Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2008. / Includes bibliographical references. / In vivo reflectance and fluorescence spectra were collected from patients with oral lesions, as well as healthy volunteers, in order to evaluate the potential of spectroscopy to serve as a non-invasive tool for the detection oral cancer. A total of 710 spectra were analyzed from 79 healthy volunteers, and 87 spectra from 67 patients. Physical models were applied to the measured spectral data in order to extract quantitative parameters relating to the structural and biochemical properties of the tissue. Data collected from healthy volunteers were used to characterize the relationship between the spectral parameters and tissue anatomy. Diagnostic algorithms for distinguishing various lesion categories were then developed using data collected from patients. The healthy volunteer study demonstrated that tissue anatomy has a strong influence on the spectral parameters. Anatomic sites could be easily distinguished from each other despite the apparent overlap in their parameter distributions. In particular, keratinized sites (gingiva and hard palate) were significantly distinct from other anatomic sites. The results of this study provide strong evidence that a robust and accurate spectroscopic based diagnostic algorithm for oral cancer needs to be applied in a site specific manner. Spectral diagnostic algorithms were developed using the data collected from patients, in combination with the data collected from healthy volunteers. The diagnostic performance of the algorithms was evaluated using the area under a receiver operator characteristic curve (ROC-AUC) and the sensitivity and specificity. The diagnostic algorithms were most successful when developed and applied to data collected from a single anatomic site or spectrally similar sites, and when distinguishing visibly normal mucosa from lesions. / (cont.) ROC-AUC values of >0.90 could be achieved for this classification. Spectral algorithms for distinguishing benign lesions from dysplastic/malignant lesions were successfully created for the lateral surface of the tongue (ROC-AUC =0.75) and for the combination of the floor of the mouth and ventral tongue (ROC-AUC =0.71). / by Sasha Alanda McGee. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2005. / Includes bibliographical references (leaves 62-65). / Alternative pre-messenger RNA splicing is a crucial step in eukaryotic gene expression, and therefore it is subject to tight regulation. Given its importance in conferring protein diversity, alternative splicing is sensitive to changes in cellular states including malignancy. We present a new paradigm by which to quantitatively study the alternative splicing of any molecule through the presented methods of quantitative exon profiling and quantitative isoform profiling which take advantage of a single-molecule based technology [Mit99]. Furthermore, we extend this paradigm to include a novel unified platform-called Isoform Convergence-to qualify particular isoforms as candidate diagnostic markers, potential therapeutic targets, and perhaps even as precursor therapeutics themselves. We apply this paradigm to quantitatively investigate the alternative splicing of CD44 in two leukemias. CD44 is an alternatively spliced cell surface receptor, which is generally implicated in cancer though the specifics are mired in controversy. In this work, we suggest several corrections to previously made claims about the presence of specific CD44 exons and of specific CD44 isoforms in leukemia as well as in non-diseased cells. / (cont.) Furthermore, we provide not only the first comprehensive characterization of CD44's (or any molecule's) alternative exon splicing in human cells, but also its resulting quantities of exons and isoforms to an average resolution on the order of 1.E+06 molecules. Finally, we identify specific isoforms in each leukemia that may serve as candidate markers or possibly as therapeutic targets. / by Chris Varma. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references (p. 123-126). / Acoustic parameters that differentiate between primary stress and non-primary full vowels were determined using two-syllable real and novel words and specially constructed novel words with identical syllable compositions. The location of the high focal pitch accent within a declarative carrier phrase was varied using an innovative object naming task that allowed for a natural and spontaneous manipulation of phrase-level accentuation. Results from male native speakers of American English show that when the high focal pitch accent was on the novel word, vowel differences in pitch, intensity prominence, and amplitude of the first harmonic, H1 * (corrected for the effect of the vocal tract filter), accurately distinguished full vowel syllables carrying primary stress vs. non-primary stress. Acoustic parameters that correlated to word stress under all conditions tested were syllable duration, HI*-A3*, as a measurement of spectral tilt, and noise at high frequencies, determined by band-pass filtering the F3 region of the spectrum. Furthermore, the results indicate that word stress cues are augmented when the high focal pitch accent is on the target word. / (cont.) This became apparent after a formula was devised to correct for the masking effect of phrase-level accentuation on the spectral tilt measurement, Hi *-A3*. Perceptual experiments also show that male native speakers of American English utilized differences in syllable duration and spectral tilt, as controlled by the KLSYN88 parameters DU and TL, to assign prominence status to the syllables of a novel word embedded in a carrier phrase. Results from this study suggest that some correlates to word stress are produced in the laryngeal region and are due to vocal fold configuration. The model of word stress that emerges from this study has aspects that differ from other widely accepted models of prosody at the word level. The model can also be applied to improve the prosody of synthesized speech, as well as to improve machine recognition of speech. / by Anthony O. Okobi. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009. / Includes bibliographical references (p. 69-83). / The use of functional magnetic resonance imaging (fMRI) to study the non-human primate brain has been developed over the past decade. Primate fMRI has many attractive features: it allows validation of previous homology assumptions between humans and monkeys, provides a model to combine imaging with invasive techniques to directly manipulate the brain, and can guide other modalities, such as electrophysiology, to new areas of interest. The frontal eye field (FEF) is a well-studied node in the oculomotor network, involved in visual target selection and saccade planning. Recent evidence has implicated FEF as a possible source of feedback signals that modulate visually-driven activity in posterior cortical areas, such as during the deployment of spatial attention. The goals of this thesis were extend the unique aspects of primate fMRI by combining it with simultaneous, intra cortical microstimulation (EM), and to use these new methods to measure how local, artificially-increased FEF output could modulate visually-driven fMRI activity in earlier cortical regions. The first outcome of this thesis was a novel form of functional tractography. FEF-EM below the threshold needed to evoke saccades yielded robust, focal fMRI activity in cortical and sub cortical structures connected with FEF. The second outcome was a demonstration that subthreshold FEF-EM produced retinotopically-specific enhancement and suppression of the representation of a stimulus presented at the saccadic endpoint, or movement field (MF), of the stimulated FEF site. Modulation occurred at multiple levels of the visual system and the signals presumably causing it appeared to be gated in the earliest cortical areas by bottom-up activity. The third outcome was a characterization of how stimulus intensity altered these modulations. / (cont.) The luminance contrast of a stimulus presented in the MF was systematically varied to generate contrast response functions for many cortical areas, which were compared with existing data. Sub-threshold FEF-EM increased fMRI activity for the lowest contrasts and had little or even a suppressive influence at the highest contrasts, mainly in support of a contrast rather than activity gain effect. From these data, a simple spatial model explaining the interaction between bottom-up and top-down signals from the FEF was constructed, which could guide future psychophysical and electrophysiological experiments. The final outcome was a demonstration that artificially-increased FEF output could alter stimulus selectivity in visual cortex independent of stimulus saliency. This suggests that FEF relays not only spatial but also feature-relevant information to specific visual cortical areas. / by Leeland Bruce Ekstrom. / Ph.D.

Thesis (Ph. D. in Biomedical Engineering)--Harvard-MIT Program in Health Sciences and Technology, 2013. / Cataloged from PDF version of thesis. "September 2013." Pages 215 and 216 blank. / Includes bibliographical references (pages 208-214). / Although many take the seemingly simple ability to balance in order to maintain posture for granted, approximately 8 million American adults have chronic balance impairment issues derived from vestibular dysfunction. For patients suffering from severe vestibular dysfunction, maintaining balance in daily activities, such as walking on an uneven surface at night, turning one's head, or attempting to stand on a moving surface, can prove extremely challenging. Unfortunately, many vestibular-loss sufferers are left with limited treatment options and can become permanently debilitated. In order to aid the vestibular-impaired population in partially restoring postural stability, it is important to develop rehabilitative solutions. For subjects suffering from severe bilateral vestibular loss, but with intact eighth nerve function, the invasive vestibular prosthesis is a potential rehabilitative solution. This must be developed and fully characterized in non-human primates in parallel with human implementation. In this research, we characterized the postural response of a severely vestibular-lesioned non-human primate instrumented with a prototype invasive vestibular prosthesis. We showed that the severely vestibular-impaired animal aided by the prosthesis was able to utilize the partially restored vestibular cues to increase its stability compared to the severely-impaired state. We also explored the impact on balance of (1) supplying an additional cue (light-touch) and (2) compensative strategies that the subject develops when suffering from mild or severe vestibular-impairment. We determined that the severely-impaired animal decreased its trunk sway when provided the light-touch cue, however a mildly-impaired animal did not. We also determined that an animal with mild vestibular impairment spontaneously compensated for its vestibular loss to stabilize itself both for stationary support surface conditions and for support surface perturbations. This thesis is the first time that animal posture measures for different levels of vestibular impairment have been used in conjunction with a feedback controller model to investigate the postural control mechanisms used. The results reported within this thesis begin to establish the baseline database of primate postural responses to a wide variety of test situations for different levels of vestibular impairment that will be needed for further investigation and evaluation of rehabilitative solutions, such as prototype vestibular implant systems. / by Lara A. Thompson. / Ph.D.in Biomedical Engineering

Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2016. / 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 107-117). / Communication in environments with multiple competing sound sources can be challenging, even for listeners with normal hearing thresholds (NHT). This difficulty in "normal" listeners is thought to arise from central sites of the auditory system with the assumption that sound encoding at the auditory nerve (AN) is robust. Despite this assumption, growing evidence from animal and human studies suggests that acoustic exposure, too modest to elevate hearing thresholds, can nonetheless cause "hidden hearing loss" that interferes with coding of supra-threshold sound. In animal studies, such noise exposure leads to cochlear synaptopathy (death of auditory nerve fibers or ANFs); however, there is no clinical test of synaptopathy in humans. In animals, synaptopathy reduces the amplitude of auditory brainstem response (ABR) wave-I. Unfortunately, ABR wave-I is difficult to measure in humans, limiting its clinical use. Here, using behavioral, otoacoustic, and electrophysiological measures in humans and mice in conjunction with computational models of sound processing by the auditory periphery and brainstem, we show that the effect of masking noise on the latency of the more robust ABR wave-V mirrors changes in ABR wave-I amplitude. In our human cohort, the effect of noise on wave-V latency predicts perceptual temporal sensitivity. Further, we show evidence that ABR wave-V latency in forward masking may be affected by ANF loss and is predictive of a listener's performance in a perceptual task related to speech intelligibility in noise. Our results suggest that measures of the effects of masking on ABR wave-V latency can be used to diagnose ANF survival in humans. / by Golbarg Mehraei. / Ph. D.

Thesis (S.M.)--Harvard-MIT Program in Health Sciences and Technology, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 27-30). / Composite hydrogels find increasing use as biomaterials because the addition of a filler often improves on the material properties of the original matrix, or provides new optical, magnetic, conductive or bioactive functionalities not inherent to the hydrogel. In this work we synthesized nanocomposite gelatin methacrylate (GelMA) hydrogels that incorporate D,L-cyclic peptide nanotubes. These nanotubes are biocompatible, stiff and their physical and chemical properties can be tailored simply by changing the amino acid sequence of the peptide. We show that the nanotubes successfully integrated into the hydrogel matrix and provided some mechanical reinforcement, without affecting hydrogel porosity or hydration characteristics. We will be using this composite system as a platform for engineering hydrogels with unique physical and biological properties to the hydrogel, for application as biological scaffolds. / by Pei Kun Richie Tay. / S.M.

Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 133-147). / Several studies over the past decade have transformed our understanding of the regulatory elements and mechanisms utilized by a human cell to drive cell type identity. In particular, epigenomic studies have revealed recurrent epigenetic signatures at enhancers and other regulatory regions, as well as their role in cellular lineage specification. However, these studies generally focused on steady-state cellular states where much of the lifespan of adult cells involves responding to extracellular cues. To better understand the gene expression changes that occur in response to stimuli, I studied a time-course stimulation of human umbilical vascular endothelial cells (HUVECs) with vascular endothelial growth factor A (VEGFA) as a model system. Using data collected from multiple genome-wide assays I modeled the dynamic changes in epigenetic, transcriptional, and transcription factor binding profiles in regulation of angiogenesis, the formation of new blood vessels. First, I identify regulatory elements involved in VEGFA-response through focal, temporal changes in chromatin structure and that p300 activity is mechanistically required for this response. Secondly, I analyze changes in combinatorial binding of transcription factors linked with VEGFA-responsive enhancers. These studies highlight general strategies to study stimulus-responsive regulatory systems, and reveal new insights into angiogenesis, human disease and therapeutic targets. Finally, I show that VEGFA-responsive genes are regulated by promoter-proximal RNA Polymerase II pausing and extend it to comprehensive analysis of gene expression and chromatin regulation by promoter-proximal pausing across cell types. / by Daniel S. Day. / Ph. D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references (leaves 39-41). / Here we describe an experimental method for measuring the acoustic transmission matrix of the middle-ear using otoacoustic emissions. The experiment builds on previous work that uses distortion product otoacoustic emissions (DPOAEs) as an intracochlear sound source to drive the middle-ear in reverse. This technique eliminates the complications introduced by needing to place an acoustic transducer inside the cochlea. Previous authors have shown how the complete 4x3 system response matrix, with its 12 unknowns, can be simplified to a 2x2 transmission matrix by de-coupling the middle-ear cavity and assuming the cochlear fluids are incompressible. This simplified description of middle-ear mechanics assumes that the input-output response at the tympanic membrane and stapes footplate is linear, one dimensional and time invariant. The technique allows for estimating the acoustic pressure and volume velocity at the tympanic membrane and the volume velocity of the stapes footplate, in both the forward and reverse direction, and under different boundary conditions at the stapes. The technique was applied to deeply anesthetized cats with widely opened middle-ear cavities over a frequency range of 200Hz to 10kHz. Results on three animals are reported and generally agree with previous data and a published middle-ear model. / by Antonio John Miller. / S.M.

Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2013. / 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 xviii-xxxvi). / Contamination of food, water, medicine and ingestible household products is a public health hazard that episodically causes outbreaks worldwide. Existing laboratory methods are often expensive, require a laboratory environment and/or trained staff to perform manual steps. The aim of this PhD thesis was to create and test methods and instruments for affordable diagnostic tests for contaminants and pathogens. To achieve this goal, the LabReader was introduced, which employs a LED-based detection scheme for four simultaneous fluorescence- and UV-measurements. Assays were developed to detect (di-)ethylene glycol in consumables ≥0.1wt% and alcohols ≥1ppb. Pathogens in water, foods and blood were detected at ≥104 CFU/ml using nonspecific intercalating dyes. To gain sensitivity and specificity for cell-based analysis, biochemical amplification methods had to be incorporated. To be deployable outside a laboratory, sample preparation needed to be automated. Automation was achieved by combining the LabReader with the already developed LabTube, a disposable platform for automated DNA extraction inside a standard centrifuge. Performing DNA amplification/readout in an external optical reader, made the LabSystem broadly deployable and flexible. DNA extraction of food bacteria (E.coli and Alicyclobacillus) was optimized inside the LabTube for 102-109 inserted DNA copies. The extracted DNA was amplified using the qualitative isothermal LAMP method and semi-quantitative, real-time PCR inside the LabReader. The combined extraction and amplification detection limit of the LAMP-LabSystem and the quantitation limit of the PCR-LabSystem were as low as 102 copies. Performing extraction and amplification inside the centrifuge/LabTube was also outlined, which may be preferable when contamination risks are high. After theoretically evaluating heating methods, a battery-driven heated LabTube was designed, in which 102-108 DNA copies of VTEC E.coli were extracted, LAMP-amplified and visually readout within 1.5 hrs. The major contribution of this thesis is the full system integration of versatile, automated sample preparation and detection systems. They offer great flexibility as they may be used with each other or in combination with other analytic methods, depending on the application. At the same time, they are frugal and deployable at low-to-medium throughput - even outside a traditional laboratory. Whilst the focus was put on food safety, the systems were also used for medical, environmental or consumer product quality applications, hence demonstrating their broad applicability. / by Melanie Margarete Hoehl. / Ph. D.