Thesis (Ph. D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2002. / Includes bibliographical references (leaves 106-120). / Our lab's long-term goal is to elucidate the circuitry of the visual cortex, to develop quantitative computational models of neuronal function in the visual cortex, and to establish how these models may relate to visual perception and visually guided behavior. Central to this goal is the analysis of functional architecture, which is crucial to an understanding of how the brain works. In my thesis research, I applied behavioral and microstimulation techniques to demonstrate the causal connections between neural activity and behavior. Understanding these relationships is one of the fundamental issues needed to be addressed in Neurobiology. Specifically, I focused on the functional analysis of the middle temporal visual area (MT) and the behavior associated with it. MT is an extrastriate area that is primarily involved in visual motion processing. A very important function within MT is a segregation of center-surround interactions which plays a critical role in processing visual motion cues. There are two types of motion center-surround interactions in MT neurons: surrounds may reinforce (at wide-field sites) or suppress (at local-motion sites) the centers' directional responses. They are important in representing the initial stages of a functional segregation between wide-field and local-contrast motion processing. To further study the computational model used by the brain to readout sensory information, I conducted microstimulation experiments in MT by changing stimulation amplitudes (from 10/LA to 160tA) and frequencies (from 25Hz to 500Hz). Microstimulation can introduce an additional velocity signal into MT and the pursuit and saccadic systems usually compute a vector average of the visually evoked and microstimulation-induced velocity signals. / (cont.) Increasing either amplitude or frequency generally increases the relative weight of the electrical velocity signal,' with the effects of amplitude being slightly more prominent. In addition, applying higher current fre-quencies appears to preserve the directionality of microstimulation better than does applying higher current amplitudes. With increasing frequencies, the magnitude of the electrical velocity signal either increased or remained constant, while its direction remained consistent. In contrast, increasing current amplitude tended to decrease the magnitude of the signal and increased its variability in direction. This finding is consistent with the idea that large current amplitudes, which presumably activate many MT columns signaling different directions, introduce noise into the behavior. My preliminary results have demonstrated that microstimulation in MT can also introduce an additional positional signal into the saccade system and that this electrical signal is combined with the visually evoked signal through a vector summation mechanism. The direction of this electrical signal is highly correlated with the position of the receptive field relative to the fixation point. To test the notion that the center-surround properties of MT neurons may be important for signaling the relative motion between object and background, we conducted behavioral experiments by using real background motion to simulate the microstimulation experiments at wide-field sites ... / by Ruilin Zhao. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / Includes bibliographical references. / Drug eluting stents have revolutionized the practice of medicine and the landscape of medical devices. Yet, more than four years after introduction clinical trial data and clinical use have still not fully clarified what drives the safety and efficacy of these devices. The goal of this thesis was to help fill this void by describing the mechanisms by which stent-eluted drugs are distributed within healthy and atherosclerotic vascular models. In the first part of the thesis we investigated the effect of drug physicochemical properties on drug deposition, retention, and distribution in a healthy vascular model. We found that hydrophobic drugs are deposited to a far greater degree than hydrophilic drugs, with longer retention times, and distribution patterns that likely track with specific and general binding sites. The second part of the thesis investigated how arterial ultrastructure in health and disease modulates the arterial deposition and distribution of hydrophobic antiproliferative drugs used with drug-eluting stents. We tracked the distribution of radiolabeled and FITC-labeled compounds and demonstrated that macrostructural changes in arterial architecture led to profound changes in drug deposition. Paclitaxel in particular was sensitive to tissue state. / (cont.) This drug binds specifically to tubulin and to lesser extent in a general manner to elastic. Drug levels fell as paclitaxel, tubulin and elastin were displaced by lipid and collagen. These observations might well explain how drugs may partition within different arterial lesions as determined by lesion composition. Finally, we demonstrated that association with these binding sites was governed by association kinetics that reflects the different components of the arterial wall compartments. Slower release kinetics yielded up to 64% higher deposition of a drug from stents implanted in rabbit iliac arteries over a 28-day period. Mathematical modeling illustrates that the dependence of drug deposition on stent release kinetics is contingent on drug retention. Further model development is implicated for predicting drug deposition profiles for different types of drugs, arterial states, and stent release kinetics. / by Neda Vukmirovic. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, February 2004. / Includes bibliographical references (p. 167-175). / This thesis explores two important factors that constrain the syntactic parser of the sentence processing mechanism, syntactic storage costs and plausibility information. It uses behavioral methods to explore the characteristics of the two factors and neuroimaging to explore the underlying neurological substrates associated with these aspects of syntactic processing. Experiment 1 behaviorally demonstrated the presence of syntactic storage costs for predictions of verbs, filler-gaps, and subcategorized prepositional phrases. It is argued that the data support the Dependency Locality Theory (Gibson, 2000) supposition of stored predicted heads as well as a theory of syntax that includes empty categories. Experiment 2 demonstrated brain regions associated with storage and integration cost demands in the contrast of subject-object (SO) and object-subject (OS) sentence structures. The results indicate that the inferior parietal cortex is part of a larger network of cortex, including inferior frontal perisylvian areas, that is involved in the processing of SO vs. OS sentences. However, the involvement is not identical to that of the inferior frontal areas and has a distinct hemodynamic character. Experiment 3 explored regions of the brain involved in the resolution of the main verb/reduced relative (MV/RR) ambiguity. Activation was seen in portions of the angular gyrus and the middle temporal gyrus for a contrast in subject noun plausibility, but not structure ambiguity, indicating that the MV interpretation was still considered even in unambiguously relative clause sentence structures. The unexpected results could imply that syntax is not the only factor that determines [theta]-role assignment and ultimately provide evidence about the brain regions involved in / (cont.) the process of plausibility information resolution in sentence interpretation. / by Evan Chen. / Ph.D.

Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 152-168). / Alzheimer's disease is a neurodegenerative disorder affecting over 5.1 million individuals in the United States today. The dementia exhibited with the disease is currently thought to be primarily due to amyloid plaques and neurofibrillary tangles. However, several other changes occur, including severe white matter damage that is yet to be fully understood. Such white matter damage includes white matter lesions (WML), which are more common in individuals with Alzheimer's disease than in non-demented individuals. WML are of presumed vascular origin because they show features of small-vessel disease and are more prevalent in individuals with vascular risk. It is currently unclear whether WML are linked to the neurodegenerative pathologies of Alzheimer's disease or are an independent factor that influences clinical course. In this work, we used sensitive diffusion MRI measures to determine that the tissue properties of WML slightly differed microstructurally between individuals with Alzheimer's disease and non-demented controls, and were strongly related to ventricular enlargement. In order to further understand the role of WML, we factored the volume of WML with four other neuroimaging markers affected in Alzheimer's disease and discovered two statistically distinct factors presumed to be due to differing underlying disease processes. One process strongly related to volume and tissue properties of WML, ventricular enlargement, age and cerebral perfusion, while the other process related to imaging markers associated with neurodegeneration. A decrease over time in the first process, interpreted as the age- and vascular-related factor, led to similar cognitive decline as the neurodegenerative factor independently, demonstrating the potential added therapeutic benefit of targeting this disease process that is distinct from the classical neurodegenerative component of the disease. / by Jean-Philippe Coutu. / Ph. D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 87). / Medicare coverage policies of medical procedures can be promulgated at a national level by the Centers of Medicare and Medicaid Services (CMS) as National Coverage Determinations (NCDs) or at a local level by Medicare contractors as Local Coverage Determinations (LCDs). Although LCDs shouldn't contradict NCDs, they can differ. In the present study, I analyze some factors that could partially account for the differences between NCDs and LCDs. Using the Medicare Coverage Database from CMS, I searched for differences between NCDs and LCDs in five benefit categories: inpatient hospital services, durable medical devices, diagnostic laboratory tests, physician's services and other diagnostic tests. There is a reasonable degree of homogeneity in coverage policies for procedures for which an NCD has been issued: 82% are exactly the same. Most of the differences took the form of exclusions from LCDs, but not from NCDs. For each state, I computed the number of times that LCDs were issued and the number of times that LCDs differed from NCDs and searched for possible linear or exponential correlation models. The following factors were initially hypothesized to account for these differences: number of Schools of Medicine, number of physicians, GDP per capita by state, state ranking according to number of Level 1 and Level 2 Trauma Centers and the profile of MEDCAC members. At a national level, I found no correlation between the number of LCDs issued or the number of differences between LCDs and NCDs and any of these variables. However, on a sub-analysis at a local level, in some regions I found a positive correlation (r2 >.94) between the following three variables: 1) number of Schools of Medicine, 2) number of physicians, and 3) state ranking according to the number of Level 1 and Level 2 Trauma Centers and the following two parameters: 1) the level of LCD issuing activity, and 2) the number of times that LCDs differ from NCDs. The correlations shown by the performed sub-analysis within regions may imply that more LCDs are issued to restrict coverage when there is a local need to control the excessive demand partially driven by the higher number of hospitals and physicians that are active in pursuing their interests. The fact that these correlations were shown only at a regional level may indicate that when local factors are disregarded, the original hypothesized factors do influence LCD activity, however, at a national level, other hypothetical local factors may have a greater influence on LCD activity and policy discrepancies. In order to have a better understanding of my results and the factors that could account for the differences between NCDs and LCDs, I interviewed four Contractor Medical Directors (CMDs). These interviews indicated that other factors could account for these differences, including the following: a history of abuse and fraud, contractor's budgets, the CMD's special interests and experience, data analysis capabilities, the number of claims and the novelty of the procedure. The impact of these variables on the differences between national and local coverage policies can be an interesting topic for future research on the subject. / by Rafael Díaz Treviño. / S.M.

Thesis (Ph. D. in Electrical and Medical Engineering)--Harvard-MIT Program in Health Sciences and Technology, 2013.. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 64-72). / Mucus is a biological hydrogel which lines the wet (non-keratinized) epithelia of the body. Mucus provides a gateway between the cells of the epithelium and the outside world, and is postulated to provide a selective filtering function which is critical to physiological functioning and has been implicated in diseases. Currently, much of the mechanisms and criteria of this selective filtering function is not well understood. In this thesis, we contribute novel microfluidic devices to characterize the selective permeability properties of the mucus barrier. Microfluidics provides the engineering ability to create channels with precise geometries, fluid flow capability, and allow chemical concentration gradients. Our devices mimic the physiological environment of the mucosa and enable improved measurements of the mucus layer selective permeability. The first microfluidic device mimics the acid barrier function of the stomach mucus layer. This device reproduces on-chip the secretion of mucus by the gastric mucosa into an acidic stomach lumen. We use this device to demonstrate that the secretion of mucins, the glycoprotein structural component of mucus, contributes significantly to the acid barrier function by continuously binding H'. The second microfluidic device probes the permeability of the mucus barrier to nanoscale peptides, as a model for drug molecules and in vivo signaling molecules. The device enabled the creation of a mucus layer next to a flowing aqueous layer, mimicking the in vivo mucus layer and lumen of the gastrointestinal, respiratory, and female reproductive tracts. Peptides added to the aqueous flow diffused across the mucus barrier interface into the mucus layer. This device demonstrated that the mucus barrier provides selective permeability to nanoscale peptides based on electrostatic interactions, and suggest novel surface functionalization strategies for drug carriers to improve mucosal drug delivery. Taken together, this thesis provides new microfluidic tools to probe the selective permeability function of the mucus barrier. Using the microfluidic tools, we show new mechanistic understanding of this barrier. / by Leon Daliang Li. / Ph.D.in Electrical and Medical Engineering

Thesis (Ph.D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2002. / Vita. Page 202 blank. / Includes bibliographical references (p. 197-201). / In the clinical management of voice patients, quantifying vocal function is becoming increasingly important both for corroborating clinicians' subjective impressions during a voice evaluation and for assessing the effectiveness of surgery or voice therapy. Current devices for quantifying vocal function measure acoustic, aerodynamic or electric signals (i.e., sound pressure, airflow, or electroglottography) during short tasks such as reading. One technique that has shown potential for measuring vocal function but has been mostly used to quantify speech-related behaviors besides phonation is measuring the acceleration of the skin near the larynx. The acceleration of the skin on the neck between the cricoid cartilage and the sternal notch arises from the airflow pulses that result from vocal-fold vibration. At least two sets of structures play a role in transforming these airflow pulses into the measured acceleration: the subglottal system, and the tissues between the subglottal airspace and the accelerometer (e.g., tracheal cartilage, skin, etc.). Advantages of measuring acceleration over current techniques include 1) the structures that filter the glottal pulses vary less over time than the vocal tract and thus they may be adequately modeled as time-invariant, making signal processing potentially easier; 2) environmental acoustic noise has a minimal influence on the measured acceleration; and 3) the accelerometer's size and placement make it more comfortable and unobtrusive for extended recordings than current techniques. This thesis work investigated the potential of using the measured acceleration for quantifying vocal function. / by Harold Arthur Cheyne, II. / Ph.D.

Thesis (Ph. D. in Biomedical Engineering)--Harvard-MIT Program in Health Sciences and Technology, 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 92-101). / Cancer is responsible for over 7.6 million deaths worldwide; the majority of patients fail to respond to drugs or become resistant over time. In order to gain a better understanding of drug efficacy in patients, we developed three diagnostic technologies to address limitations in sample acquisition and improve the scale and sensitivity of current cancer diagnostic tools. In the first section, we describe a hybrid magnetic and size sorting microfluidic device that isolates rare circulating tumor cells from peripheral blood. The self-assembled magnetic sorter creates strong magnetic fields and effectively removes leukocytes tagged with magnetic nanoparticles. The size sorting region retains the remaining cells in single cell capture sites, while allowing small red blood cells to pass through 5pm gaps. The device achieves over 103 enrichment, up to 96% recovery of cancer cells and allows for on-chip molecular profiling. In the second section we use a magnetic nanoparticle decorated with small molecule drugs to assay target expression and drug binding in mock clinical samples of cancer cells spiked into whole blood. Specifically, we modify a PARP inhibitor (Olabarib) and conjugate it to a dextran coated iron oxide nanoparticle. We measure the presence of the drug nanosensor based on the change in T2 relaxation time using a miniaturized, handheld NMR sensor for point-of-care diagnosis. In the final section, we detail a photocleavable DNA barcoding method for understanding treatment response via multiplexed profiling of cancer cells. We validate our method with a 94 marker panel on different cell lines with varying treatments, showing high correlations to gold standard methods such as immunofluorescence and flow cytometry. Furthermore, we demonstrate single cell sensitivity, and identify a number of expected biomarkers in response to cell treatments. Finally, we demonstrate the potential of our method to help in clinical monitoring of patients by examining intra- and inter-patient heterogeneity, and by correlating pre and post-treatment tumor profiles to patient response. Together, we show how these technologies can help overcome clinical limitations and expedite advancements in cancer treatment. / by Adeeti Ullal / Ph.D.in Biomedical Engineering

Thesis: Ph. D. in Medical Engineering, Harvard-MIT Program in Health Sciences and Technology, 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 108-122). / Angiogenesis- the growth of new capillaries from existing vessels- is required for tumor growth; however, tumor vessels exhibit abnormal structure and function, which impairs the targeted delivery of anti-cancer agents. While directional migration of capillary endothelial cells is critical for normal angiogenesis, the mechanism by which oriented capillary cell migration is controlled or how it is deregulated during tumorigenesis is unknown. Recently our lab reported that the focal adhesion protein, paxillin, is required for directional migration of fibroblasts. Endothelial cells also express paxillin and localize it in their focal adhesions. Thus, I set out to analyze whether paxillin influences directional migration of endothelial cells. When the expression of paxillin is knocked down in endothelial cells, this enhances their migration but decreases their directional persistence in vitro and in vivo in migration, angiogenesis and developmental assays. Having confirmed that paxillin plays a central role in controlling oriented capillary cell migration, I then studied the mechanism by which it contributes to normal microvessel network formation and tumor angiogenesis. I found that paxillin knockdown increases microvessel density but causes loss of sprout orientation. These characteristics resemble those of tumor vasculature, and, in fact, studies revealed that tumors inhibit paxillin expression in endothelial cells in vitro and in vivo by secreting soluble factors, such as the potent angiogenic factor VEGF. Mechanistically, paxillin knockdown decreases expression of the VEGF receptor neuropilin 2 (NRP2) but not VEGF receptor 2, and this is mediated by the transcription factor GATA2. Direct knockdown of NRP2 also increases endothelial cell migration and vessel density in vitro and in vivo and these effects are rescued by over expressing paxillin. In summary, these studies have led to the discovery of a new mechanism for control of directional endothelial cell migration during angiogenesis that is mediated by paxillin-NRP2 signaling. Importantly, this previously unknown mechanism is deregulated in tumor angiogenesis, which may contribute to the enhanced, disorganized microvasculature that is hallmark of cancer. These findings also revealed a new function for the focal adhesion protein, paxillin, as a mediator of tumor angiogenesis, and elucidated a novel mechanism for control of the expression of NRP2. / by Alexandra Elisa German. / Ph. D. in Medical Engineering

Thesis (Ph. D. in Biomedical Engineering and Computational Biology)--Harvard-MIT Program in Health Sciences and Technology, February 2013. / "September 2012." Cataloged from PDF version of thesis. / Includes bibliographical references (p. 147-160). / The adaptive immune system is one of the primary mediators in almost every major human disease, including infections, cancer, autoimmunity, and inflammation-based disorders. It fundamentally functions as a molecular classifier, and stores a memory of its previous exposures. However, until recently, methods to unlock this information or to exploit its power in the form of new therapeutic antibodies or affinity reagents have been limited by the use of traditional, low-throughput technologies. In this thesis, we leverage recent advances in high-throughput DNA sequencing technology to develop new methods to characterize and probe the immune repertoire in unprecedented detail. We use this technology to 1) characterize the rapid dynamics of the immune repertoire in response to influenza vaccination, 2) characterize elite neutralizing antibodies to HIV, to better understand the constraints for designing an HIV vaccine, and 3) develop new methodologies for discovering auto-antigens, and assaying large libraries of protein antigens in general. We hope that these projects will serve as stepping-stones towards filling the gap left by low-throughput methods in the development of antibody technologies. / by Uri Laserson. / Ph.D.in Biomedical Engineering and Computational Biology