Thesis (Ph. D.)--Harvard-MIT Program in Health Sciences and Technology, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The delivery of nucleic acids has the potential to revolutionize medicine by allowing previously untreatable diseases to be clinically addressed. Viral delivery systems have been held back by immunogenicity and toxicity concerns, but synthetic vectors have lagged in transfection efficiency. This thesis describes the rational design and systematic study of three classes of bioresponsive polymers for nucleic acid delivery. A central theme of the study was understanding how the structure of the polymers impacted each of the intracellular steps of delivery, rather than solely the end result. A powerful tool for efficiently quantifying endosomal escape was developed and applied to each of the material systems described. First, a linear-dendritic poly(amido amine) -poly(ethylene glycol) (PAMAM-PEG) block copolymer system previously developed in our lab was evaluated and its ability to overcome the sequential barriers of uptake, endosomal escape, and nuclear import were characterized. Next, a class of crosslinked linear polyethyleimine (xLPEI) hyperbranched polymers, which can contain disulfideresponsive linkages, were synthesized and investigated. It was demonstrated that free polymer in solution, not the presence of a functional bioresponsive domain, was responsible for the highly efficient and relatively nontoxic DNA delivery of this promising class of crosslinked polyamines. Finally, this analysis was applied to siRNA delivery by a library of amine-functionalized synthetic polypeptides. The pH-responsive secondary structure, micelle formation, and ester hydrolysis were studied prior to the discrete barrier-oriented analysis of the siRNA delivery potential of this library. It is hoped that the tools, materials, and systemic analysis of structure-function relationships in this thesis will enhance the process of discovery and development of clinically relevant gene carriers. / by Daniel Kenneth Bonner. / Ph.D.

Thesis (M. Eng.)--Harvard-MIT Division of Health Sciences and Technology, 2004. / Includes bibliographical references (p. 54-55). / (cont.) nucleus and at the nuclear surface. / Mutations in the lamin A/C gene (Lmna) and the lamin-associated protein emerin gene (EM) cause a variety of human diseases including Emery-Dreifuss muscular dystrophy, dilated cardiomyopathy, familial partial lipodystrophy, Charcot-Marie-Tooth Neuropathy and Hutchinson-Gilford progeria syndrome. The molecular mechanisms underlying the varied phenotypes are unknown, and both a mechanical stress hypothesis and an altered gene expression hypothesis have been proposed to explain the tissue specific effects observed in laminopathies. To investigate the role of emerin in mechanotransduction, lamin A/C deficient (Lmna⁻/⁻) fibroblasts, and emerin deficient (EM⁻/y) fibroblasts were studied for nuclear mechanical properties, cytoskeletal stiffness, and mechanical strain-induced signaling. EM⁻/y fibroblasts exhibited similar cell sensitivity, nuclear and cytoskeletal properties compared to wild type cells under stress and strain. Interestingly, both Lmna⁻/⁻ and EM⁻/y fibroblasts had impaired mechanotransduction, characterized by attenuated expression of the mechanosensitive genes egr-1, iex-1, and txnip in response to mechanical stimulation. In addition, NF-rB signaling appeared disturbed in Lmna⁻/⁻ cells, but normal in EM⁻/y fibroblasts. The relationship between changes in cytoskeletal stiffness recently discovered in Lmna⁻/⁻ cells and nuclear mechanics under strain was explored using a computational finite elemental model. Analysis of the several models using variations in material properties and cell geometry revealed that nuclear shape, material properties of the cytoskeleton and nucleus, as well as the size and location of strain application on the cell are important parameters in determining the magnitude of stress and strain within the / by Janet Hsiao. / M.Eng.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 123-133). / Amyloids and prion proteins are clinically and biologically important beta-structures, whose supersecondary structures are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Recent work has indicated the utility of templates and pairwise probabilistic statistics in betastructure prediction. A new suite of programs, BETASCAN, STITCHER, and HELIXCAP, are presented to address the problem of amyloid structure prediction. BETASCAN calculates likelihood scores for potential beta-strands and strand-pairs based on correlations observed in parallel beta-sheets. The program then determines the strands and pairs with the greatest local likelihood for all of the sequence's potential beta-structures. BETASCAN suggests multiple alternate folding patterns and assigns relative ab initio probabilities based solely on amino acid sequence, probability tables, and pre-chosen parameters. STITCHER processes the output of BETASCAN and uses dynamic programming to 'stitch' structures from flexible abstract templates defined by constraints for amyloid-like all-beta structures. The 'stitched' structures are evaluated by a free-energy-based scoring algorithm incorporating BETASCAN scores, bonuses for favorable side-chain stacking, and penalties for linker entropy. The analyses of STITCHER structures emphasize the importance of side-chain stacking ladders in amyloid formation. HELIXCAP detects a class of end-caps, called beta-helix caps, which stabilize known beta-helix structures. These structures are known to stabilize globular beta-helix proteins and prevent their amyloidogenesis; their presence in a sequence is a powerful negative predictor of amyloid potential. Together, these algorithms permit detection and structural analysis of protein amyloidogenicity from sequence data, enhancing the experimental investigation of amyloids and prion proteins. / by Allen Wayne Bryan, Jr. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Layer-by-layer assembly has become a quintessential tool for the creation of versatile, dynamic nanostructured materials able to dictate cellular behavior through exquisite surface functionality and delivery of bioactive agents. The primary aim of this work was to use layer-by-layer assembly to advance ophthalmic drug delivery modalities post cataract surgery to overcome the challenges of traditional postoperative therapy. Hydrolytically degradable multilayer films were used to create a multi-drug delivery coating for intraocular lenses (IOL). The establishment of a drug delivery coating for intraocular lenses required key advances in ultrathin film technology. This thesis focused on rational polymer design for tailored release, incorporation of hydrophobic small molecule therapeutics, and controlled multi-agent release. Fabrication rules and design tools necessary to create hydrolytically degradable polyelectrolyte multilayer films with preprogrammed advanced engineered release kinetics were investigated. A correlation between polycation hydrophobicity, as determined using octanol:water coefficients, allowed for the reliable prediction of release dynamics. A novel ultrathin system able to produce programmable zero order release kinetics of uncharged or hydrophobic small molecule therapeutics was developed. Charged cyclodextrin polymers were essential for the trapping of cyclodextrin-drug complexes in stable, surface eroding films capable of sustained drug release without altering therapeutic activity. In vitro investigation of cellular interactions with hydrolytically degradable multilayer films containing anti-inflammatory agents was conducted. These anti-inflammatory films controlled inflammation over physiologically relevant timescales and maintained the transparency and optical clarity of the IOL. Lastly, the first multilayer thin film system able to address the demands of both infection and inflammation, using small molecule pharmaceutics is described. The power, versatility, and utility of this multi-functional system were highlighted by the creation of functional drug coatings on intraocular lenses, bandage, and sutures. These combination devices effectively prevented bacterial growth while suppressing the production of inflammatory cytokines. Combined, these efforts surmounted key challenges toward the development of intraocular lenses able to prevent complications of cataract surgery and enhanced the fundamental understanding of layer-by-layer systems. / by Renée Chivon Smith. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 85-87). / The aim of this thesis was to look at the impact of acquiring the CE marking approval on the outcome of early stage medical device companies, specifically its impact on strategic acquisition opportunities and on valuation. We gathered data on acquisitions of 237 companies over the past ten years, from April 01, 2002 to March 31, 2011. These data were gathered from various sources, and information on the date of acquisition, enterprise value, funds invested to date, date of incorporation, status and dates of CE and FDA approvals, patent status, type of regulatory clearances (PMA versus 510K), type of sales models (direct versus distributorship), capitalization status and last twelve month stock returns of the acquirer was acquired. These data were then analyzed using basic statistical methods and multivariate linear regression analyses to determine the significance of the CE marking on the outcomes of these companies. Our results support the claim that the CE mark does significantly improve outcomes for early stage medical device companies, in terms of time to strategic acquisition, which is by far the commonest exit route for these companies. On the other hand, we did not find any statistically significant impact of acquisition of the CE mark on the valuation or valuation multiples of these companies. These results have potential implications for management of these early stage medical device companies in making strategic decisions and for investors who are concerned about the exit opportunities and valuations, especially as it relates to funds invested. There could also be some policy implications in terms of the effort, duration and cost of getting a CE approval versus that of an FDA approval, which is especially important given the current growing concern about increasingly stringent regulation, rising costs and increasing delays in FDA approvals for medical devices. / by Ashish Kothari. / S.M.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2004. / Includes bibliographical references (leaves 46-51). / One important purpose for creating clinical practice guidelines is to improve quality of care by reducing variations in practice. In the current healthcare environment, guidelines are being advocated as a means to disseminate research findings, standardize care, improve quality of care, and increase the cost-effectiveness of health care services. Unfortunately, compliance with text-based clinical practice guidelines is unsatisfactory. On the other hand, adherence to guideline recommendations is increased when providers receive patient-specific recommendations during the patient-provider consultation. Guideline-based point of care decision support systems have been shown to increase provider consultation. Guideline-based point of care decision support systems have been shown to increase provider adherence to guideline recommendations. Computer-interpretable formats for clinical practice guidelines are a prerequisite for decision support systems. The development process of a text-based clinical practice guideline is long and arduous and in most cases this process is repeated when text-based guidelines are revised to include new medical knowledge. Clearly, once text-based guideline knowledge is translated into a computer-interpretable format, the computer-interpretable guideline would also require periodic revisions to maintain the integrity of its evidence-base. Therefore, representation formalisms for encoding guideline knowledge into computer-interpretable formats should enable easy revisions of the encoded guidelines. This thesis describes a study I conducted to demonstrate that modular knowledge representation of clinical practice guidelines facilitates easy guideline revisions. To test the hypothesis / (cont.) hypothesis, I used a methodology for modular representation of guidelines, HieroGLIF, developed by Decision Systems Group, Brigham and Women's Hospital, Boston Massachusetts. HieroGLIF uses Axiomatic Design theory to encode "guideline knowledge modules" into a hierarchical tree structure. Axiomatic Design theory was developed in the field of engineering as a principled approach to product design. I applied HieroGLIF to encode parts of three outdated guidelines. I revised these designs to model updated guideline releases. Quantitative metrics assessed the adequacy of the tool to encode generic setting-independent guidelines and to facilitate revisions in encoded guidelines without complete recoding of the model. This work explores the use of HieroGLIF and Axiomatic Design theory to facilitate revisions of computer-interpretable guidelines. / by Alicia Scott-Wright. / S.M.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2008. / Includes bibliographical references. / Evidence suggests that morphological changes of neuroanatomical structures may reflect abnormalities in neurodevelopment, or relate to a variety of disorders, such as schizophrenia and Alzheimer's disease (AD). Advances in high-resolution Magnetic Resonance Imaging (MRI) techniques allow us to study these alterations of brain structures in vivo. Previous work in studying the shape variations of brain structures has provided additional localized information compared with traditional volume-based study. However, challenges remain in finding an accurate shape presentation and conducting shape analysis with sound statistical principles. In this work, we develop methods for automatically extracting localized and multi-scale shape features and conducting statistical shape analysis of neuroanatomical structures obtained from MR images. We first develop a procedure to extract multi-scale shape features of brain structures using biorthogonal spherical wavelets. Using this wavelet-based shape representation, we build multi-scale shape models and study the localized cortical folding variations in a normal population using Principal Component Analysis (PCA). We then build a shape-based classification framework for detecting pathological changes of cortical surfaces using advanced classification methods, such as predictive Automatic Relevance Determination (pred-ARD), and demonstrate promising results in patient/control group comparison studies. Thirdly, we develop a nonlinear temporal model for studying the temporal order and regional difference of cortical folding development based on this shape representation. Furthermore, we develop a shape-guided segmentation method to improve the segmentation of sub-cortical structures, such as hippocampus, by using shape constraints obtained in the wavelet domain. / (cont.) Finally, we improve upon the proposed wavelet-based shape representation by adopting a newly developed over-complete spherical wavelet transformation and demonstrate its utility in improving the accuracy and stability of shape representations. By using these shape representations and statistical analysis methods, we have demonstrated promising results in localizing shape changes of neuroanatomical structures related to aging, neurological diseases, and neurodevelopment at multiple spatial scales. Identification of these shape changes could potentially lead to more accurate diagnoses and improved understanding of neurodevelopment and neurological diseases. / by Peng Yu. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2011. / Vita. Cataloged from PDF version of thesis. / Includes bibliographical references (p. 91-97). / This thesis investigates the commercial viability of developing and commercializing targeted oncology drugs directed at a specific tumor mutation instead of all forms and mutations of a single target. While oncologic drugs targeted to aberrant or overexpressed pro-proliferative proteins have revolutionized cancer treatment, tumors treated for long periods may mutate over time, gain resistance to these drugs and proliferate rapidly again. I hypothesize that drugs developed to inhibit specific resistant tumor genotypes can be commercially viable from a pharmaceutical manufacturer's perspective. To assess this hypothesis empirically, I construct a patient flow model in order to quantify the treatment of CML, a relatively rare and indolent hematological malignancy with extensive clinical data available and well-delineated disease phases and response criteria. To represent the rate of diagnosis, patients are "added" to the model every month, and thereafter there is a probability that a patient may either 1) become sufficiently intolerant to his drug in order to discontinue treatment, 2) fail to respond to treatment but remain in the same disease phase, 3) fail to respond to treatment and progress to the next phase of disease, or 4) adequately respond to treatment and stay on the same drug in the same phase. Patients that fail to respond (categories 2 and 3 above) have a chance of manifesting a resistance mutation that is adequately controlled by a hypothetical drug (in addition to their current treatment) but is otherwise untreatable. The aim of this analysis is to track the number of patients that accrue the chosen resistance mutation and thus would be good candidates to receive the hypothetical drug. Patient treatment rates are converted to sales figures, and are weighed against clinical development costs, timelines, and probabilities to determine the net present value (NPV) of a project to develop the hypothetical drug. In addition, parameters are varied in order to conduct a sensitivity analysis and determine the "boundary conditions" that make a drug profitable or unprofitable. To supplement the model results and confirm the model dynamics, I interviewed investment analysts, clinical oncology thoughtleaders, academic cancer researchers and clinical, commercial and regulatory personnel from drug manufacturers to gauge their opinions on the CML market and the hurdles particular to developing drugs aimed at resistant genotypes. The conclusion I reach from this analysis is that development of a specific mutation-directed therapy for resistant CML is unlikely to be profitable. Given the significantly smaller patient population, favorable conditions in pricing and clinical development would be required to make the hypothetical candidate even marginally profitable. / by Joseph P. Sterk. / S.M.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 150-159). / This thesis builds on previous efforts to develop tactile speech-reception aids for the hearing-impaired. Whereas conventional hearing aids mainly amplify acoustic signals, tactile speech aids convert acoustic information into a form perceptible via the sense of touch. By facilitating visual speechreading and providing sensory feedback for vocal control, tactile speech aids may substantially enhance speech communication abilities in the absence of useful hearing. Research for this thesis consisted of several lines of work. First, tactual detection and temporal order discrimination by congenitally deaf adults were examined, in order to assess the practicability of encoding acoustic speech information as temporal relationships among tactual stimuli. Temporal resolution among most congenitally deaf subjects was deemed adequate for reception of tactually-encoded speech cues. Tactual offset-order discrimination thresholds substantially exceeded those measured for onset-order, underscoring fundamental differences between stimulus masking dynamics in the somatosensory and auditory systems. Next, a tactual speech transduction scheme was designed with the aim of extending the amount of articulatory information conveyed by an earlier vocoder-type tactile speech display strategy. The novel transduction scheme derives relative amplitude cues from three frequency-filtered speech bands, preserving the cross-channel timing information required for consonant voicing discriminations, while retaining low-frequency modulations that distinguish voiced and aperiodic signal components. Additionally, a sensorimotor training approach ("directed babbling") was developed with the goal of facilitating tactile speech acquisition through frequent vocal imitation of visuo-tactile speech stimuli and attention to tactual feedback from one's own vocalizations. A final study evaluated the utility of the tactile speech display in resolving ambiguities among visually presented consonants, following either standard or enhanced sensorimotor training. Profoundly deaf and normal-hearing participants trained to exploit tactually-presented acoustic information in conjunction with visual speechreading to facilitate consonant identification in the absence of semantic context. Results indicate that the present transduction scheme can enhance reception of consonant manner and voicing information and facilitate identification of syllableinitial and syllable-final consonants. The sensorimotor training strategy proved selectively advantageous for subjects demonstrating more gradual tactual speech acquisition. Simple, low-cost tactile devices may prove suitable for widespread distribution in developing countries, where hearing aids and cochlear implants remain unaffordable for most severely and profoundly deaf individuals. They have the potential to enhance verbal communication with minimal need for clinical intervention. / by Theodore M. Moallem. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references. / Bilateral cochlear implantation is becoming more common as clinicians attempt to provide better sound-source localization and speech reception in noise for cochlear implant (CI) users. While some improvement over the abilities of monolateral implantees has been documented, bilateral performance for CI users is far from that achieved with normal hearing. Identifying factors that limit bilateral performance has been difficult because little is understood about CI listeners' localization abilities, their sensitivity to interaural cues, and the relationships between them. To better understand bilateral electric hearing, five bilateral CI users' abilities to locate sound sources and their sensitivities to interaural time difference (ITD) were studied in this thesis. Unlike past studies, monolateral and bilateral performance was recorded before and after exposure to daily, bilateral-CI listening using constant- and roving-level stimuli. For constant-level stimuli, increasing bilateral-listening experience improved all subjects' bilateral performance but degraded two subjects' monolateral performance. Using roving-level stimuli, increasing bilateral-listening experience also improved bilateral performance but did not alter monolateral performance. / (cont.) Our results show that depending on the method of evaluation, the benefit of bilateral CIs over monolateral CI could be overstated for some subjects. A simple decision model was used to predict subjects' localization performance based on their sensitivity to interaural time and level differences (TD and ILD) measured through their sound processors. The predicted performance indicated that the measured performance could be accounted for by subjects' ILD sensitivity but not by their ITD sensitivity alone. Poor ITD sensitivity may be one reason that bilateral CI users' localization performance is poor compared to that of normal-hearing (NH) listeners. To improve ITD sensitivity, a first step is to characterize ITD sensitivity on single, interaural electrode pairs because data in the literature is incomplete. In particular, the dependence of ITD sensitivity on the repetition rate and the number of pulses in the unmodulated pulse trains was studied. Just noticeable difference (JND) of ITD was measured with four subjects on their most ITD-sensitive, interaural electrode pair. At low rate (50 pps), ITD JND improved with increasing number of pulses, indicating integration of ongoing ITD cues. The best ITD JNDs were 85 - 354 pts. Using 800-pps trains, two subjects' ITD JND degraded with increasing number of pulses. / (cont.) Two subjects were insensitive to ITD up to 2 ms for 800-pps trains. To begin studying the impact of CI processing on ITD sensitivity, ITD JND was also measured using low-rate (50 pps) pulse trains delivered to the external input of the subjects' sound processors. ITD JND improved with increasing number of pulses. While subjects were insensitive to ongoing ITD in unmodulated, high-rate pulse trains delivered to single, interaural electrode pairs, they were sensitive to ongoing ITDs in the low-frequency modulator of high-rate pulse trains in the through-processor case. A next step toward greater understanding of bilateral electric hearing is to fully investigate the degree to which subjects are sensitive to ITD using modulated pulse trains. The results of this thesis show that there is significant localization benefit with bilateral CIs even though performance is not at the level of NL listeners. Further studies to improve ITD sensitivity may improve localization ability, which will further justify the risks and cost associated with bilateral implantation. / by Becky Bikkei Poon. / Ph.D.