Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2008. / Includes bibliographical references. / Genetic mapping by association is an unbiased approach to discover genes and pathways influencing disease traits and response to drugs and environmental exposures. There are two key obstacles to mapping in humans: (1) The full sequence of study subjects cannot yet be obtained; and (2) There are substantial limits to the phenotypes that can be safely elicited or measured. Geneticists thus rely on practically measurable sets of genotypes to proxy for the sequence and human in-vitro models that proxy for in-vivo genetics and physiology while allowing for perturbation and characterization in high throughput. This thesis presents the development of one important class of proxy genotypes, those that capture most common genetic variation, as well as an evaluation and refinement of proxy phenotypes offered by one commonly used in-vitro model, the lymphoblastoid cell-line.Capturing common human genetic variation for genome-wide association studies requires genotyping a feasible subset of proxy (or "tag") SNPs. We investigated selection and analysis of tag SNPs, examined the relationship between investment in genotyping and statistical power, and evaluated whether power is compromised when tags are selected from an incomplete resource such as HapMap. We demonstrate an efficient haplotypebased tagging approach and other methods that dramatically increase tagging efficiency. Examining all observed haplotypes for association increases power to detect rare causal alleles, while reducing power for common alleles. Power is robust to completeness of the reference panel and holds across demographically related groups.Lymphoblastoid cell lines (LCLs) are being developed into an in-vitro model where genetics of human gene expression, drug response, and other traits can be studied under controlled conditions. However, the impact of the immortalization process, the relative influence of non-genetic factors, and reproducibility of measured traits are not yet understood. / (cont.) We addressed these questions while mapping loci for response to chemotherapy and found that traits in LCLs are subject to substantial confounders and are only modestly reproducible in independent experiments. Despite this, RNA expression of many genes is affected by genetic variation and predicts response to drugs; integrating SNPs, RNA, and drug response can identify novel pharmacogenetic variation mediated by RNA. / by Roman Yelensky. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 25). / The influence of middle-ear disease on hearing in mice is not well understood. We investigated middle-ear function and structure in a small group of dopamine beta hydroxylase (DBH)- knockout mice, which are known to be susceptible to middle-ear disease. We measured auditory brainstem response (ABR) and distortion-product otoacoustic emission (DPOAE) thresholds, as well as sound-induced umbo velocity, and used standard histological techniques to study normal and pathological middle-ear anatomy. Anatomical analyses included observation of tympanic membrane and ossicular structures, reconstruction of middle ear volume, and estimation of the volume of lightly or darkly stained middle-ear fluid. Lightly stained fluid in diseased ears was located throughout the middle ear, whereas darkly stained fluid, when present, was usually seen near the round window. The ABR and DPOAE thresholds and the umbo velocity produced by lower- and middle-frequency sound stimuli were strongly correlated with middle-ear air volume. The volume of darkly stained fluid was correlated with the DPOAE and ABR thresholds for lower- and middle-frequency sounds. The volume of lightly stained fluid was correlated with the umbo velocity in the middle and upper frequencies. Regression analyses between the thresholds and velocity show the DPOAE threshold about twice the ABR threshold in the middle frequencies, while the ABR threshold was roughly inversely proportional to the umbo velocity at lower stimulus frequencies. The correlations between histological and functional results are consistent with a decrease in middle-ear air volume and the presence of lightly stained fluid affecting the motion of the TM, while the darkly stained fluid near the round window acts to reduce the middle ear vibrations that reach the cochlea. The inverse relationship between the ABR threshold and the umbo velocity is consistent with a conductive hearing loss produced by reduced middle-ear air volume. / by Suh-Kyung Lee. / S.M.

Thesis (Ph. D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2001. / Leaves 141 and 142 reversed in binding and microfilming process. / Includes bibliographical references (leaves 143-150). / Aim: To examine the effects of cellular and tissue pharmacokinetics on control released growth factors. Motivation: The resurgence of interest in controlled drug delivery reflects the increasing appreciation of the importance of local pharmacokinetics in defining the efficacy and potency of bioactive compounds. Despite promising data in vitro, growth factor use in vivo has generally failed to live up to its full potential. Without a theoretical framework to consider local pharmacology, there remains no consensus approach for improving the clinical outcomes of control released growth factors. As a result, a series of experiments incorporating cellular pharmacokinetics, computational modeling, and tissue pharmacokinetics were conducted. CellularPharmacokinetics: The effect of ligand-receptor trafficking was examined on the potency of sustained release versus bolus administration of two growth factors that differed by intracellular trafficking kinetics. Sustained delivery potency was demonstrated to be dependent on both ligand and receptor trafficking and could be predicted based on trafficking considerations. / (cont.) Computational Models: Computational models were conceptualized to describe the relationship between controlled-delivery, transport, receptor ligand pharmacokinetics, and tissue response. Theoretical predictions were made about potential approaches for optimizing local delivery and about the spatial correlation of tissue concentrations with tissue response. Tissue Pharmacokinetics: The roles of physiological transport forces and proteolytic constraints on control released growth factor were examined. Partitioning and convection were shown to be dominant forces in governing drug distribution. A novel method based on intramolecular fluorescence quenching was implemented to describe the proteolytic constraints of local fibroblast growth factor delivery in an ex vivo carotid explant model. Conclusion: Both experimental and theoretical models of cellular and tissue interactions of growth factors have suggested concepts that may be relevant for local growth factor delivery. / by David Wu. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references (p. 54-58). / Industry-sponsored clinical research of investigational drugs (also called clinical development) has traditionally been carried out in relatively developed countries in the North American, Western European, and Pacific regions. However, lately it has been widely reported that clinical trials starting now are becoming increasingly diffused globally, with significant growth of activity in so-called emerging economies in Eastern Europe, Latin America, and Southeast Asia. This change in location of clinical development activities has numerous implications for patients, health care providers, pharmaceutical companies, regulatory agencies and governments around the globe. Even though there is much debate about the topic, a public systematic quantitative assessment of the current status of the globalization of clinical drug development phenomenon is lacking. The objective of this thesis research is to provide such objective quantification while addressing some issues that are currently in active discussion. This thesis documents that the participation of emerging countries is still relatively small (13%) and they most commonly participate in very large (involving more than five countries) phase Ilb or III trials. / (cont.) Albeit perceived as small, this participation is growing at a rapid pace (23% average annual growth rate) and the number of clinical sites of global clinical trials located in all emerging countries (11,038) is comparable with the sum of Germany, France, U.K., and Italy (11,061). Eastern European and Latin American countries have the greatest participation in clinical trials among emerging countries, but Southeast Asia is the region that is experiencing fastest growth. Meanwhile, Western Europe has experienced negative average annual growth of -8%, and North America has seemingly been stable. This thesis discusses findings and key drivers behind the globalization process. I also consider the argument that the sustainability of this model will depend on stringent protection of patients in these emerging countries and continued development of these nations, with eventual creation of an attractive market for pharmaceutical products. The extension of this process of globalization of clinical trials, if coupled with substantial improvements in health care delivery and research capacity in these emerging economies, has the potential of revolutionizing medical product development within the next two decades. / by Fabio Albuquerque Thiers. / S.M.

Includes bibliographical references (p. 197-212). / Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2004. / (cont.) Our methods analyze the coupling between instantaneous lung volume and heart rate and, subsequently, derive representative indices of parasympathetic and sympathetic control based on physiological and experimental findings. The validity of each method is evaluated via experimental data collected following interventions with known effect on the parasympathetic or sympathetic control. With the above techniques, this thesis explores an important topic in the field of space medicine: effects of simulated microgravity on cardiac autonomic control and orthostatic intolerance (OI). Experimental data from a prolonged bed rest study (simulation of microgravity condition) are analyzed and the conclusions are: 1) prolonged bed rest may impair autonomic control of heart rate; 2) orthostatic intolerance after bed rest is associated with impaired sympathetic responsiveness; 3) there may be a pre-bed rest predisposition to the development of OI after bed rest. These findings may have significance for studying Earth-bound orthostatic hypotension as well as for designing effective countermeasures to post-flight OI. In addition, they also indicate the efficacy of our proposed methods for autonomic function quantification. / System identification is an effective approach for the quantitative study of physiologic systems. It deals with the problem of building mathematical models based on observed data and enables a dynamical characterization of the underlying physiologic mechanisms specific to the individual being studied. In this thesis, we develop and validate a new linear time-invariant system identification approach which is based on a weighted-principal component regression (WPCR) method. An important feature of this approach is its asymptotic frequency-selective property in solving time-domain parametric system identification problems. Owing to this property, data-specific candidate models can be built by considering the dominant frequency components inherent in the input (and output) signals, which is advantageous when the signals are colored, as are most physiologic signals. The efficacy of this method in modeling open-loop and closed-loop systems is demonstrated with respect to simulated and experimental data. In conjunction with the WPCR-based system identification approach, we propose new methods to noninvasively quantify cardiac autonomic control. Such quantification is important in understanding basic pathophysiological mechanisms or in patient monitoring, treatment design and follow-up. / by Xinshu Xiao. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references (p. 171-175). / The inferior colliculus, the primary nucleus in the mammalian auditory midbrain, occupies a central position in the ascending auditory pathway. Nearly all ascending neural pathways converge and synapse in the central nucleus of the inferior colliculus (ICC). Further, the anatomical arrangement of axons and neurons in the ICC suggests the existence of functional regions which may play a role in organizing different types of physiological information. To investigate this organization, we characterized the response properties of neighboring neurons in the ICC. To record reliably from neighboring neurons, we adopted a relatively new electrophysiological technique, tetrode recordings. Tetrodes have four closely spaced recording sites (<20[mu]m) which record multi-unit activity from a small number of neighboring neurons. The recorded signals contain action potentials originating from more than one neuron. Based on action potential wave shape differences across the four channels, we can reconstruct the contributions of individual neurons. Applying tetrode recordings to the ICC of anesthetized cats, we successfully reconstructed individual spike trains for 190 neurons at 52 recording sites. / (cont.) To quantify the advantage of tetrodes, we compared our multi-channel recording results with waveform sorting from single-channel electrode recordings. At best, only 32% of the single-units from tetrode sorting were correctly identified using single-channel recordings. We used tetrode to characterize pure tone responses of neighboring neurons in the ICC in terms of frequency selectivity, level dependence, temporal discharge patterns, and sensitivity to interaural time differences. We find similarities in best frequency and pure-tone threshold among neighboring neurons; however, we find large disparities in bandwidth, level dependence, temporal discharge patterns, and sensitivity to interaural time differences. These results suggest that neighboring neurons in ICC can greatly differ in membrane properties and/or their patterns of synaptic input from different brainstem nuclei and tonotopic regions. Using tetrode recordings, we investigated how well multi-unit responses represent the response properties of the contributing single-unit responses. / (cont.) We find that multi-unit responses represent single-unit best frequency, pure-tone threshold and level dependence well, and they represent single-unit bandwidth and interaural phase sensitivity poorly. These results suggest caution must be used not to infer single-unit responses from multi-unit recordings. / by Chandran V. Seshagiri. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2004. / "June 2004." / Includes bibliographical references (leaves 152-156). / Current implementations of patient information review on Personal Digital Assistants (PDAs) are gaining traction in the in-patient hospital setting. There are tremendous patient safety and satisfaction, workflow improvement and physician satisfaction improvements possible if similar technology is optimized and used in the ambulatory care setting. We have performed a study of Partners HealthCare System (PHS) physicians to determine user requirements, implemented a formal method (not previously used within the PHS Information Systems division) to create a Software Requirements Specification (SRS), and developed a prototype user interface for a future LMR2go application (a mobile adjunct for the ambulatory care Longitudinal Medical Record system in use at PHS). The results of the study provided a core set of functions for the LMR2go application which physicians would like to use while on-call and substantiated the potential adoption of such an application. After an analysis of current software and hardware technologies, review of the study results and components of the actual SRS, a sample run through of a typical on-call physician workflow on the LMR2go User Interface is provided. / by Sameer A. Bade. / S.M.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2008. / 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. 173-178). / Over the past three decades, much research in motor neuroscience has focused on understanding how humans make coordinated reaching movements, yielding valuable insight into the planning and control of reaching movements, and establishing a foundation for robot-assisted rehabilitation. The goal of this doctoral research was to provide a quantitative characterization of humans' wrist rotations, paving the way for intelligent robot-assisted wrist rehabilitation. More specifically, we have characterized the kinematics, dynamics, and adaptation of wrist rotations, and discussed implications for planning and control. Kinematics: It is well known that humans make relatively straight reaching movements, suggesting that reaching movements are primarily under kinematic control of hand position. We used a motion capture system to test if wrist rotations are also under kinematic control. We found that wrist rotations exhibit a pattern with significantly more path curvature and variability than reaching movements (p = 0.001). While the increased path curvature could indicate that wrist rotations are not under kinematic control, this work provides evidence that the curvature is instead due to imperfect peripheral execution.Dynamics: In order to determine the exact cause of path curvature, an anatomically-accurate, mathematical model of the wrist was developed, including recent measurements of passive wrist stiffness. Combining experimentally-measured kinematics from human subjects with the wrist model revealed that moderately-sized wrist rotations can be approximated by a very simple model with virtually no loss in accuracy.Interaction torques, for which the nervous system compensates in reaching movements, are present but negligible in wrist rotations. / (cont) Rather, wrist rotation dynamics are dominated by stiffness, which was shown to be the likely cause of path curvature.Adaptation: When perturbed during reaching movements, humans adapt by straightening their paths, confirming that kinematics play a prominent role in planning reaching movements. We found that subjects consistently adapted to a conservative,velocity-dependent force field. Interestingly, this adaptation was more difficult to detect than in perturbation studies involving reaching movements. Taken together, these results suggest that wrist rotations are also primarily under kinematic control (albeit imperfect). / by Steven K. Charles. / Ph.D.

Thesis (Ph. D. in Health Sciences and Technology)--Harvard-MIT Program in Health Sciences and Technology, 2012. / Cataloged from PDF version of thesis. In title on title page, double underscored "v̳" appears as subscript. / Includes bibliographical references (p. 73-83). / Voltage-gated sodium (Nav) channels are diverse, comprising nine known mammalian subunits, which are classified pharmacologically into tetrodotoxin-sensitive (TTX-S) and tetrodotoxin-insensitive (TTX-1) categories. The pattern of Nav channel expression shapes response properties of neurons, while changes in these expression patterns are related to many pathological conditions. Previous RT-PCR results indicated the expression of a variety of Nav channel subunits in the vestibular ganglion, the sensory ganglion that conveys information about motion and orientation. The expressed subunits included several TTX-1 subunits with unique biophysical properties that have been extensively characterized in somatosensory neurons and the heart, but never reported in published electrophysiological studies of the vestibular ganglion. Using whole-cell patch clamp, we show the presence of two types of TTX-l Nav currents in acutely dissociated rat vestibular ganglion neurons (VGNs) from the first postnatal week: a fast and negatively-inactivating current (midpoint of inactivation: ~-100 mV) that resembled current previously described for the Nav1.5 subunit, and a slower current with a depolarized voltage range of inactivation (midpoint ~-30 mV) which had properties consistent with Nav1.8 channels. All neurons also expressed TTX-S Nav currents with similar properties to those previously described in VGN (midpoint of inactivation: ~-75 mV). The Nav1.5-like current contributed about 10% of the total Nav current, was expressed in most VGNs on the first postnatal day (P1), and gradually decreased in prevalence throughout the first week. The Nav1.8-like current was present in ~25% of cells and was correlated with broader action potentials, higher voltage thresholds, and minimal spike height accommodation. We confirmed the expression of Nav1.8 using a reporter mouse in which fluorescence is restricted to Nav1.8- expressing cells; intense fluorescent signal was seen in many VGN cell bodies and peripheral processes. These results suggest that Nav1.8 may be expressed in non-somatosensory peripheral neurons. Nav channel expression in immature VGNs may contribute to development, while differential expression in adulthood may underlie diversity of mature response properties. / by Xiao-Ping Liu. / Ph.D.in Health Sciences and Technology

Thesis: Ph. D. in Medical Engineering and Bioastronautics, Harvard-MIT Program in Health Sciences and Technology, 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 126-139). / Bone adapts its mass and architecture in response to its mechanical environment. Yet control of this process by mechanical cues is poorly understood, particularly for unloading. Defining the fundamental mechano-regulation of bone adaptation is critical for the better understanding and mitigation of bone loss in astronauts as well as clinical conditions such as spinal cord injury, stroke, muscular dystrophy, and bed rest. The overall goal of this work was to study skeletal adaptation to varying amounts of reduced loading to help delineate the relationship between mechanical stimuli and skeletal adaptation. We first examined the relative contribution of muscle and gravitational forces to the maintenance of skeletal health in mice, using botulinum toxin (BTX) to induce muscle paralysis and hindlimb unloading to eliminate external loading on the hindlimbs, alone and in combination. BTX led to greater bone loss than hindlimb unloading, while the combination of interventions led to the most detrimental effects overall, suggesting that both muscle and gravitational forces play a role in skeletal maintenance, with greater contributions from muscle forces. We then characterized skeletal adaptation to controlled reductions in mechanical loading of varying degrees employing a novel model that enables long-term exposure of mice to partial weightbearing (PWB). We found that declines in bone mass and architecture were linearly related to the degree of unloading. Even mice bearing 70% of their body weight exhibited significant bone loss, suggesting that the gravity of the moon (0.16 G) and Mars (0.38 G) will not be sufficient to prevent bone loss on future exploration missions. Finally, since bone remodeling is highly site-specific, we used gait analysis and inverse dynamics to determine the mechanical environment during PWB, and then developed a finite element model of the tibia to resolve the local strain-related stimulus proposed to drive changes in bone mass. We found modest correlations between cortical bone architecture at different PWB levels and strain energy density. Altogether this work provides a critical foundation and rationale for future studies that incorporate detailed quantification of the mechanical stimuli and longitudinal changes in bone architecture to further advance our understanding of the skeletal response to reduced loading. / by Rachel Ellman. / Ph. D. in Medical Engineering and Bioastronautics