Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2005. / Includes bibliographical references (leaves 91-100). / Advances in microarray technology facilitate the study of biological systems at a genome-wide level. Meaningful analysis of these transcriptional profiling studies, however, demands the concomitant development of novel computational techniques that take into account the size and complexity of the data. We have devised statistical algorithms that use replicate microarrays to define a genome-wide expression profile of a given cell type and to determine a list of genes that are significantly differentially expressed between experimental conditions. Applying these algorithms to the study of cultured human umbilical vein endothelial cells (HUVEC), we have found approximately 54% of all genes to be expressed at a detectable level in HUVEC under basal conditions. The set of highest expressed genes is enriched in nucleic acid binding proteins, cytoskeletal proteins and isomerases as well as certain known markers of endothelium, and the complete list of genes can be found at ... We have also studied the effect of a 4-hour exposure of HUVEC to 10 U/mL of IL-1, and detected 491 upregulated and 259 downregulated statistically significant genes, including several chemokines and cytokines, as well as members of the TNFAIP3 family, the KLFfamily and the Notch pathway. Applying these rigorous statistical techniques to genome-wide expression datasets underscores known patterns of endothelial inflammatory gene regulation and unveils new pathways as well. / (cont.) Finally, we performed a direct comparison of direct-labeled microarrays with amplified RNA microarrays for an initial assessment of the effect of the additional noise of amplification on the outputs of the statistical algorithms. These techniques can be applied to additional genome-wide profiling studies of endothelium and other cell types to refine our understanding of transcriptomes and the gene regulatory network governing cellular function and pathophysiology. / by Sripriya Natarajan. / S.M.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2008. / Includes bibliographical references (p. 193-201). / It is now widely accepted that cells are capable of processing both mechanical and chemical signals from the extracellular environment. Exactly how these two factors affect the cell biology in the context of physiological circumstances is an area of intense interest that has given rise to an entire field of study called cell mechanotransduction. The unambiguous decoupling of mechanical and chemical properties that stimulate cell development and phenotypic change is challenging from an experimental standpoint. This thesis describes some of the first studies of chemomechanical coupling arising from anchorage-dependent forces between cells and a versatile class of chemically and mechanically tunable polymer thin films, termed polyelectrolyte multilayers. Specifically, investigation of the effects of extracellular chemomechanical stimulation on cell morphology and adhesion in the eukaryotic cells such as vascular endothelial cells and fibroblasts; and the adhesion of prokaryotic cells S. epidermidis and E. coli are presented. Endothelial cells (EC) comprise a major portion of the cell population in the human body. Because of the extensive distribution of endothelial cells in various tissues, they function across a broad range of mechanical and chemical environments. Furthermore, a general understanding of how mechanical forces contribute to the development of cellular function is an important aspect in the development of therapeutic techniques and materials capable of addressing a wide spectrum of human diseases and injuries. Cell adhesion to extracellular matrices and tissues can be indicative of underlying molecular processes in both healthy and disease states. / (cont.) Through the use of a mechanically tunable class of polymer thin films called polyelectrolyte multilayers (PEMs) developed by Rubner et al., we have demonstrated that the adhesion and morphology of human microvascular endothelial cells depend directly on the mechanical stiffness of these synthetic substrates, as quantified by the nominal elastic modulus E. Characterization of the mechanical properties and surface features of PEMs is attained via scanning probe microscopy (SPM) and SPM-enabled nanoindentation. Typical cellular response to increased substrata stiffness includes increased number of cells adhered per unit substratum area. We have further demonstrated that the chemical and mechanical signals imposed at the cell-substrata interface can be decoupled, thereby providing two independent parameters capable of controlling cell behavior. This capacity of the cell to sense and/or exert chemical and mechanical forces, in addition to initiating a sustained molecular response, is termed the chemomechanical response element. Finally, adhesion dependent mechanosensation in bacteria is explored, with respect to the chemomechanical response elements common to eukaryotic and prokaryotic cells. Potential applications towards the development of therapeutic materials and compounds for treatment of various disease states are discussed, with particular attention to limiting hospital acquired infections. / by Michael Todd Thompson. / Ph.D.

Thesis (Ph.D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2002. / Vita. / Includes bibliographical references. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / The temporal envelope of sound strongly influences the intelligibility of speech, pattern analysis, and the grouping of sequential stimuli. This thesis examined the coding of sound temporal envelope in the time-patterns of population neural activity of the human auditory pathway. Traditional microelectrode recordings capture the fine time-pattern of neural spiking in individual neurons, but do not necessarily provide a good assay of temporal coding in neural populations. In contrast, functional magnetic resonance imaging (fMRI), the technique chosen for the present study, provides an indicator of population activity over a time-scale of seconds, with the added advantage that it can be used routinely in human listeners. In a first study, it was established that the time-pattern of cortical activity is heavily influenced by sound repetition rate, whereas the time-pattern of subcortical activity is not. In the inferior colliculus, activity to prolonged noise burst trains (30 s) increased with increasing rate (2/s - 35/s), but was always sustained throughout the train. In contrast, the most striking sound rate dependence of auditory cortex was seen in the time-pattern of activity. Low rates elicited sustained activity, whereas high rates elicited "phasic" activity, characterized by strong adaptation early in the train and a robust response to train offset. These results for auditory cortex suggested that certain sound temporal envelope characteristics are encoded over multiple seconds in the time-patterns of cortical population activity. A second study tested this idea more fully by using a wider variety of sounds (e.g., speech, music, clicks, tones) and by systematically varying different sound features. / (cont.) Important for this test was the development of a new set of basis functions for use in a general linear model that enabled the detection and quantification of the full range of cortical activity patterns. This study established that the time-pattern of cortical activity is strongly dependent on sound temporal envelope, but not sound level or bandwidth. Namely, as either rate or sound-time fraction increases, the time-pattern shifts from sustained to phasic. Thus, shifts in the time-pattern of cortical activity from sustained to phasic signal subsecond differences in sound temporal envelope. These shifts may be fundamental to the perception of successive acoustic transients as either distinct or grouped acoustic events. / by Michael Patrick Harms. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 83-90). / Tinnitus, the ongoing perception of sound in the absence of a physical stimulus, and hyperacusis, the intolerance of sound intensities considered comfortable by most people, are two often co-occurring clinical conditions lacking effective treatments. This thesis identified neural correlates of these poorly understood disorders using functional magnetic resonance imaging (fMRI) and auditory brainstem responses (ABRs) to measure sound-evoked activity in the auditory pathway. Subjects with clinically normal hearing thresholds, with and without tinnitus, underwent fMRI or ABR testing and behavioral assessment of sound-level tolerance (SLT). The auditory midbrain, thalamus, and primary auditory cortex (PAC) showed elevated fMRI activation related to reduced SLT (i.e. hyperacusis). PAC, but not midbrain or thalamus, showed elevated fMRI activation related to tinnitus, perhaps reflecting undue attention to the auditory domain. In contrast to fMRI activation, ABRs showed relationships only to tinnitus, not SLT. Wave I of the ABR, which reflects auditory nerve activity, was reduced in tinnitus subjects, while wave V, reflecting input activity to the midbrain, was elevated. Wave I reduction in tinnitus subjects suggests that auditory nerve dysfunction apparent only above threshold is a factor in tinnitus. Because ABRs reflect activity in only one of multiple pathways from cochlear nucleus to midbrain, the wave V elevation implicates this particular pathway in tinnitus. The results directly link tinnitus and hyperacusis to hyperactivity within the central auditory system. Because fMRI and ABRs reflect different aspects of neural activity, the dependence of fMRI activation on SLT and ABR activity on tinnitus in the midbrain raises the possibility that tinnitus and hyperacusis arise in parallel from abnormal activity in separate brainstem pathways. / by Jianwen Wendy Gu. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2008. / Includes bibliographical references (p. 101-110). / Sound-evoked vibrations transmitted into the mammalian cochlea produce traveling waves that provide the mechanical tuning necessary for spectral decomposition of sound. These traveling waves of motion propagate along the basilar membrane (BM) and ultimately stimulate the mechano-sensory receptors. The tectorial membrane (TM) plays a key role in this stimulation process, but its mechanical function remains unclear. Here we show that the TM supports traveling waves that are an intrinsic feature of its visco-elastic structure. Radial forces applied at audio frequencies (1-20 kHz) to isolated TM segments generate longitudinally propagating waves on the TM with velocities similar to those of the BM traveling wave near its best frequency (BF) place. We compute the dynamic shear storage modulus and shear viscosity of the TM from the propagation velocity of the waves and show that segments of the TM from the basal turn are stiffer than apical segments are. Analysis of loading effects of hair bundle stiffness, the limbal attachment of the TM, and viscous damping in the subtectorial space suggests that TM traveling waves can occur in vivo. To test how TM waves may participate in cochlear function, we investigated waves in genetically modified mice lacking beta-tectorin, a glycoprotein found exclusively in the TM. Tectb-/- mutant mice were previously shown to exhibit significant loss of cochlear sensitivity at low frequencies and sharpened frequency tuning compared to wild types. We show that the spatial extent and propagation velocity of TM traveling waves are significantly reduced in Tectb-/- mice compared to wild types, consistent with the concept that there is a reduction in the spread of excitation via TM waves and less TM wave interaction with the BM traveling wave in Tectb-/- mice. / (cont.) The differences in TM wave properties between mutants and wild types arise from changes to the mechanical properties of the TM; mutant TMs are significantly less stiff than wild type TMs are. Our results show the presence of a traveling wave mechanism through the TM that can functionally couple a significant longitudinal extent of the cochlea and may interact with the BM wave, suggesting that TM waves are crucial for cochlear sensitivity and tuning. / by Roozbeh Ghaffari. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references (p. 110-118). / Healthy ears generate sounds known as otoacoustic emissions that can be evoked and measured in the ear-canal using small, low-noise microphones. The ability to measure acoustic signals that originate within the cochlea provides noninvasive access to what in humans is an almost inaccessible organ. Although otoacoustic emissions (OAEs) are frequently used as noninvasive probes of cochlear function in both the clinic and the laboratory, their utility is limited by incomplete knowledge of their generating mechanisms. A recently proposed model suggests that most OAEs are mixtures of -emissions arising by two fundamentally different mechanisms: 1) nonlinear distortion induced by cochlear traveling: waves and 2) linear reflection 6f those waves from pre-existing micromechanical impedance perturbations. The model predicts that OAEs generated by wave-induced perturbations manifest a phase that is nearly-frequency invariant whereas OAEs generated by reflection from pre-existing perturbations manifest a phase that rotates rapidly with frequency. The model suggests that the relative contribution from each mechanism to any emission measurement depends on factors such as the type and intensity of the evoking stimulus. / (cont.) In this thesis we tested the relationships between common OAE measurements and the two proposed mechanisms of OAE generation. We tested the two-mechanism model by measuring and comparing OAEs evoked with single tones and broad-band clicks, as well as those evoked by two-tone complexes at frequencies not contained in the stimulus, so-called distortion-product emissions. Our results indicate that click-evoked and tone-evoked OAEs, previously regarded as different types of emission based on the characteristics of the stimuli used to evoke them, are really the same emission evoked in different ways. The phase characteristics of both emission types are consistent with those predicted for emissions originating by linear-reflection from pre-existing perturbations. In addition, we demonstrate that distortion-product OAEs are often mixtures of two components. By separating the two components we show that one component arises by linear reflection and the other component arises by induced distortion. Our results provide strong empirical support for the two-mechanism model of OAE generation. Since the two emission mechanisms depend on fundamentally different aspects of cochlear mechanics, measurements that isolate each emission type should improve the power and specificity of OAEs as non-invasive probes of cochlear function. / by Radha Kalluri. / Ph.D.

Thesis (Ph. D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2002. / Includes bibliographical references. / A cell with extraordinary motile ability exists in our inner ear, the outer hair cell. Outer hair cell (OHC) motility can occur at acoustic frequencies and play a key role in mammalian cochlear frequency selectivity and hearing sensitivity. To date, the mechanism of cochlear amplification is not well understood and remains a matter of controversy. In order to understand the role of OHC motility in cochlear micromechanics we developed a technique to measure the mechanical responses within the organ of Corti (OC) due to OHC forces. We used an excised cochlea preparation because it provided a good view of the organ and allowed us to compare the resulting responses of hundreds of cells simultaneously. The tissue was stimulated electrically using sinusoidal current, and the resulting motion was captured at specific phases within the stimulus period using stroboscopic video microscopy. Animations of this motion were created, and the displacement magnitude and phase for each structure were calculated using two dimensional cross-correlation. With these techniques we were able to detect displacements as low as ten nanometers. The frequency responses of electrically-evoked vibrations from the apical and middle turn had low pass filtering characteristics with cutoff frequencies near or below the estimated characteristic frequency of the imaging location. Using a simple one dimensional electrical model of our excised cochlea preparation, we hypothesize that the electrical properties of the stria vascularis play an important role in shaping the frequency response of individual structures. / (cont.) The vibration pattern of the organ was complex and changed with frequency. These changes suggest that at least two OC vibration modes are excited by OHC motility. At all frequencies OHC motility induced oscillatory fluid flow in the tunnel of Corti. We modeled the tunnel of Corti as an elastic tube and showed that it can support a traveling wave. The tunnel of Corti wave could travel without significant attenuation for distances larger than the wavelength of the cochlear traveling wave at its peak. The classical view of cochlear partition vibration is that the structure simply bends in phase along the radial dimension, and that there is no coupling between adjacent sections other than that provided by the fluid above and below the OC. Our findings challenge the classical view of cochlear partition vibration, and support the existence of multiple vibration modes. In addition, the presence of fluid flow in the tunnel of Corti in response to OHC contractions suggests that a second traveling wave provides longitudinal coupling between adjacent sections. Such coupling may be critical for cochlear amplification. / Kiriaki Domenica Karavitaki. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2003. / Includes bibliographical references (leaves 164-169). / Hemodynamics has long been identified as a major factor in the determination and localization of atherosclerotic lesions. While the precise mechanism by which different hemodynamic factors act is not yet clear, the fact that they correlate highly with atherogenesis suggests that local disturbances in flow through blood vessels can promote arterial disease. These issues have become increasingly acute as physicians seek to alter the pathological arterial anatomy with bypass grafting or endovascular manipulations such as angioplasty or stenting. We proposed that local vascular interventions might cause previously unforeseen effects elsewhere in the arterial tree. As an example of these interactions, manipulation of one branch of a bifurcation might adversely affect the contralateral branch of the bifurcation. The goal of this work was to study the distant impact of local flow alterations, as well as to classify and evaluate the different parameters that determine their severity. Dynamic flow models of the arterial system were developed that allowed for the continuous alteration of model geometry in a controlled fashion to simulate the healthy and diseased states as well as the entire range in between. Moreover, these models permit simulation of different strategies of clinical intervention. Flow through the models was investigated using both qualitative and quantitative tools. Boundary layer separation and vascular resistance in one location of the arterial tree varied with geometrical alterations in another. In-vivo models were developed that allowed investigation of the effect of side branch occlusion or dilation on the acute and chronic outcome of main branch stenting in a bifurcation. Chronic side branch occlusions were protective of main branch stenting as reflected by a reduction in in-stent neo-intimal hyperplasia. / (cont.) This protective influence was mediated by an acute modulation of monocyte adhesion and accumulation on the lateral wall of the main branch, correlating with the location of flow disturbance demonstrated by the flow models. Chronic main branch vascular remodeling plays a major role in achieving this beneficial effect. The results of this study could have important implications for the diagnosis, treatment and long-term follow-up of the large number of patients who suffer from complex arterial diseases and undergo vascular interventions. In clinical manipulation of one arterial site one may well need to consider the hemodynamic impact on vascular segments at a distance. / by Yoram Richter. / Ph.D.

Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 86-94). / Humans have the ability to precisely sense the position, speed, and torque of their body parts. This sense is known as proprioception, and is essential to human motor control. In the many attempts to create human-mechatronic interactions, there is still no robust, repeatable methodology to reflect proprioceptive information from a synthetic device onto the nervous system. As a solution to this shortcoming, I present the agonist-antagonist myoneural interface (AMI). The AMI is comprised of 1) a surgical construct made up of two muscle-tendons - an agonist and an antagonist - surgically connected in series so that contraction of one muscle stretches the other, and 2) a bi-directional efferent-afferent neural control architecture. The AMI preserves dynamic muscle relationships that exist within native anatomy, thereby allowing proprioceptive signals from biological sensors within both muscles to be communicated to the central nervous system. Each AMI is designed to send control signals to one joint of a prosthesis, and to provide proprioceptive feedback pertaining to the movement of that joint. The doctoral work presented in this thesis constitutes the pre-clinical and early clinical validation of the AMI. The AMI concept is first described and validated in small (murine) and large (caprine) pre-clinical models. A detailed surgical methodology for implementation of the AMI during primary below-knee amputation is then described and evaluated in three human patients. Characterization of independent neural control of prosthetic joint position and impedance is presented for one AMI patient, as compared to a group of four persons with traditional amputation. Data are shown evidencing improved volitional control over the prosthesis in the AMI patient, as well as an emergence of natural reflexive behaviors during stair ambulation that do not exist in the traditional amputation cohort. These results provide a framework for reconsidering the integration of bionic systems with human physiology. / by Tyler R. Clites. / Ph. D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Vita. / Includes bibliographical references (p. 52-56). / Post-marketing surveillance of medical pharmaceuticals and devices has received a great deal of media, legislative, and academic attention in the last decade. Among medical devices, these have largely been due to a small number of highly publicized adverse events, some of them in the domain of cardiac surgery and interventional cardiology. Phase three clinical trials for these devices are generally underpowered to detect rare adverse event rates, are performed in near-optimal environments, and regulators face significant pressure to deliver important medical devices to the public in a timely fashion. All of these factors emphasize the importance of systematic monitoring of these devices after being released to the public, and the FDA and other regulatory agencies continue to struggle to perform this duty using a variety of voluntary and mandatory adverse event rate reporting policies. Data quality and comprehensiveness have generally suffered in this environment, and delayed awareness of potential problems. However, a number of mandatory reporting policies combined with improved standardization of data collection and definitions in the field of interventional cardiology and other clinical domains have provided recent opportunities for nearly "real-time" safety monitoring of medical device data. / (cont.) Existing safety monitoring methodologies are non-medical in nature, and not well adapted to the relatively heterogeneous and noisy data common in medical applications. A web-based database-driven computer application was designed, and a number of experimental statistical methodologies were adapted from non-medical monitoring techniques as a proof of concept for the utility of an automated safety monitoring application. This application was successfully evaluated by comparing a local institution's drug-eluting stent in-hospital mortality rates to University of Michigan's bare-metal stent event rates. Sensitivity analyses of the experimental methodologies were performed, and a number of notable performance parameters were discovered. In addition, an evaluation of a number of well-validated external logistic regression models, and found that while population level estimation was well-preserved, individual estimation was compromised by application to external data. Subsequently, exploration of an alternative modeling technique, support vector machines, was performed in an effort to find a method with superior calibration performance for use in the safety monitoring application. / by Michael E. Matheny. / S.M.