Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, February 2006. / Includes bibliographical references (leaves 73-85). / Proteomics has been revolutionized in the last couple of years through integration of new mass spectrometry technologies such as -Enhanced Laser Desorption/Ionization (SELDI) mass spectrometry. As data is generated in an increasingly rapid and automated manner, novel and application-specific computational methods will be needed to deal with all of this information. This work seeks to develop a Bayesian framework in mass-based proteomics for protein identification. Using the Bayesian framework in a statistical signal processing manner, mass spectrometry data is filtered and analyzed in order to estimate protein identity. This is done by a multi-stage process which compares probabilistic networks generated from mass spectrometry-based data with a mass-based network of protein interactions. In addition, such models can provide insight on features of existing models by identifying relevant proteins. This work finds that the search space of potential proteins can be reduced such that simple antibody-based tests can be used to validate protein identity. This is done with real proteins as a proof of concept. Regarding protein interaction networks, the largest human protein interaction meta-database was created as part of this project, containing over 162,000 interactions. A further contribution is the implementation of the massome network database of mass-based interactions- which is used in the protein identification process. / (cont.) This network is explored in terms potential usefulness for protein identification. The framework provides an approach to a number of core issues in proteomics. Besides providing these tools, it yields a novel way to approach statistical signal processing problems in this domain in a way that can be adapted as proteomics-based technologies mature. / by Gil Alterovitz. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2005. / Includes bibliographical references (leaves 80-88). / Neutrophils traversing the pulmonary microcirculation are subjected to mechanical stimulation during their deformation into narrow capillaries. To better understand the time- dependant changes caused by this mechanical stimulus, in the first part of the thesis, neutrophils were caused to flow into a microchannel, which allowed simultaneous visualization of cell morphology, and passive rheological measurement by tracking the Brownian motion of endogenous granules. Above a threshold stimulus, mechanical deformation resulted in neutrophil activation with pseudopod projection. The activation time was inversely correlated to the rate of mechanical deformation experienced by the neutrophils. A reduction in shear moduli was observed within seconds after the onset of the mechanical stimulus, suggesting a sudden disruption of the neutrophil cytoskeleton when subjected to mechanical deformation. However, the magnitude of the reduction in moduli was independent of the degree of deformation. Recovery to nearly the initial values of viscoelastic moduli occurred within one minute. These observations confirm that mechanical deformation of neutrophils, similar to conditions encountered in the pulmonary capillaries is not a passive event; rather, it is capable of activating the neutrophils and enhancing their migratory tendencies. The second part of the thesis seeks to understand the changes in the cytoskeletal structure and the extent of biological activation as a result of this deformation process. Neutrophils were passed through narrow polycarbonate filter pores under physiological driving pressures, fixed and stained downstream in order to visualize the F-actin content and distribution. / (cont.) Below a threshold capillary size, the cell remodeled its cytoskeleton through initial F-actin depolymerization, followed by recovery and increase in F-actin content associated with formation of pseudopods. 'This rapid depolymerization and subsequent recovery of F-actin was consistent with our previous observation of an immediate reduction in moduli with eventual recovery when the cells were subjected to deformation. Results also show that neutrophils must be retained in their elongated shape for an extended period of time for pseudopod formation, suggesting that a combination of low driving pressures and small capillary diameters promotes cellular activation. These observations show that mechanical deformation of neutrophils into narrow pulmonary capillaries have the ability to influence cytoskeletal structure, the degree of cellular activation and migrational capabilities of the cells. / by Belinda Yap. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / Includes bibliographical references (leaves 158-172). / The overall goal of this research is to acquire a more complete picture of the neurological processes of visual influences on speech perception and to investigate effects of hearing status on AV speech perception. More specifically, functional magnetic resonance imaging (fMRI) was used to investigate the brain activity underlying audio-visual speech perception in three groups of subjects: (1) normally hearing, (2) congenitally deafened signers (American Sign Language) who do not use hearing aids, and (3) congenitally hearing impaired individuals with hearing aids. FMRI data were collected while subjects experienced three different types of speech stimuli: video of a speaking face with audio input, audio speech without visual input, and video of a speaking face without audio input. The cortical areas found to be active for speechreading included: visual cortex, auditory cortex (but not primary auditory cortex), speech motor network areas, supramarginal gyrus, thalamus, superior parietal cortex and fusiform gyrus. For hearing impaired subjects, in addition to the areas listed above, Heschl's gyrus, right angular gyrus (AG), cerebellum and regions around right inferior frontal sulcus (IFS) in the frontal lobe were also found to be active. / (cont.) Results from our study added to existing evidence of the engagement of motor-articulatory strategies in visual speech perception. We also found that an individual's speechreading ability is related to the amount of activity in superior temporal cortical areas, including primary auditory cortex, pre-SMA, IFS and right AG during visual speech perception. Results from effective connectivity analyses suggest that posterior superior temporal sulcus may be a potential AV speech integration site; and that AG serves a critical role in visual speech perception when auditory information is absent for hearing subjects, and when auditory information is available for hearing impaired subjects. Also, strong excitatory projections from STS to inferior frontal gyrus (IFG) and premotor/motor areas, and a strong inhibitory projection from IFG to STS seem to play an important role in visual speech perception in all subject groups. Finally, correlation analyses revealed that in hearing aid users, the amount of acoustic and speech signal gained by using hearing aids were significantly correlated with activity in IFG. / by Julie J. Yoo. / Ph.D.

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. 124-135). / When viewed under the microscope, biological tissues reveal an exquisite microarchitecture. These complex patterns arise during development, as cells interact with a multitude of chemical and mechanical cues in the surrounding extracellular matrix. Tissue engineers have sought for decades to repair or replace damaged tissue, often relying on porous scaffolds as an artificial extracellular matrix to support cell development. However, these grafts are unable to recapitulate the complexity of the in vivo environment, limiting our ability to regenerate functional tissue. Biomedical engineers have developed several methods for printing two- and three-dimensional patterns of proteins for studying and directing cell development. Of these methods, laser microprinting of proteins has shown the most promise for printing sub-cellular resolution gradients of cues, but the photochemistry remains too slow to enable large-scale applications for screening and therapeutics In this work, we demonstrate a novel high-speed photochemistry based on multi-photon photobleaching of fluorescein, and we build the fastest 2-D and 3-D laser microprinter for proteins to date. First, we show that multiphoton photobleaching of a deoxygenated solution of biotin-4-fluorescein onto a PEG monolayer with acrylate end-group can enable print speeds of almost 20 million pixels per second at 600 nanometer resolution. We discovered that the mechanism of fluorescein photobleaching evolves from a 2-photon to 3- and 4-photon regime at higher laser intensities, unlocking faster printing kinetics. Using this 2-D printing system, we develop a novel triangle-ratchet method for directing the polarization of single hippocampal neurons. This ability to determine which neurite becomes an axon, and which neuritis become dendrites is an essential step for developing defined in vitro neural networks. Next, we modify our multiphoton photobleaching system to print in three dimensions. For the first time, we demonstrate 3-D printing of full length proteins in collagen, fibrin and gelatin methacrylate scaffolds, as well as printing in agarose and agarose methacrylate scaffolds. We also present a novel method for 3-D printing collagen scaffolds at unprecedented speeds, up to 14 layers per second, generating complex shapes in seconds with sub-micron resolution. Finally, we demonstrate that 3-D printing of scaffold architecture and protein cues inside the scaffold can be combined, for the first time enabling structures with complex sub-micron architectures and chemical cues for directing development. We believe that the ultra-rapid printing technology presented in this thesis will be a key enabler in the development of complex, artificially engineered tissues and organs. / by Mark Andrew Scott. / Ph.D.in Electrical and Medical Engineering

Thesis (Ph. D. in Speech and Hearing Bioscience and Technology)--Harvard-MIT Program in Health Sciences and Technology, 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 118-125). / Many hearing aids introduce nonlinear compressive gain to accommodate the reduced dynamic range that often accompanies hearing loss. Unfortunately, when applied independently at either ear, this gain can introduce fluctuations in interaural level difference (ILD), which is an important cue for spatial perception and attending to sounds in an acoustic mixture. Moreover, natural sounds produce complicated interactions between different sounds in a mixture, as a compressor's gain is driven by whichever source dominates the mixture within a specified temporal window. While independent compression can interfere with spatial perception of sound, it does not always interfere with localization accuracy or speech identification. This thesis investigates the role of dynamic range compression on the ability to attend to target speech in the presence of interfering speech. First, the fundamental concepts behind dynamic range compression and its use are introduced, and used to develop a framework to understand some of the possible effects on ILD and spatial perception. This framework is applied toward the interpretation of the existing literature regarding dynamic range compression and spatial perception, bringing together a seemingly contradictory range of results. In particular, the framework presented here predicts that dynamic range compression will only affect performance in tasks for which relatively small spatial separations are tested, whereas many existing studies compare only large spatial separations to no spatial separation. We describe and analyze the results of an experiment designed to test this prediction by systematically varying the spatial separation between different speech sources that normal-hearing listeners attended to. We found a robust but modest detrimental effect of dynamic range compression on listeners' performance. Linking the left and right compressors so that ILD was unaltered restored performance. Lastly, we develop a model to describe the utility of ILD for such tasks. The results of this model provide insight into the reported behavioral results, and generate predictions for how hearing impairment may alter the observed pattern of results. / by Andrew H. Schwartz. / Ph.D.in Speech and Hearing Bioscience and Technology

Thesis (Ph. D.)--Harvard University--Massachusetts Institute of Technology Division of Health Sciences and Technology, Program in Medical Engineering and Medical Physics, 1990. / Includes bibliographical references (leaves 185-203). / by Gregory Alexander Brown. / Ph.D.

Thesis (Ph. D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2001. / Includes bibliographical references (p. 223-240). / When bone is loaded beyond its failure point, it develops damage in the form of microcracks. Normally, microcracks are repaired by the remodeling process, limiting the number of in vivo microcracks. However, if the rate of microdamage accumulation increases or the rate of remodeling slows, microdamage can accumulate, reducing bone stiffness and strength and may lead to stress fractures or fragility fractures. A new technique for visualizing microdamage in vitro has been developed that uses chelating fluorochromes to label microcracks. Sequential staining is used to distinguish between microdamage that occurred before testing and damage created during testing. Microdamage parameters quantified include the total number of microcracks, total length of microcracks, damaged area, the number of trabeculae containing microcracks, the pattern of microcracking, the extent of microdamage across the thickness of the trabeculae, and the size of the damage-containing region in the specimen. The chelating fluorochrome marker technique was used to label and quantify microdamage in specimens of bovine trabecular bone damaged in uniaxial compression and compressive fatigue, and relationships between microdamage parameters and changes in mechanical properties (maximum compressive strain, modulus reduction) were quantified. / (cont.) The progressions of damage accumulation during a single compression cycle and during fatigue to failure were determined. Comparisons were made between specimens tested in different loading modes, including uniaxial compression, compressive fatigue, and compressive creep (Pierce, 1999). Microdamage accumulation increases with increasing specimen strain and with increasing stiffness loss. A model was developed to predict modulus reductions based on observed microdamage using cellular solid principles. The predictions were compared to experimentally measured changes in mechanical properties during uniaxial compressive loading and compressive fatigue. There was good agreement between model predictions and experimental results for specimens tested in uniaxial compression. The model predictions were less accurate when applied to specimens tested in compressive fatigue. / by Tara L. Arthur Moore. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, February 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 171-180). / Dysarthria is a motor speech disorder characterized by weak or uncoordinated movements of the speech musculature. While unfamiliar listeners struggle to understand speakers with severe dysarthria, familiar listeners are often able to comprehend with high accuracy. This observation implies that although the speech produced by an individual with dysarthria may appear distorted and unintelligible to the untrained listener, there must be a set of consistent acoustic cues that the familiar communication partner is able to interpret. While dysarthric speech has been characterized both acoustically and perceptually, most accounts tend to compare dysarthric productions to those of healthy controls rather than identify the set of reliable and consistently controlled segmental cues. This work aimed to elucidate possible recognition strategies used by familiar listeners by optimizing a model of human speech recognition, Stevens' Lexical Access from Features (LAFF) framework, for ten individual speakers with dysarthria (SWDs). The LAFF model is rooted in distinctive feature theory, with acoustic landmarks indicating changes in the manner of articulation. The acoustic correlates manifested around landmarks provide the identity to articulator-free (manner) and articulator-bound (place) features. / (cont.) SWDs created weaker consonantal landmarks, likely due to an inability to form complete closures in the vocal tract and to fully release consonantal constrictions. Identification of speaker-optimized acoustic correlate sets improved discrimination of each speaker's productions, evidenced by increased sensitivity and specificity. While there was overlap between the types of correlates identified for healthy and dysarthric speakers, using the optimal sets of correlates identified for SWDs adversely impaired discrimination of healthy speech. These results suggest that the combinations of correlates suggested for SWDs were specific to the individual and different from the segmental cues used by healthy individuals. Application of the LAFF model to dysarthric speech has potential clinical utility as a diagnostic tool, highlighting the fine-grain components of speech production that require intervention and quantifying the degree of impairment. / by Thomas M. DiCicco, Jr. / Ph.D.

Thesis (S.M. in Health Sciences and Technology)--Harvard-MIT Program in Health Sciences and Technology, 2012. / "September 2012." Cataloged from PDF version of thesis. / Includes bibliographical references (p. 37-40). / Successful translation of scientific discovery into new medicines is most successful with collaboration between academics - scientists and physicians - and industry. In recent years, there has been increasing concern at academic medical centers about the impact of relationships with industry on patient care and student education. This has generally resulted in more stringent conflict-of-interest rules. This paper seeks to better understand the impact of these conflict-of-interest rules. In the first part, it explores research to-date on the importance of relationships between industry and academia and discusses some of the concerns that have arisen. In the second part, this relationship is better characterized with clinical trial data. The findings suggest that there is a strong trend towards schools with higher conflict-of-interest rules having fewer clinical trials. This suggests that although there may be benefits to stricter regulation, there are trade-offs in terms of clinical translation. / by Elyssa Sarah Campbell. / S.M.in Health Sciences and Technology

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2007. / Includes bibliographical references (leaves 56-61). / It has been widely reported that pharmaceutical drug discovery innovation began its major decline somewhere in the last decade of the 20th century. After reaching a historical high of 53 new molecular entities (NMEs) in 1996, the industry has since witnessed a steady decline of NME filings (down to 18 in 2006) with the Center for Drug Evaluation and Research (CDER)---despite rapidly escalating R&D spending among the world's major pharmaceutical firms (the "majors"). Industry leaders, researchers, and observers have all but acknowledged this drug discovery productivity crisis, much of it attributed to the industry's preference for and eventual exhaustion of simple, single molecular targets-the so-called "low-hanging fruit" whose discovery is characteristically attributed to serendipity. Collectively, pharmacological compounds were identified that targeted the products of -400-500 genes in the human body over the past five decades. These single-molecular targets-the majority of which are mechanistically overrepresented by the G-protein coupled receptors and key enzymes--are now believed to have been mostly discovered and commercialized into the ubiquitous blockbuster drugs on the market, ranging from statins to proton-pump inhibitors (PPIs). / (cont.) Historically and nearly coincident with this apparent dearth of new molecular targets was the advent of the 99% completed euchromatic sequence' of the human genome in 2004, as reported by the International Human Genome Sequencing Consortium (IHGSC). Launched in 1990, the Human Genome Project (HGP) thus made available thousands of the approximately 30,000-40,000 estimated human genes that could be potentially associated with disease. Given the therapeutic promise of the supposed -3,000 druggable genes2, the major pharmaceutical firms have allocated sizeable investment into genomics-based drug discovery. The realization of senior research executives that future drug innovation will likely be based on a multi-gene, systems biology-based model for understanding complex disease mechanisms of action has resulted in a shift away from reliance on serendipity toward a model informed by genomic elucidation of inter-pathway connectivity. In my research, I examined the level and type of genomics-related investments made by selected majors in the West (U.S., Europe) and Japan. Moreover, I have leveraged genomics as a "lens" to assess the nature and role of serendipity in drug discovery-which I have posited can be deconstructed into the two different facets of technological capability and organizational design. / (cont.) Thirdly, the impact of personal-, firm-, and country-level ethnic & national identity, cultural & historical legacy, and social factors on productivity are investigated. Through the use of personal interviews with senior pharmaceutical industry research executives, an online survey questionnaire completed by research managers and staff, and publicly available information, it was found that the Western and Japanese majors shared major similarities surrounding the original impetus to invest in genomics. While Western firms were found to reap significant benefits from superior scale and decisively 'permeated' genomics as the central platform technology throughout their drug discovery organizations, Japanese firms were found to exhibit greater efficiency in resource utilization in genomics-based discovery. Furthermore, the finding of 3 distinctive national culture characterizations for Western, Japanese, and Chinese firms revealed differential influences on their respective firms' drug discovery practices and productivity. Finally, the state of China's genomics and life sciences firms was evaluated. Prescriptive recommendations for the development of the nascent pharmaceutical industry in China, based on conclusions drawn above, are provided. / by Trent Yen-wei Lu. / S.M.