Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2005. / Includes bibliographical references (leaves 34-36). / Objectives: There are several ongoing efforts aimed at developing formal models of medical knowledge and reasoning to design decision-support systems. Until now, these efforts have focused primarily on representing content of clinical guidelines and their logical structure. The present study aims to develop a computable representation of health-care providers' intentions to be used as part of a framework for implementing clinical decision-support systems. Our goal is to create an ontology that supports retrieval of plans based on the intentions or goals of the clinician. Methods: We developed an ontological representation of medical goals, plans, clinical scenarios and other relevant entities in medical decision-making. We used the resulting ontology along with an external ontology inference engine to simulate selection of clinical recommendations based on goals. The ontology instances used in the simulation were modeled from two clinical guidelines. Testing the design: Thirty-two clinical recommendations were encoded in the experimental model. Nine test cases were created to verify the ability of the model to retrieve the plans. For all nine cases, plans were successfully retrieved. Conclusion: The ontological design we developed supported effective reasoning over a medical knowledge base. / (cont.) The immediate extension of this approach to be fully developed in medical applications may be partially limited by the lack of available editing tools. Many efforts in this area are currently aiming to the development of needed technologies. / by Davide Zacacagnini [i.e. Zaccagnini]. / S.M.

Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2014. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references (pages 123-142). / Studies of human brain function require technologies to non-invasively image neuronal dynamics with high spatiotemporal resolution. The electroencephalogram (EEG) and magnetoencephalogram (MEG) measure neuronal activity with high temporal resolution, and provide clinically accessible signatures of brain states. However, they have limited spatial resolution for regional dynamics. Combinations of M/EEG with functional and anatomical magnetic resonance imaging (MRI) can enable jointly high temporal and spatial resolution. In this thesis, we address two critical challenges limiting multimodal imaging studies of spatiotemporal brain dynamics. First, simultaneous EEG-fMRI offers a promising means to relate rapidly evolving EEG signatures with slower regional dynamics measured on fMRI. However, the potential of this technique is undermined by MRI-related ballistocardiogram artifacts that corrupt the EEG. We identify a harmonic basis for these artifacts, develop a local likelihood estimation algorithm to remove them, and demonstrate enhanced recovery of oscillatory and evoked EEG dynamics in the MRI scanner. Second, M/EEG source imaging offers a means to characterize rapidly evolving regional dynamics within an estimation framework informed by anatomical MRI. However, existing approaches are limited to cortical structures. Crucial dynamics in subcortical structures, which generate weaker M/EEG signals, are largely unexplored. We identify robust distinctions in M/EEG field patterns arising from subcortical and cortical structures, and develop a hierarchical subspace pursuit algorithm to estimate neural currents in subcortical structures. We validate efficacy for recovering thalamic and brainstem contributions in simulated and experimental studies. These results establish the feasibility of using non-invasive M/EEG measurements to estimate millisecond-scale dynamics involving subcortical structures. Finally, we illustrate the potential of these techniques for novel studies in cognitive and clinical neuroscience. Within an EEG-fMRI study of auditory stimulus processing under propofol anesthesia, we observed EEG signatures accompanying distinct changes in thalamocortical dynamics at loss of consciousness and subsequently, at deeper levels of anesthesia. These results suggest neurophysiologic correlates to better interpret clinical EEG signatures demarcating brain dynamics under anesthesia. Overall, the algorithms developed in this thesis provide novel opportunities to non-invasively relate fast timescale measures of neuronal activity with their underlying regional brain dynamics, thus paving a way for enhanced spatiotemporal imaging of human brain function. / by Pavitra Krishnaswamy. / Ph. D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / Includes bibliographical references (leaves 36-39). / The goal of this study is to explore the economic conditions that favor the joint development of therapeutics and companion diagnostics. I hypothesize that predictive biomarkers can generate economic value in drug development by increasing success rates. I construct an economic model of the development of a hypothetical new therapy, and devote particular attention to parameters regarding safety, efficacy, cost, and market size, within a decision-theoretic framework. The results include a characterization of the dynamic net present value trade-offs between stratum size and biomarker success, as well as the identification of two complementary concepts of stratified medicine, namely, disease reclassification and value-based reimbursement. I also identify a strong potential incentive mechanism in the hands of public policy makers that could facilitate a resolution of the tension between patient interests and the interests of pharmaceutical sponsors. The conclusion is that a biomarker can compensate for smaller stratum by increasing success probabilities. However, the effects of longer development time due to biomarker inclusion counter the effects of improved success probabilities. Longer exclusivity periods for stratified medicine may be required in order to resolve the tension between patient interests and the interests of pharmaceutical sponsors. / by Amir Goren. / S.M.

Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 86-97). / Human pluripotent stem (hPS) cells have the ability to reproduce indefinitely and differentiate into any cell type of the body, making them a potential source of cells for medical therapy and an ideal system to study fate decisions in early development. However, hPS cells exhibit a high degree of heterogeneity, which may be an obstacle to their clinical translation. Heterogeneity is at least partially induced as an artifact of removing the cells from the embryo and culturing them on a plastic dish. hPS cells grow in spatially patterned colony structures, which necessitates in situ quantitative single-cell image analysis. This dissertation offers a tool for analyzing the spatial population context of hPS cells that integrates automated fluorescent microscopy with an analysis pipeline. It enables high-throughput detection of colonies at low resolution, with single-cellular and sub-cellular analysis at high resolutions, generating seamless in situ maps of single-cellular data organized by colony. We demonstrate the tool's utility by analyzing inter- and intra-colony heterogeneity of hPS cell cycle regulation and pluripotency marker expression. We measured the heterogeneity within individual colonies by analyzing cell cycle as a function of distance. Cells loosely associated with the outside of the colony are more likely to be in G1, reflecting a less pluripotent state, while cells within the first pluripotent layer are more likely to be in G2, possibly reflecting a G2/M block. Our analysis tool can group colony regions into density classes, and cells belonging to those classes have distinct distributions of pluripotency markers and respond differently to DNA damage induction. Our platform also enabled noninvasive texture analysis of live hPS colonies, which was applied to monitoring subtle changes in differentiation state. Lastly, we demonstrate that our pipeline can robustly handle high-content, high-resolution single molecular mRNA FISH data by using novel image processing techniques. Overall, the imaging informatics pipeline presented offers a novel approach to the analysis of hPS cells, which includes not only single cell features but also spatial configuration across multiple length scales. / by Bryan Robert Gorman. / Ph. D.

Thesis: Ph. D. in Medical Engineering and Medical Physics, Harvard-MIT Program in Health Sciences and Technology, 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 163-173). / The objective of this work was to translate the diagnostic capabilities of magnetic resonance imaging (MRI) to the patient bedside, specifically for the purpose of quantifying fluid overload. MRI is used extensively in clinical medicine, but it is still not used for routine diagnostics due to high cost, limited availability, and long scan times. Many of these impracticalities come from the hardware requirements associated with generating images. Images, however, are not necessary to harness some of magnetic resonance's (MR's) diagnostic potential. This thesis demonstrates that that a single-voxel MR sensor can obtain the same results as a traditional MRI in both phantoms and humans. A clinical study with hemodialysis patients and age-matched healthy controls was performed at MGH. The T2 relaxation times of study participants' legs were quantified at multiple time points with both a 1.5T clinical MRI scanner and a custom 0.27T single-voxel MR sensor. The results showed that the first sign of fluid overload is an increase in the relative fraction of extracellular fluid in the muscle. The relaxation time of the extracellular fluid in the muscle eventually increases after more fluid accumulates. Importantly, these MR findings occur before signs of lower-extremity edema are detectable on physical exam. Two healthy control subjects became dehydrated over the course of the study and the relative fraction of their extracellular fluid decreased. This incidental finding suggests MR can measure the full spectrum of hydration states. Furthermore, a single MRI measurement at a single time point can distinguish fluid overloaded patients from healthy controls. The amplitude associated with extracellular fluid most closely correlates to fluid loss, and these amplitude decreases are detectable with both the MRI and MR sensor. The results of this work point towards a promising future of using cheaper, faster MR sensors for bedside diagnostics. / by Lina Avancini Colucci. / Ph. D. in Medical Engineering and Medical Physics

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references. / There is a constant demand for enormous numbers of high quality hepatocytes in the fields of cell transplantation, pharmacotoxicology, tissue engineering, and bioartificial assist devices. The scarcity of viable hepatocytes necessitates the use of suboptimal sources including damaged donor organs that are not transplantable. Many of these organs have potentially reversible pathologies however, that could be treated via ex vivo perfusion thereby increasing their cell yield. With the intent to translate organ recovery by perfusion into the clinic, we engineered a very simple room temperature-operated ex vivo organ perfusion system to test a rat liver model of uncontrolled non-heart beating donors. Seventeen times as many hepatocytes were recovered from livers exposed to an hour of warm ischemia (WI, 34*C) compared to untreated WI livers in only 3 hours of perfusion. Further, fresh liver hepatocyte yields were also increased by 32% postperfusion, demonstrating that both damaged and healthy donor livers could benefit from this methodology. A linear correlation between cell yield and tissue ATP content was established. This enables an accurate prediction of cell recovery during preservation and can be used as a direct measure of organ viability and the trajectory of organ recovery during perfusion resuscitation. Further, a strong correlation between perfusion flow rate and cell yield was also established supporting the use of flow rates as low as possible without causing hypoperfusion or oxygen deprivation. Morphologically and functionally, perfusion-isolated hepatocytes generally performed comparably or better than fresh hepatocytes in cell suspension and plate culture. Cumulatively, these findings strongly support the ubiquitous use of organ perfusion systems in the clinic for optimal enhancement of donor grafts. / by Maria-Louisa Izamis. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 56-58). / In this thesis I have developed a map of Healthcare Information Technology applications used in the United States for care delivery, healthcare enterprise management, clinical support, research and patient engagement. No attempt has previously been made to develop such a taxonomy for use by healthcare policy makers and on-the-spot decision makers. Using my own fifteen years of experience in HIT, along with an extensive set of literature reviews, interviews and on-site research I assembled lists of applications and organized them into categories based on primary workflows. Seven categories of HIT systems emerged, which are Practice Tools, Advisory Tools, Financial Tools, Remote Healthcare Tools, Clinical Research Tools, Health 2.0 Tools and Enterprise Clinical Analytics, each of which have different operational characteristics and user communities. The results of this pilot study demonstrate that a map is possible. The draft map presented here will allow researchers and investors to focus on developing the next generation of HIT tools, including software platforms that orchestrate a variety of healthcare transactions, and will support policy makers as they consider the impact of Federal funding for HIT deployment and adoption. Further studies will refine the map, adding an additional level of detail below the seven categories established here, thus supporting tactical decision making at the hospital and medical practice level. / by William Charles Richards Crawford. / S.M.

Thesis (Ph. D. in Medical Engineering and Medical Physics)--Harvard-MIT Program in Health Sciences and Technology, 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 93-96). / Vaccines have revolutionized medicine by increasing the life expectancy of children and substantially decreasing the morbidity of multiple infectious diseases worldwide. Over several decades, we have acquired significant gains in the understanding of the underlying mechanisms involved in developing protective immunity, yet vaccine development has progressed comparatively slowly. This thesis serves to explore two polymeric nanoparticle platforms to demonstrate the therapeutic potential of synthetic nanocarriers as vaccines with the aim of 1) providing greater spatiotemporal release of small molecule adjuvant to secondary lymphoid sites and 2) providing a tunable surface for loading B cell antigen epitopes in a specific conformation to drive epitope-specific antibody response. In recent decades, TLR mechanisms have been elucidated and novel agonists have been developed, yet our generation still has not seen paramount progress in the clinical translation of these agonists due to risks of systemic toxicity and off target effects. In the first section, we synthesized 223±18 nm poly(lactic-co-glycolic acid)- poly(ethylene glycol)/ poly(lactic acid)-R848 (PLGA-PEG/PLA-R848) nanoparticle vaccine that is designed to deliver a combination of antigen and control release of a small molecule adjuvant R848 (tl/2= 42 hours) to drive a potent antigen-specific immune response. Using ovalbumin as a model protein, this vaccine is able to enhance antigen presentation and co-stimulatory molecules on dendritic cells and subsequently enhanced proliferation of antigen-specific naive CD8+ cells in vitro. Upon vaccination, our delivery system is able to increase cell-mediated and humoral response in comparison to its soluble form, thereby illustrating the potential to bring novel small molecule adjuvants to the clinics. In the second section, we developed a nanoparticle vaccine platform that allows selective orientation of peptide epitopes to enhance B cell response in an application that has therapeutic potential for treatment for cardiovascular disease (CVD). Utilizing epitopes discovered through in silico modeling for human PCSK9, a plasma protein that plays an important role in LDL cholesterol (LDL-c) levels in the blood, our nanoparticle allows selective orientation through biotin-streptavidin conjugation. Upon vaccination with CPG, selected synthetic epitopes conjugated to polymeric nanoparticles trended to reduce serum LDL-c and serum PCSK9 in murine models. Additionally, antibodies in the serum showed promise to increase LDL-receptor levels in HepG2 cells transfected in with WT-hPCSK9 and GOF-hPCSK9 separately suggesting that this vaccine has the potential to reduce risks of CVD. These studies demonstrate that designing polymeric nanoparticles for applications to stimulate the immune system can help define new, cost-effective treatment options in applications for prophylaxis against infectious diseases that are unresponsive to traditional routes of vaccination or for immunotherapy against cardiovascular disease and cancer. / by Pamela A. Basto. / Ph.D.in Medical Engineering and Medical Physics

Thesis: Ph. D. in Biomedical Engineering, Harvard-MIT Program in Health Sciences and Technology, 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 149-166). / Accurate, timely, and effective diagnosis is the first step in appropriately treating disease. Many diseases have confusing symptoms, nonspecific biomarkers, or require invasive biopsy; these factors and others contribute to the low rates of early diagnosis for noncommunicable diseases like cancer, clotting disorders, or fibrotic diseases. A promising approach is the introduction of pro-diagnostic agents that interact with pathologic processes to produce a readout. In this vein, our group has developed responsive nanomaterials that, upon cleavage by disease-associated proteases, release reporters into the urine. This thesis sought to improve these tools by enabling the noninvasive quantification of disease-associated protease activity, deskilling complex diagnostic procedures, and developing a pipeline for extending these tools to additional diseases. Drawing inspiration from existing diagnostics, we modified our protease nanosensors to release ligand-encoded reporters compatible with clinical ELISA and paper-based lateral flow assays. These detection techniques enable simple and inexpensive quantification of our synthetic disease reporters by ensuring compatibility with existing diagnostic resources and infrastructure. To demonstrate our platform's versatility, we adapted it to a highly sensitive single molecule array (SiMoA) assay and validated disease detection in mice using 1000-fold lower doses of nanosensors. We next used disease-specific protease expression data to develop an inhalable formulation of our protease nanosensors and investigated direct tissue delivery. Finally, we built a pipeline to improve protease substrate sensitivity and specificity. Using liver fibrosis as a model, we identified target proteases, designed a peptide-screening assay, and nominated peptide candidates that efficiently classify diseased tissue. The protease nanosensors developed here provide a noninvasive, quantitative, and otherwise unavailable glimpse of the complex proteolytic milieu of disease and health. These tools form a framework for developing new diagnostics that simply, rapidly, and inexpensively identify protease-driven diseases without complex equipment or specialized personnel. / by Andrew David Warren. / Ph. D. in Biomedical Engineering

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references (p. 183-198). / In this thesis we address the whole-brain tractography segmentation problem. Diffusion magnetic resonance imaging can be used to create a representation of white matter tracts in the brain via a process called tractography. Whole brain tractography outputs thousands of trajectories that each approximate a white matter fiber pathway. Our method performs automatic organization, or segmention, of these trajectories into anatomical regions and gives automatic region correspondence across subjects. Our method enables both the automatic group comparison of white matter anatomy and of its regional diffusion properties, and the creation of consistent white matter visualizations across subjects. We learn a model of common white matter structures by analyzing many registered tractography datasets simultaneously. Each trajectory is represented as a point in a high-dimensional spectral embedding space, and common structures are found by clustering in this space. By annotating the clusters with anatomical labels, we create a model that we call a high-dimensional white matter atlas. / (cont.) Our atlas creation method discovers structures corresponding to expected white matter anatomy, such as the corpus callosum, uncinate fasciculus, cingulum bundles, arcuate fasciculus, etc. We show how to extend the spectral clustering solution, stored in the atlas, using the Nystrom method to perform automatic segmentation of tractography from novel subjects. This automatic tractography segmentation gives an automatic region correspondence across subjects when all subjects are labeled using the atlas. We show the resulting automatic region correspondences, demonstrate that our clustering method is reproducible, and show that the automatically segmented regions can be used for robust measurement of fractional anisotropy. / by Lauren Jean O'Donnell. / Ph.D.