Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Active motility in outer hair cells (OHCs) amplifies basilar-membrane (BM) and auditory-nerve (AN) responses to low-level sounds. The recent finding that medial olivocochlear (MOC) efferents (which innervate OHCs) inhibit AN initial peak (ANIP) responses from mid-to-high-level clicks, but do not inhibit initial BM responses, suggests a coupling of OHC motility to inner-hair-cell (IHC) stereocilia that is not through the BM. The main thesis objective was to test whether different OHC mechanisms produce AN responses to low-level sounds versus ANIP from mid-to-high-level clicks by comparing the suppressive effects of low-frequency "bias-tones" on these responses. Bias tones suppress by pushing OHC stereocilia into low-slope regions of their mechanoelectric transduction functions thereby lowering OHC amplification, particularly for probe tones near an AN-fiber's characteristic frequency (CF). This suppression occurs at opposite bias-tone phases, with one suppression typically larger than the other. Bias-tone effects were measured on cat AN-fiber responses using 50 Hz bias tones. In the first thesis part, bias-tone suppressive effects on AN responses to low-level clicks and low-level CF-tones were found to be similar, as expected but never previously shown. Then, in the main thesis focus, bias-tone suppressions of AN responses to low-level clicks and ANIP responses were studied. Both responses were suppressed twice each bias-tone cycle, but their major suppressions were at opposite bias-tone phases, which indicates that both ANIP and low-level AN responses depend on the slope of OHCstereocilia mechanoelectric-transduction, but with some significant difference. In the last thesis part, bias-tone suppression effects on low-CF (<4 kHz) AN-fiber responses to low-level CF and off-CF (by >0.7 octaves) tones were studied. Previous work found differences in AN-response group delays between CF and off-CF frequency regions that might arise from two different IHC-drive mechanisms, and the objective was to test this hypothesis. Our results showed similar bias-tone effects in both regions. Overall, the results demonstrate differences and similarities in the OHC mechanisms that produce ANIP and traditional, low-level cochlear amplification, and the results are consistent with the ANIP drive coupling OHC motility to IHC stereocilia without going through BM motion. / by Hui S. Nam. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2005. / Includes bibliographical references (p. 56-57). / Cancer development and progression typically features genomic instability frequently resulting in genomic changes involving DNA copy number gains or losses. Identifying the genomic location of these regional alterations provides important opportunities for the discovery of potential novel oncogenes and tumor suppressors. Recently, array based competitive genomic hybridization (array-CGH) has become available as a powerful approach for genome-wide detection of DNA copy number changes. Array-CGH assesses DNA copy number in tumor samples through competitive hybridization on microarrays containing probes for thousands of genes. The datasets generated are complex and require statistical methods to accurately define discrete and uniform copy number from the data and to identify transitions between genomic regions with altered copy number. Several approaches based on different statistical frameworks have been developed. However, a fundamental informatic issue in array-CGH analysis remains unsolved by these methods. In particular, sample-specific data compression, a result of tumor cells being commonly admixed with normal cells in many tumor types, must be accounted for in each sample analyzed. Additionally, in order to accurately assess deviations from normal copy number, the copy number readout must be shifted to faithfully represent the baseline copy number in each tumor sample. Failure to appropriately address these issues reduces the accuracy of the data in hard-threshold based high-level analysis. / (cont.) By using the natural framework Hidden Markov Models (HMM) to model the distribution of array-CGH signals, a method infer the absolute copy number and identify change points has been developed to address the above problems. This method has been validated on independent dataset and its utility in inference on array-CGH data is demonstrated here. / by Yunyu Zhang. / S.M.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / Includes bibliographical references (p. 163-181). / High-throughput molecular data are revolutionizing biology by providing massive amounts of information about gene expression and regulation. Such information is applicable both to furthering our understanding of fundamental biology and to developing new diagnostic and treatment approaches for diseases. However, novel mathematical methods are needed for extracting biological knowledge from high-dimensional, complex and noisy data sources. In this thesis, I develop and apply three novel computational approaches for this task. The common theme of these approaches is that they seek to discover meaningful groups of genes, which confer robustness to noise and compress complex information into interpretable models. I first present the GRAM algorithm, which fuses information from genome-wide expression and in vivo transcription factor-DNA binding data to discover regulatory networks of gene modules. I use the GRAM algorithm to discover regulatory networks in Saccharomyces cerevisiae, including rich media, rapamycin, and cell-cycle module networks. I use functional annotation databases, independent biological experiments and DNA-motif information to validate the discovered networks, and to show that they yield new biological insights. Second, I present GeneProgram, a framework based on Hierarchical Dirichlet Processes, which uses large compendia of mammalian expression data to simultaneously organize genes into overlapping programs and tissues into groups to produce maps of expression programs. I demonstrate that GeneProgram outperforms several popular analysis methods, and using mouse and human expression data, show that it automatically constructs a comprehensive, body-wide map of inter-species expression programs. / (cont.) Finally, I present an extension of GeneProgram that models temporal dynamics. I apply the algorithm to a compendium of short time-series gene expression experiments in which human cells were exposed to various infectious agents. I show that discovered expression programs exhibit temporal pattern usage differences corresponding to classes of host cells and infectious agents, and describe several programs that implicate surprising signaling pathways and receptor types in human responses to infection. / by Georg Kurt Gerber. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2005. / Includes bibliographical references (v. 2, leaves 192-205). / Thrombosis is an initiating response to vascular injury. Physiologically, this process aids in the repair and remodeling of the vessel wall. However, if left unchecked, luminal occlusion may rapidly occur. The coronary vascular bed is a life-sustaining environment in which pathological thrombosis can lead to devastating outcomes such as acute coronary syndromes or post-interventional thrombosis. In order to study these coronary thrombotic reactions, it is essential to consider the physical environment in which they occur. We have developed an in vitro method for creating pulsatile flows to mimic the coronary hernodynamic setting on a beat-to-beat basis. Furthermore, he have developed techniques and protocols to parametrically vary both the biological and physical aspects of thrombosis and in doing so, have investigated the effects of real-world temporal and spatial flow perturbations on local site platelet adhesion. Not only do such variations create quantitative differences in local reactions, but qualitative differences as well as various receptors must interact to create stable adhesions in a given hemodynamic environments. These findings have implications on the propensity for certain individuals to form clot under certain conditions, as well as the environment-dependent efficacy of various clinically relevant anti-thrombotic strategies. / by Kumaran Kolandaivelu. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references (p. 136-148). / Arterial remodeling is a major pathophysiological mechanism underlying clinical cardiovascular disorders such as hypertension, atherosclerosis and restenosis. We examined heparan sulfate proteoglycan homeostasis as a mechanism of regulation of arterial vascular remodeling in response to altered mechanical environments such as hypertension and injury. We first studied the effect of in-vitro mechanical strain on the ability of endothelial cells to inhibit vascular smooth muscle cell proliferation. Under these conditions we found mechanical strain increased endothelial inhibition of smooth muscle cell proliferation through increased production of heparan sulfate proteoglycans. Using inhibitors to p38 MAPK and ERK, we showed that activation of both of these pathways was essential for load-induced heparan sulfate production, TGF-,f1 activation, smad-2 activation and increased FGF-2 uptake. Further, we exposed cells to strain in the presence of a neutralizing antibody to TGF-P 1 and demonstrated that autocrine TGF-1l signaling was essential for load-induced HSPG production and sustained p38 MAPK and ERK activation. / (cont.) We also examined the endothelium of spontaneously hypertensive rats using immunohistochemical staining for heparan sulfate proteoglycan core proteins, TGF-31 and phosphorylated signaling intermediates and found results that correlated well with our in-vitro experiments. Taken together these results imply a novel paradigm of vascular remodeling to mechanical stimuli in which net arterial remodeling is controlled by the dynamic interplay between pro-growth signals from vascular smooth muscle cells and anti-growth signals from endothelial cells. In a second portion of this work, we examined the role of heparanase in vascular remodeling. Using siRNA gene silencing and overexpression techniques, we showed that alterations in heparanase expression lead to a profound modulation in endothelial inhibition of vascular smooth muscle cell proliferation. In vivo, we quantified heparanase expression in animal models of hypertension, vascular disease and injury. Immunohistochemical analysis of the aortae of hypertensive rats revealed an increase in endothelial production of heparanase that strongly correlated with increased aortic structural remodeling. / (cont.) Studies of vascular injury with stenting in the Zucker rat model of diabetes showed a relationship between neointimal heparanase expression and lesion thickness. Our results define a new role for heparanase as a key molecular controller of vascular remodeling in diverse disease states. / by Aaron B. Blair. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 69-71). / The history of private philanthropy in the US has been dominated by family foundations with arms-length philanthropy practices that largely existed in separation from commercial enterprise and business operations. This paper looks at emerging organizational and funding models being used in a wide range of disease areas in which philanthropy has shifted towards a more "venture-oriented" model sometimes referred to as disease foundation venture philanthropy (DFVP) as practiced by disease focused foundations (DFFs). More specifically, this research seeks to understand how these models map onto the range of translational challenges confronted by those engaged in bringing ideas from the bench to the bedside and it explores our current understanding of DFVP best practices. It concludes by raising questions and addressing issues designed to assist those who seek to setup successful collaborations between DFFs and industry partners. / S.M.

Includes bibliographical references (leaves 87-89). / Thesis (M. Eng.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / (cont.) The EWS models were then tested in a forward, casual manner on a random cohort of 500 ICU patients to mimic the patients' stay in the unit. The model with the highest performance achieved a sensitivity of 0.85 and a positive predictive value (PPV) of 0.70. Of the 35 episodes of hypotension despite fluid resuscitation present in the random patient dataset, the model provided early warnings for 29 episodes with a mean early warning time of 582 ± 355 minutes. / Early goal-directed therapy (EGDT) in severe sepsis and septic shock has shown to provide substantial benefits in patient outcomes. However, these preventive therapeutic interventions are contingent upon an early detection or suspicion of the underlying septic etiology. Detection of sepsis in the early stages can be difficult, as the initial pathogenesis can occur while the patient is still displaying normal vital signs. This study focuses on developing an early warning system (EWS) to provide clinicians with a forewarning of an impending hypotensive crisis-thus allowing for EGDT intervention. Research was completed in three main stages: (1) generating an annotated septic shock dataset, (2) constructing multivariate logistic regression EWS models using the annotated dataset, and (3) testing the EWS models in a forward, causal manner on a random cohort of patients to simulate performance in a real-life ICU setting. The annotated septic shock dataset was created using the Multi-parameter Intelligent Monitoring for Intensive Care II (MIMIC II) database. Automated pre-annotations were generated using search criteria designed to identify two patient types: (1) sepsis patients who do not progress to septic shock, and (2) sepsis patient who progress to septic shock. Currently, manual review by expert clinicians to verify the pre-annotations has not been completed. Six separate EWS models were constructed using the annotated septic shock dataset. The multivariate logistic regression EWS models were trained to differentiate between 107 high-risk sepsis patients of whom 39 experienced a hypotensive crisis and 68 who remained stable. The models were tested using 7-fold cross validation; the mean area under the receiver operating characteristic (ROC) curve for the best model was 0.940 ± 0.038. / by Dewang Shavdia. / M.Eng.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 165-180). / Vocal hyperfunction refers to "conditions of abuse and/or misuse of the vocal mechanism due to excessive and/or 'imbalanced' muscular forces" (Hillman, Holmberg, Perkell, Walsh, & Vaughan, 1989), characterized by excessive laryngeal and paralaryngeal tension (Aronson, 1980; M. D. Morrison, Rammage, Belisle, Pullan, & Nichol, 1983; N. Roy, Ford, & Bless, 1996). There is no widely accepted diagnostic measure of the presence and degree of vocal hyperfunction, and currently, assessment during diagnosis is often primarily based on subjective impressions given the patient's history and presentation of symptoms such as auditory-perceptual and visual or tactile discrimination of muscle tension (e.g., laryngeal palpation). Clinical care is hindered by the lack of a "gold standard" objective measure for the assessment of vocal hyperfunction. The first study in this thesis evaluated a novel experimental design for the study of vocal hyperfunction, making use of the established clinical procedure of injection laryngoplasty. This work found that the use of injection laryngoplasty as a platform for the study of some types of vocal hyperfunction is limited, but may offer a convenient opportunity to study selected associated parameters. Particular promising objective measures were investigated in the remaining four studies: kinematics of the vocal folds, root-mean-squared (RMS) measures of surface electromyography (sEMG), and spectral characteristics of sEMG. Kinematic features of vocal fold abduction and adduction were shown to discriminate between individuals with muscle tension dysphonia and controls. / (cont.) RMS measures of sEMG were investigated through correlation with current clinical neck palpation techniques in voice therapy patients and via a cross-sectional study of individuals with vocal fold nodules. Correlations between RMS neck sEMG and palpation ratings were low, and although some individuals with nodules displayed RMS neck sEMG patterns that were inconsistent with those seen in controls, overall the RMS measures were unable to discriminate between disordered and control groups. Mean coherence between two neck sEMG locations in individuals with vocal nodules was significantly lower in the 15 - 35 Hz band relative to controls, possibly agreeing with past subjective accounts of "imbalanced" muscle activity. / by Cara Elizabeth Stepp. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, September 2011. / "August, 2011." Vita. Cataloged from PDF version of thesis. / Includes bibliographical references. / One of the primary functions of the human auditory system is to separate the complex mixture of sound arriving at the ears into neural representations of individual sound sources. This function is thought to be crucial for survival and communication in noisy settings, and allows listeners to selectively and dynamically attend to a sound source of interest while suppressing irrelevant information. How the brain works to perceptually organize the acoustic environment remains unclear despite the multitude of recent studies utilizing microelectrode recordings in experimental animals or non-invasive human neuroimaging. In particular, the role that brain areas outside the auditory cortex might play is, comparatively, vastly understudied. The experiments described in this thesis combined classic behavioral paradigms with electrical recordings made directly from the cortical surface of neurosurgical patients undergoing clinically-indicated invasive monitoring for localization of epileptogenic foci. By sampling from widespread brain areas with high temporal resolution while participants simultaneously engaged in streaming and jittered multi-tone masking paradigms, the present experiments sought to overcome limitations inherent in previous work, namely sampling extent, resolution in time and space, and direct knowledge of the perceptual experience of the listener. In experiment 1, participants listened to sequences of tones alternating in frequency (i.e., ABA-) and indicated whether they perceived the tones as grouped ("1 stream") or segregated ("2 streams"). As has been reported in neurologically-normal listeners since the 1950s, patients heard the sequences as grouped when the frequency separation between the A and B tones was small and segregated when it was large. Evoked potentials from widespread brain areas showed amplitude correlations with frequency separation but surprisingly did not differ based solely on perceptual organization in the absence of changes in the stimuli. In experiment 2, participants listened to sequences of jittered multi-tone masking stimuli on which a regularly-repeating target stream of tones was sometimes superimposed and indicated when they heard the target stream. Target detectability, as indexed behaviorally, increased throughout the course of each sequence. Evoked potentials and high-gamma activity differed strongly based on the listener's subjective perception of the target tones. These results extend and constrain theories of how the brain subserves auditory perceptual organization and suggests several new avenues of research for understanding the neural mechanisms underlying this critical function. / by Andrew R. Dykstra. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / Includes bibliographical references (p. 133-141). / Inquiry into intracellular and cytoskeletal mechanics requires an intracellular mechanical sensor to verify models of sub-cellular structure dynamics. To this end, the green fluorescent protein (GFP) is considered as a mechanical sensor candidate with many desirable characteristics. Implicit solvent molecular dynamics CHARMM simulations demonstrated details inaccessible by AFM and OT methods, such as the linkage dependency of fluorophore environment changes and the energy exchanges between protein components during protein unfolding. Theoretical considerations and in vitro experiments explored the parameters important to GFP conjugation by N-hydroxysuccinimide (NHS) ester chemistry, and the complexities associated with a polymer approach to a controlled distribution of force across fluorescent proteins in a polyacrylamide (PAM) gel. / by Taro M. Muso. / S.M.