using a combination of systematic complementation experiments and computational sensitivity analysis, we show that the phosphorelay module is robust to changes in the kinetic parameters characterizing signal propagation through the module while signaling through the MAPK module can be tuned by changing the rate constants. Furthermore, we show that pathway robustness to rate constant changes has consequences for the evolvability of the osmosensing cascade. Populations of yeast cells challenged to alter the input/output relationship of the cascade saw their MAPK proteins preferentially targeted by natural selection over their phosphorelay counterparts. To explore how a simple regulatory element can be both robust and tunable, we turn our attention to gene regulation by microRNA (miRNA). MiRNAs are short regulatory RNA molecules that repress gene expression in a sequence-dependent manner. By observing the strength of miRNA-mediated repression in individual cells, we show that the strength of repression depends strongly on the relative abundance of the miRNA and its target. Below a threshold level of target message miRNA robustly silences the conversion of mRNA input into protein output, but above this threshold miRNAmediated repression generates an ultrasensitive response to mRNA input allowing the strength of repression to be tuned over a wide variety of values. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / Includes bibliographical references (p. 111-118). / The Magnetic Guidance Keyboard System (MaGKeyS) embodies a new haptic guidance technology designed to facilitate sensorimotor training and rehabilitation. MaGKeyS works by employing active magnetic force to guide finger pressing movements during sensorimotor learning that involves sequential key presses, such as playing the piano. By combining this haptic guidance with an audiovisual learning paradigm, we have created a core technology with possible applications to such diverse fields as musical training, physical rehabilitation, and scientific investigation of sensorimotor learning. Two embodiments of this new technology were realized in this thesis. The first embodiment, the MaGKeyS Prototype, is a 5-key acrylic USB keyboard designed for a stationary right hand. A set of three behavioral experiments were executed to investigate the manner in which haptic guidance, via the MaGKeyS Prototype, facilitates rhythmic motor learning. In particular, the experiments examined the independent effects of haptic guidance on ordinal learning, which is the order of notes in a sequence, and temporal learning, which is the order of timing variations in a rhythmic sequence. A transfer test and 24-hour retention test were also administered. Our results provide conclusive evidence that haptic guidance can facilitate learning the ordinal pattern of a key press sequence. Furthermore, our results suggest that the advantage gained with haptic guidance can both transfer to learning a new rhythmic sequence, as well as extend to a demonstrable advantage a day later. The second embodiment, the MaGKeyS Trainer Piano, is an upright piano in which the keyboard has been modified and outfitted with electromagnets in a manner similar to the MaGKeyS Prototype. The Trainer Piano helps to teach by "feel" by providing an experience in which the user feels his or her fingers being pulled down into the correct piano keystrokes as the piano plays itself. / by Craig Edwin Lewiston. / Ph.D.