Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 131-147). / Prostate cancer persists as a major public health issue in the United States and remains the second leading cause of cancer death in men. Early detection and disease monitoring in prostate cancer can significantly improve a patient's prognosis. The advent of prostate-specific antigen (PSA) screening has allowed physicians to monitor the levels of a specific protein, or biomarker, as a correlate of disease progression. This thesis focuses on optical detection of prostate tumors through the development of biomarker-targeted molecular imaging probes. In the first part of this work, engineered human prostate cancer cell lines were developed and characterized to determine the dynamics of post-translational processing for PSA proteolytic activity and to establish potential small animal models for validating protease-activatable imaging probes. Target-activatable gold nanoparticle imaging probes that can be self-assembled in a one-step reaction were then developed to detect biomarker proteases in vivo. The activated probes demonstrated a 5 to 8-fold fluorescence signal amplification, extended circulation time, and high image contrast in a mouse tumor model. Lastly, differential phage display selection was performed on human prostate cancer cells with low and high metastatic potentials to (1) identify cell-surface biomarkers specific to highly aggressive tumors, and (2) develop molecular imaging probes for detecting prostate cancer metastases. / (cont.) One peptide, LN4P-1, demonstrated preferential binding to highly metastatic PC3M-LN4 cells and identified a highly expressed protein on their cell surface. Fluorescently labeled LN4P-1 was able to detect PC3MLN4 tumors in vivo. In summary, this thesis outlines the development of molecular imaging probes for targeting tumors both at the primary site, through evaluation of biomarker protease activity, and at the metastatic site, through affinity-based analysis of biomarker expression. / by Chunyao Jenny Mu. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references. / Understanding intensity coding and auditory learning are basic concerns of research on the auditory central pathway. There is no unifying model of intensity coding but several mechanisms have been proposed to play a role. The first aim of this thesis was to determine the mechanisms of intensity coding in the central auditory pathway from the cochlear nucleus to the auditory cortex. The Fos labeling method was used to assess neuronal activation in the central auditory system. This technique allows one to study large regions of the brain in awake animals. Increasing sound pressure level led to: (1) spreading of labeling towards neurons with higher best frequencies; (2) spread of labeling orthogonal to the tonotopic axis; (3) and increased density of labeling within the tonotopic band. In addition to encoding the physical features of a stimulus, it is fundamental for survival that we learn about the meaning of sounds and put them in a behavioral context. The second aim of this thesis was to study how learning, in particular auditory fear conditioning, changes the pattern of neuronal activation of neurons, as measured with Fos labeling, in the central nervous system. Conditioning led to an increase in Fos labeling in central auditory nuclei. / (cont.) This increase in labeling was similar to the effects of increasing sound intensity. The present results support the idea that auditory fear memories are stored in the auditory pathway. / by Teresa P.G. Santos. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 145-159). / Epilepsy is a neurological disorder characterized predominantly by an enduring predisposition to generate epileptic seizures. The apprehension about injury, or even death, resulting from a seizure often overshadows the lives of those unable to achieve complete seizure control. Moreover, the risk of sudden death in people with epilepsy is 24 times higher compared to the general population and the pathophysiology of sudden unexpected death in epilepsy (SUDEP) remains unclear. This thesis describes the development of a wearable electrodermal activity (EDA) and accelerometry (ACM) biosensor, and demonstrates its clinical utility in the assessment of epileptic seizures. The first section presents the development of a wrist-worn sensor that can provide comfortable and continuous measurements of EDA, a sensitive index of sympathetic activity, and ACM over extensive periods of time. The wearable biosensor achieved high correlations with a Food and Drug Administration (FDA) approved system for the measurement of EDA during various classic arousal experiments. This device offers the unprecedented ability to perform comfortable, long-term, and in situ assessment of EDA and ACM. The second section describes the autonomic alterations that accompany epileptic seizures uncovered using the wearable EDA biosensor and time-frequency mapping of heart rate variability. We observed that the post-ictal period was characterized by a surge in sympathetic sudomotor and cardiac activity coinciding with vagal withdrawal and impaired reactivation. The impact of autonomic dysregulation was more pronounced after generalized tonic-clonic seizures compared to complex partial seizures. Importantly, we found that the intensity of both sympathetic activation and parasympathetic suppression increased approximately linearly with duration of post-ictal EEG suppression, a possible marker for the risk of SUDEP. These results highlight a critical window of post-ictal autonomic dysregulation that may be relevant in the pathogenesis of SUDEP and hint at the possibility for assessment of SUDEP risk by autonomic biomarkers. Lastly, this thesis presents a novel algorithm for generalized tonic-clonic seizure detection with the use of EDA and ACM. The algorithm was tested on 4213 hours (176 days) of recordings from 80 patients containing a wide range of ordinary daily activities and detected 15/16 (94%) tonic-clonic seizures with a low rate of false alarms (<; 1 per 24 h). It is anticipated that the proposed wearable biosensor and seizure detection algorithm will provide an ambulatory seizure alarm and improve the quality of life of patients with uncontrolled tonic-clonic seizures. / by Ming-Zher Poh. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Program in Health Sciences and Technology, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Temporal and spatial variation of histone methylation is an important factor in mammalian development. Deciphering the details of such epigenetic phenomena has the potential to enrich both stem cell biology and therapeutics, as well as offer insight into various pathologies. While the enzymatic machinery responsible for these transitions is well known, it is their localization to specific genomic regions that controls cell fate, and this has largely remained a mystery. The goal of this thesis was to use an integrative genomics approach to elucidate the role of cis elements in the establishment of repressive chromatin domains. To this effect, we determined the genetic basis for localization of Polycomb repressive complexes (PRCs) in mammalian embryonic stem (ES) cells. First, by generating genomewide chromatin state maps in mouse and human by high throughput sequencing, we utilized a comparative and motif dictionary approach to computationally identify potential Polycomb recruitment elements. Surprisingly, we found that PRC recruitment is best explained by localization to clusters of unmethylated CpG dinucleotides, elements originally associated with gene activation. Next, in a series of transgenic assays involving human and E. coli sequence, we were able to reconstitute the chromatin state of an epigenetic memory element in mouse ES cells. Finally, we found that as somatic identity is reset during induced pluripotent stem (iPS) cell reprogramming, these same elements are central to a coordinated response in which active chromatin domains are established prior to and independently of transcription. Taken together, these studies highlight the role of a particular cis element in the establishment of both active and repressive chromatin domains. Furthermore, this dynamic underscores how a static genetic element can be utilized to enable the chromatin-based plasticity required of stem cell differentiation and lineage specification. / by Richard Patrick Koche. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 103-114). / Human Immunodeficiency Virus (HIV) is the cause of Acquired Immune Deficiency Syndrome (AIDS) and has killed over 25 million people since the disease was first recognized in 1981. As of 2007, 33 million people globally are infected with HIV and this number is growing. HIV infects and depletes CD4+ helper T cells, affecting the ability of the immune system to defend the host against common infections. While anti-retroviral therapy has decreased morbidity and mortality, these drugs are not curative. In addition, they are beyond the financial reach of many HIV infected patients. Thus, the development of strategies to control HIV spread is a high priority. The most relevant animal model for studying HIV is the Simian Immunodeficiency Virus (SIV) - infected rhesus monkey. While HIV research has focused on studying peripheral blood specimens, mucosal sites have recently been identified as a focal point for HIV replication and tissue destruction. They are usually the sites of primary infection in the setting of sexual transmission and they are also important sites of immune depletion. If methods for controlling the replication of the virus early after infection in mucosal sites are available, it may be possible to eliminate the virus prior to systemic spread. While strategies for generating strong neutralizing antibody responses have not yet been developed, emerging data suggest that CD8+ cytotoxic T cells can contribute substantially to early virus control. It is important to study CD8+ T cells in the setting of SIV infection in rhesus monkeys, particularly in mucosal sites, using functional as well as transcriptional assays. / (cont.) One of the challenges in studying mucosal cellular immunity is the limited number of cells available in biopsies, making traditional assay systems such as flow cytometry very difficult to employ. Here, technologies for isolating rare cell populations and extracting RNA from these cells for gene expression analysis were developed. These technologies were then applied to peripheral blood specimens, looking at gene expression differences between virus-specific CD8+ T cells in Mamu-A*01+ and Mamu-A*02+ monkeys. The ultimate goal of these studies is to gain a better understanding of SIV immunopathogenesis (as a model for HIV immunopathogenesis) and to find a way to control or eliminate the virus. / by Amy Shi. / S.M.

Thesis: S.M., Harvard-MIT Program in Health Sciences and Technology, 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (page 30). / This work investigates the nature of the memory mechanisms utilized in language comprehension. Through the use of the Speed Accuracy Tradeoff (SAT) paradigm (Wickelgren, 1977), healthy young adults were studied for the use of parallel or serial search mechanisms to understand syntactically complex sentences with multiple embeddings. Systematically designed sentence stimuli tested whether the relevant memory mechanism differs when reanalysis is required. Results indicated that sentence length and syntactic ambiguity affected overall accuracy of sentence comprehension. The rate in which information was retrieved did not vary for most sentence types, but may have been affected by length in one type of sentence (ambiguous "early closure" sentences). The data support a parallel, content-addressable retrieval mechanism for information in most sentences but may provide evidence for serial search in ambiguous sentences that require complex syntactic reanalysis. / by Jordan Ashley Whitlock. / S.M.

Thesis (Ph.D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2000. / Includes bibliographical references. / Understanding how the human brain works, in both health and disease, requires data with both high spatial and temporal resolution. This thesis develops and applies a spatiotemporal neuroimaging method. I describe a linear estimation inverse approach, which is a method for the combination of functional magnetic resonance imaging (fMRI) with electroencephalography (EEG) and magnetoencephalography (MEG). fMRI provides millimeter spatial resolution, while EEG and MEG provide millisecond temporal resolution. The thesis is divided into two broad sections: Monte Carlo modeling studies and experimental studies. Improvements to both the bioelectromagnetic forward and inverse solutions are demonstrated. Through modeling studies, I characterize the accuracy of the method with and without functional and anatomic constraints, the effects of various model mis-specifications, and as a function of EEG/MEG sensor configuration. I describe a noise sensitivity normalization to the traditional linear estimation operator that improves the point spread function (a measure of spatial resolution), increases the spatial homogeneity of the point spread, and allows interpretation of the localization in terms of a statistical measure (F-statistic). Using experimentally generated current dipoles implanted an epilepsy patient, I examine the accuracy of both a realistic and spherical EEG head model. This experimental data demonstrates the improved accuracy of the realistic head model, and gives us confidence in using this realistic head model for EEG source localization. The optimized and validated forward and inverse methods are then applied to a variety of empirical measurements. First, the combined multi modality imaging approach is used to simultaneous EEG/fMRI measurements of a visual stimulus, demonstrating the feasibility of measuring and localizing simultaneously acquired electric potential and hemodynamic measurements. Second, combined MEG/fMRI measurements are used to analyze the spatiotemporal characteristics of a cortical network that is responsive to visual motion coherency. Finally, in epilepsy patients, I compare the non-invasive MEG localization of interictal spikes with verification from invasive recordings and surgical results. These studies, in both normal volunteers and patients, clearly demonstrate the utility, accuracy, and power of the combined use of fMRI, EEG and MEG. The tools demonstrated here provide "real time movies" of the human brain at work during a given task or behavior. This information is required to develop computational models of how the human brain/mind works. / by ARthur K. Lui. / Ph.D.

Thesis: Ph. D. in Biomedical Engineering, Harvard-MIT Program in Health Sciences and Technology, 2017. / 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 120-125). / The cochlea is part of the peripheral auditory system that has unique and intriguing features - for example it acts as a wave-based frequency analyzer and amplifies traveling waves. The human cochlea is particularly interesting due to its critical role in our ability to process speech. To better understand how the cochlea works, we develop a model of the mammalian cochlea. We develop the model using a mixed physical-phenomenological approach. Specifically, we utilize existing work on the physics of classical box-representations of the cochlea, as well as the behavior of recent data-derived wavenumber estimates. We provide closed-form expressions for macromechanical responses - the pressure difference across the Organ of Corti (OoC), and the OoC velocity, as well as the response characteristics - such as bandwidth and group delay. We also provide expressions for the wavenumber of the pressure traveling wave and the impedance of the OoC that underlie these macromechanical responses and are particularly important variables which provide us with information regarding how the cochlea works; they are a window to properties such as effective stiffness, positive and negative damping or amplifier profile, incremental wavelengths, gain and decay, phase and group velocities, and dispersivity. The expressions are in terms of three model constants, which can be reduced to two constants for most applications. Spatial variation is implicitly incorporated through an assumption of scaling symmetry, which relates space and frequency, and reduces the problem to a single independent dimension. We perform and discuss various tests of the model. We then exemplify a model application by determining the wavenumber and impedance from observable response characteristics. To do so, we determine closed-form expressions for the model constants in terms of the response characteristics. Then, using these expressions, along with values for human response characteristics that are available from psychoacoustic measurements or otoacoustic emissions, we determine the human wavenumber and impedance. In addition, we determine the difference in the wavenumber and impedance in the human base (where the OoC velocity responds maximally to high frequencies), and the human apex (where the OoC velocity responds maximally to low frequencies) and discuss their interpretations. The model is primarily valid near the peak region of the traveling wave, and is linear - therefore the model, as is, does not account for cochlear nonlinearity, and hence is primarily suitable for low stimulus levels. Finally, we discuss other scientific and engineering model applications which we can pursue, as well as potential modifications to the model, including suggestions regarding incorporating nonlinearity. / by Samiya A Alkhairy. / Ph. D. in Biomedical Engineering

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2008. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 84-85). / Valuing medical device companies and technologies is a complex process. Several different approaches and models are often used in combination to determine a transaction valuation. This research uses the Enterprise Value to Forward Sales model as a tool for valuing mergers and acquisitions in the device industry. This model was selected for its transportability across industry segments, ease of calculation, broad acceptance, and lack of detailed forecasting assumptions. This research seeks to: 1) explore the importance of 20 commonly cited factors in determining a medical device company EV/Sales multiple, 2) develop a model for forecasting the EV/Sales multiple of medical device transactions, and 3) assess the explanatory power of these factors in determining the enterprise value (measured in dollars) of pre-revenue transactions. For purposes of this analysis valuation was approached from a sector neutral or portfolio diversification perspective. Multivariate regression analysis was performed on a database of 352 M&A transactions announced between January 1, 1996 and December 31, 2007 to assess the importance of various factors and develop a model for forecasting EV/Sales multiples. Consistent with our expectations, supernormal growth, industry growth, market size, sector beta, position in market, venture funding, and IPO status were all significant factors in determining the multiple. Based on these factors, we developed a model that was 95% accurate in forecasting the EV/Sales multiple of medical device transactions that occurred between January and May of 2008. / (cont.) Based on the success of this model, we then explored the utility of these factors in determining the gross enterprise value of pre-revenue M&A transactions. As expected, this approach was not successful. Varying discount rates, timing assumptions, difficult to determine value synergies, and emotion are confounding factors which make it difficult to reliably forecast absolute dollar transaction valuations. / by Jason S. Robins. / S.M.

Thesis: Ph. D. in Biomedical Engineering, Harvard-MIT Program in Health Sciences and Technology, February 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 101-114). / MRI based cerebral oxygenation measures could enable brain-centered clinical care and improve understanding of brain energy use throughout human development. We made technical improvements to two MR oxygenation imaging techniques, and explored the concordance between various methods to quantify the cerebral metabolic rate of oxygen consumption (CMRO2 ) and other aspects of cerebral metabolism in neonates with congenital heart disease (CHD). Using a turbo gradient spin echo readout we reduced the scan time of the existing QUantitative Imaging of eXtraction of Oxygen and TIssue Consumption (QUIXOTIC) technique for measurements of global oxygen extraction fraction by eightfold while improving robustness to physiological noise and motion. We also corrected the effect of residual cerebrospinal fluid signal on transverse relaxation time quantification. The detected change in oxygen extraction fraction in the visual cortex during visual stimulation, demonstrated the technique's suitability for absolute quantitative functional MRI experiments. T2-Relaxation Under Spin Tagging (TRUST) has been used in several studies, including one with neonates, to quantify blood oxygen saturation. We investigated how involuntary subject motion affects quantification by incorporating volume navigators into TRUST to monitor motion during scans. We demonstrated that motion causes an upward bias in venous oxygen saturation quantification. Finally, we used TRUST and phase contrast MRI to measure CMRO2 in neonates with congenital heart disease (CHD) and explored the link between CMRO2 and other aspects of metabolism examined by MR spectroscopic imaging. We found a relationship between cerebral oxygenation and lactate and glutathione concentrations in white matter. We also sought to extend the reach of absolute MRI-based quantification by comparing it to bedside near infrared spectroscopy-based measurements. We found good agreement between oxygenation measurements, but no agreement between cerebral blood flow measurements, suggesting that hemodynamics vary more rapidly than oxygenation. Robust MR-based oxygenation imaging would improve clinical care and our understanding of how abnormal oxygen delivery affects brain development. Seeking a complete picture of cerebral metabolism throughout development, future work will perfect techniques to monitor cerebral hemodynamics, oxygenation and metabolism from midgestation to old age. / by Jeffrey Neil Stout. / Ph. D. in Biomedical Engineering