Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 161-176). / Nearly all listening environments-indoors and outdoors alike-are full of boundary surfaces (e.g., walls, trees, and rocks) that produce acoustic reflections. These reflections interfere with the direct sound arriving at a listener's ears, distorting the binaural cues for sound localization. Yet, human listeners have little difficulty localizing sounds in most settings. This thesis addresses fundamental questions regarding the neural basis of sound localization in everyday reverberant environments. In the first set of experiments, we investigate the effects of reverberation on the directional sensitivity of low-frequency auditory neurons sensitive to interaural time differences (ITD), the principal cue for localizing sound containing low frequency energy. Because reverberant energy builds up over time, the source location is represented relatively faithfully during the early portion of a sound, but this representation becomes increasingly degraded later in the stimulus. We show that the directional sensitivity of ITD-sensitive neurons in the auditory midbrain of anesthetized cats and awake rabbits follows a similar time course. However, the tendency of neurons to fire preferentially at the onset of a stimulus results in more robust directional sensitivity than expected, suggesting a simple mechanism for improving directional sensitivity in reverberation. To probe the role of temporal response dynamics, we use a conditioning paradigm to systematically alter temporal response patterns of single neurons. Results suggest that making temporal response patterns less onset-dominated typically leads to poorer directional sensitivity in reverberation. In parallel behavioral experiments, we show that human lateralization judgments are consistent with predictions from a population rate model for decoding the observed midbrain responses, suggesting a subcortical origin for robust sound localization in reverberant environments. In the second part of the thesis we examine the effects of reverberation on directional sensitivity of neurons across the tonotopic axis in the awake rabbit auditory midbrain. We find that reverberation degrades the directional sensitivity of single neurons, although the amount of degradation depends on the characteristic frequency and the type of binaural cues available. When ITD is the only available directional cue, low frequency neurons sensitive to ITD in the fine-time structure maintain better directional sensitivity in reverberation than high frequency neurons sensitive to ITD in the envelope. On the other hand, when both ITD and interaural level differences (ILD) cues are available, directional sensitivity is comparable throughout the tonotopic axis, suggesting that, at high frequencies, ILDs provide better directional information than envelope ITDs in reverberation. These findings can account for results from human psychophysical studies of spatial hearing in reverberant environments. This thesis marks fundamental progress towards elucidating the neural basis for spatial hearing in everyday settings. Overall, our results suggest that the information contained in the rate responses of neurons in the auditory midbrain is sufficient to account for human sound localization in reverberant environments. / by Sasha Devore. / Ph.D.

Thesis (Ph. D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2001. / Includes bibliographical references (p. 147-154). / The human tongue is a versatile, lithe and structurally complex muscular organ that is of paramount importance for many physiological tasks. The lingual musculature is composed of various orthogonally oriented myofiber populations. Furthermore, coupling this knowledge of tissue myoarchitecture with patterns of regional deformation offers the ability to explore complex structure-function relationships in the organ. Tongue myoarchitecture was studied with Diffusion Tensor MRI (DTI), which derived the spatial diffusion tensor field in the tongue. Since, diffusivity relates directly to myofiber orientation, this in vivo technique successfully produced a virtual anatomical atlas. In order to relate this 3D myoarchitecture to physiological deformations, in vivo strain was quantified by an MRI tagging technique. This technique tagged lingual tissue with a rectilinear grid, which was subsequently imaged to track and quantify deformation through 3D strain measures. Anterior protrusion, sagittal bending, and oral stage deglutition were studied with this technique. The results demonstrated that synergistic co-contraction between various muscle populations produced the necessary deformations in global tongue shape. In order to delineate specific muscular contributions to sagittal bending, the tongue was modeled by a thermal bimetal strip analog wherein thermal contraction approximated muscle fiber activation. / (cont.) The results confirmed our hypothesis that sagittal bending resulted from synergistic co-contraction of two distinct myofiber populations. In conclusion, tongue deformation is intimately related to the lingual musculature, and our results confirm the characterization of the tongue as a muscular hydrostat - an organ whose musculature produces deformation as well as the structural support for that deformation. / by Vitaly J. Napadow. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / Includes bibliographical references (p. 91-101). / Recent advances in systems biology and bioinformatics have highlighted that no cell population is truly uniform and that stochastic behavior is an inherent property of many biological systems. As a result, bulk measurements can be misleading even when particular care has been taken to isolate a single cell type, and measurements averaged over multiple cell populations in a tissue can be as misleading as the average height at an elementary school. Unfortunately, there are relatively few experimental systems available at present that can provide a combination of single cell resolution, large cell populations, and the ability to track individual cells over multiple time points. Those systems that do exist are often difficult to automate and require extensive user intervention simply to generate the raw data sets for later analysis. The goal of this thesis project was to develop a powerful, inexpensive, and easy-to-use system that meets the above requirements and can serve as a platform for single cell bioinformatics. Our current system design is composed of two basic parts: 1) a customizable PDMS device consisting of one or more microwell arrays, each with associated alignment and identification features, and 2) a suite of custom software tools for automated image processing and data analysis. The system has a number of significant advantages over competing technologies such as flow cytometry and standard image cytometry. Unlike flow cytometry, the cells are not in suspension, and individual cells can be tracked across multiple time points or examined before and after a treatment. / (cont.) Unlike most image cytometry approaches, the cells are arranged in a spatially defined pattern and physically separated from one another, greatly simplifying the required image analysis. The automated analysis tools require only a minimal amount of user intervention and can easily generate multi-channel fluorescence time courses for tens of thousands of individual cells in a single experiment. For visualization purposes, tools are provided to annotate the original fluorescence images or movies with the results of later analysis, and several quality control routines are available to identify improperly seeded wells or debris. The microwell array cytometry platform has allowed us to investigate a number of biological problems that would be difficult or impossible to tackle with standard techniques. Our earliest work focused on correlating pre-stress cell states with post-stress outcomes, with a major focus on the cryopreservation of primary hepatocytes. In particular, we wanted to know whether cell survival was dominated by extrinsic factors such as ice crystal nucleation, or intrinsic factors such as the energetic state of the cell. In one set of studies, we found that cells with a high initial mitochondrial content or mitochondrial membrane potential, as measured by Rh123 or JC-1 staining, were significantly less likely to survive the freezing process. This demonstrated that intrinsic cell factors do play a major role in cryopreservation survival, but perhaps more importantly demonstrated the power and versatility of the microwell system by tracking individual cells across a treatment as extreme as freezing the entire device. In another set of cryopreservation experiments, cells were transiently transfected with a GFP-tagged protective protein and the resulting cell population, with its range of expression levels, was used to generate dose response curves with single cell resolution for the protein's protective effect. / (cont.) More recently, our efforts have focused on generating single cell fluorescence time courses and using bioinformatics techniques such as hierarchical and k-means clustering to visualize the data and extract interesting features. More specifically, the behavior of primary hepatocytes under oxidative stress and protective metabolic manipulation was examined using a combination of mitochondrial and free radical sensitive dyes. The resulting time courses could not only be compared between the treatment groups, but a number of distinct response patterns could be identified within each treatment group. This variation in response patterns represent potentially important information that would be missed using bulk techniques or flow cytometry. In addition, membership in each response cluster was correlated between multiple dyes and with the initial state of each cell. Using a live / dead methodology, dose response curves, survival curves, and survival time distributions were also generated for each treatment condition and further subdivided based on the initial cell state and cluster assignments. We believe that our microwell array cytometry platform will have general utility for a wide range of questions related to cell population heterogeneity, biological stochasticity, and cell behavior under stress conditions. We have really just begun exploring rich data sets of this type, and with additional work there is a great potential for groundbreaking results in many areas of biology and bioinformatics. Though we have applied techniques from gene expression analysis, there are a number of significant differences between the type of data generated by gene chips and that generated in high-throughput single cell experiments. These differences also make single cell biology a fruitful area for the development of novel bioinformatics techniques and theories. / by Kenneth L. Roach. / Ph.D.

Thesis (Ph.D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2002. / Includes bibliographical references (p. 216-225). / Osteoarthritis is a painful degenerative joint disease affecting millions of people in the U.S. The pathogenesis of articular cartilage disease is characterized by softening of cartilage and loss and disruption of constituent macromolecules including proteoglycans and collagen. In current orthopaedic surgical practice, the gold standard for evaluating articular cartilage integrity is the use of a hand probe during arthroscopy. Mechanical probing, however, is invasive and requires anesthesia. Tightly confined areas of the articular surface can be difficult to reach and assess, and manual probing provides a subjective rather than a quantitative assessment of cartilage mechanical integrity. This thesis was motivated by the desire for a noninvasive and nondestructive means to map the variation in mechanical stiffness of an articular surface. Such a method could potentially have application to guiding surgeons during procedures and quantitatively assessing the efficacy of medical and surgical therapies. It could also potentially provide patient-specific, in vivo tissue mechanical property data for surgical simulation and preoperative procedure planning. The macromolecule glycosaminoglycan (GAG) is a significant determinant of cartilage stiffness. GAG content can be assessed noninvasively in vivo and in vitro by an MRI-based technique known as delayed gadolinium-enhanced magnetic resonance imaging of cartilage (dGEMRIC), which measures the MRI parameter TI after equilibration with the ionic contrast agent Gd(DTPA)2-. With dGEMRIC, TlGd serves as an index of GAG content: we therefore examined whether cartilage stiffness could be related to dGEMRIC-measured TlGd in samples of human tibial plateaus. / (cont.) We developed an experimental methodology to permit indentation test sites and regions in dGEMRIC scans to be registered with submillimeter accuracy. We found that the load response to focal indentation (a measure of local stiffness) and locally-averaged TlGd were in general highly correlated (Pearson correlation coefficients r = .80, .90, .64, .81 (p < .002) for four different patient samples, 130 total test locations). We further demonstrated that the observed correlation is not a simple consequence of cartilage thickness effects. We observed that the parameters of the stiffness-TIGd relationship differed in some samples between the region of the tibial plateau covered by the meniscus in vivo and the more central region normally in contact with the femoral condyle. This suggests that another factor such as surface architecture or collagen integrity also influences the indentation response of the articular surface. / by Joseph Thomas Samosky. / Ph.D.

Thesis (Ph.D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2000. / "September 1999." / Includes bibliographical references (leaves 139-145). / In asthma, the key effector driving acute airway narrowing is thought to be airway smooth muscle (ASM); as the muscle surrounding the airways shortens, the airway lumen narrows. Airway hyperresponsiveness (AHR) - the excessive narrowing of the airways - is one of the cardinal features of asthma. Yet, the mechanism(s) regulating the airway lumenal radius, and perhaps the failure of these mechanisms to prevent excessive airway constriction, remains largely unexplained. This thesis shows that the regulation of ASM length corresponds to a dynamically equilibrated steady-state, not the static mechanical equilibrium that had been previously assumed. This dynamic steady state requires as an essential feature a continuous supply of external mechanical energy (derived from tidal lung inflations) that act to perturb the interactions of myosin with actin, drive the molecular state of the system far away from thermodynamic equilibrium, and bias the muscle toward lengthening. This mechanism leads naturally to the suggestion that excessive airway narrowing in asthma may be associated with the destabilization of that dynamic process and its resulting collapse back to static equilibrium. With this collapse the muscle undergoes a phase transition and virtually freezes at its static equilibrium length. This mechanism may help to elucidate several unexplained phenomena including the multi-factorial origins of AHR, how allergen sensitization leads to AHR, and the inability in asthma of deep inspiration to relax ASM. / by David Shoichi Inouye. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 107-112). / Obtaining accurate needle placement is of critical importance in many medical scenarios. In the setting of fine needle aspiration biopsy (FNAB), manual palpation is often the only cue for determining the optimal position of the needle. As a result, FNAB procedures frequently yield non-diagnostic tissue. When not guided by an imaging modality, breast and thyroid FNAB's only obtain diagnostic tissue in approximately 65% of cases. Although the addition of noninvasive imaging technology has been shown to increase FNAB yield, it is time-consuming, relatively expensive, and often requires additional personnel with specialized expertise. A need exists for low-cost, small, simple to use technologies that can provide active feedback during needle placement. One promising method for guiding needle placement would be to integrate an optical sensor that could identify tissue type at the tip of the needle in order to avoid non]diagnostic sampling. Optical technologies are well suited to this challenge because sensors can be made using optical fiber which is as thin a human hair. Optical frequency domain ranging (OFDR) is an optical ranging technique that is capable of measuring depth-resolved (axial, z) tissue structure, birefringence, flow (Doppler shift), and spectra at a micrometer level resolution. Analysis of the OFDR depth reflectivity profiles yields information about the nature of the tissue being interrogated at the tip of the probe and algorithms can be developed to automatically differentiate between tissue types. The overall goal of this thesis is to develop a small, portable, point-of-care optical system that can be used to differentiate human breast tissue and guide needle placement in the setting of FNAB. We will investigate enabling technologies that allow for efficient simplification and miniaturization of an OFDR system including signal processing algorithms for automatically differentiating tissue type, a miniature battery-powered laser, and a study of the effect of reduced-bit depth acquisition for OFDR systems. Throughout, we will focus on trade offs between size and performance while taking into account usability, robustness, and overall cost which are key features of point-of-care technologies. / by Brian David Goldberg. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / "September 2006." / Includes bibliographical references. / Transitive inference (TI) refers to inferences on relations between items based on other known relations of those items. Using a paradigm where participants first learn a series of four overlapping pairs that constitute the ordered sequence A>B>C>D>E and are then tested on the novel TI pair BD and non-TI pair AE, animal experiments demonstrated that intact function of the hippocampus is necessary for TI but not for non-TI. We performed three functional magnetic resonance imaging (fMRI) experiments to identify neural correlates of TI in healthy humans. First, we show hippocampal activation in learning overlapping pairs that constitute an ordered sequence but not non-overlapping individual pairs. Second, we demonstrate hippocampal recruitment in inferences on the ordered sequence of overlapping pairs (TI) but not on non-overlapping pairs (non-TI, e.g., if a>b and c>d then a>d). We then demonstrate the specificity of hippocampal activation to TI on pairs that are devoid of sequence end-items (e.g., B>D vs. A>C). The results support the relational flexibility account of hippocampal function. / (cont.) Under this account, the hippocampus plays a special role in declarative memory in that it acts to rapidly bind common features into a unified representation that supports flexible inferential memory expression. Other brain areas that were activated in TI included prefrontal cortex, pre-supplementary and supplementary motor areas, insula, anterior and posterior cingulate cortex, lateral temporal cortex, precuneus, posterior parietal cortex, cerebellum, thalamus, ventral striatum and midbrain (the TI network). In schizophrenia, TI performance is impaired. Could this deficit be linked to hippocampal abnormalities in SZ? We used the findings from studies of TI in healthy participants to interpret an fMRI study of TI in SZ. In SZ, we confirmed the deficit in TI on pairs devoid of end-items (e.g., B>D) but not on pairs including an end-item (e.g., A>C) and linked it to reduced hippocampal activation. Further, we uncovered aberrant function in two points of the TI network - anterior cingulate and inferior parietal cortices - in SZ. / by M. Zalesak. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, February 2007. / "September 2006." / Includes bibliographical references. / The main goal of this thesis was to systematically characterize the detection sensitivity, temporal response, and spatial resolution of IRON contrast for fMRI within the awake, behaving monkey. Understanding these issues provides insights into the physiology of the functional response to local changes in brain activity, enables researchers to optimize experimental designs, and delineates the advantages and limitations of neuroimaging within this important animal model. The injection of the iron oxide contrast agent (MION) provided a 9-fold increase in efficiency for block designs relatively to BOLD contrast. Because the hemodynamic response function acts as a low-pass filter on neural activation to attenuate the size of differential responses to alternate stimuli, this factor dropped to approximately 2 for rapidly presented stimuli. Detection efficiency for event-related stimulus designs for BOLD and IRON contrasts could be optimized using random or semi-random distributions for interstimulus intervals. Small increases in predictability could be traded for large gains in efficiency, particularly for the IRON method. A general linear model was successfully employed to describe IRON and BOLD impulse response functions. Both responses were accurately described by a bimodal exponential model with similar time constants, a fast (4.5 sec) and a slow (13.5 sec). / (cont.) The slow response comprised 80% of IRON signal, and was responsible for the BOLD post-stimulus undershoot. It likely encompasses changes in post-arteriole blood volume. Optimized IRON activation maps do not show activation in draining veins or draining tissue, in contrast with BOLD contrast. To examine what happens at the level of small vessels and capillaries, we used point-image stimuli to measure IRON and BOLD point spread functions (PSF) in V1. We estimated an IRON PSF no larger than approximately 0.4 mm, and a BOLD PSF with twice the size. Severe image distortions arising from monkey's body motion outside of the field of view currently limit the achievable spatial resolution. Preliminary data suggests multi-shot EPI with navigators may be useful in improving image stability at higher resolution for IRON fMRI, which can employ short echo times to minimize phase variations, while achieving maximum efficiency by increasing the MION dose. / by Francisca Maria Pais Horta Leite. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2008. / Vita. / Includes bibliographical references (p. 147-155). / Parallel MRI techniques allow acceleration of MR imaging beyond traditional speed limits. In parallel MRI, radiofrequency (RF) detector coil arrays are used to perform some degree of spatial encoding which complements traditional encoding using magnetic field gradients. As the acceleration factor increases, coil design becomes critical to the overall image quality. The quality of a design is commonly judged on how it compares with other coil configurations. A procedure to evaluate the absolute performance of RF coil arrays is proposed. Electromagnetic calculations to compute the ultimate intrinsic signal-to-noise ratio (SNR) available for any physically realizable coil array are shown, and coil performance maps are generated based on the ratio of experimentally measured SNR to this ultimate intrinsic SNR. Parallel excitation, which involves independent transmission with multiple RF coils distributed around the body, can be used to improve the homogeneity of RF excitations and minimize the RF energy deposited in tissues - both critical issues for MRI at high magnetic field strength. As its use is explored further, it will be important to investigate the intrinsic constraints of the technique. We studied the trade-off between transmit homogeneity and specific absorption rate (SAR) reduction with respect to main magnetic field strength, object size and acceleration. We introduced the concept of ultimate intrinsic SAR, the theoretical smallest RF energy deposition for a target flip angle distribution, and we calculated the corresponding ideal current patterns. Knowledge of these optimal current patterns will serve as an important guide for future high-field coil designs. / by Riccardo Lattanzi. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Cochlear nucleus (CN), the exclusive destination of the auditory nerve, is the gateway for all central processing of auditory information. The CN comprises three major subdivisions: anteroventral, posteroventral and dorsal (AVCN, PVCN and DCN, respectively), each of which contains anatomically and physiologically distinct neurons projecting onto different targets. This research used focal electric stimulation of small, confined parts of the CN in anesthetized guinea pigs to resolve the roles of the CN divisions, in two contexts. Part i explored the effect of stimulation on the gross neural potential (electrically evoked auditory brainstem response, EABR). In AVCN and PVCN away from the 8th nerve fibers entering the brainstem, stimulation consistently evoked waveforms comprising 3 waves, suggesting a diffuse distribution of cellular generator of the EABR. On the other hand, in vestibular structures (vestibular nerve root and Scarpa's ganglion), the characteristic waveform comprised only two waves. Stimulation of multiple neural structures, as seen with higher stimulus levels or stimulation in auditory nerve root area generally produced more complex and variable waveforms. Part 2 explored the effects of stimulation on the activation of one type of auditory reflex, medial olivocochlear (MOC) reflex. The reflex was monitored through its effects on distortion product otoacoustic emission (DPOAE). The MOC reflex was activated bilaterally by stimulating PVCN or AVCN shell, but not AVCN core. These results suggest that there are two groups of MOC interneurons in specific parts of CN. / by Ryuji Suzuki. / Ph.D.