Thesis (S.M. in Health Sciences and Technology)--Harvard-MIT Program in Health Sciences and Technology, 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 67-70). / Targeted, especially stratified or biomarker-guided, therapies offer significant advantages over traditional oncology therapies in certain settings. Selecting patients most likely to respond to a drug increases the therapeutic efficacy while reducing toxicities and may accelerate regulatory approval since smaller clinical trials are needed to demonstrate benefit. Several drugs, including vemurafenib and crizotinib have demonstrated these benefits along with commercial success. However, significant risk exists for the drug developer since approval may be threatened if they fail to meet unclear and differing yet parallel requirements for both the drug and the required companion diagnostic. Tumor biology is also increasingly complex since recent studies suggest that there are limited numbers of individual driver mutations, complicated interactions throughout signaling pathways as well as extensive tumor heterogeneity, all of which will challenge the effectiveness of targeted therapies. Clinical trial strategy decisions can greatly impact the success of a targeted therapy due to these challenges. While therapeutic efficacy is considered important, biomarker prevalence and companion diagnostic performance have been shown to be as important, yet more informative at the time decisions are made. I hypothesized that common prevalence and companion diagnostic performance thresholds are being used to guide biomarker-guided clinical trial strategy decisions for targeted oncology therapies. Seventeen interviews with preclinical, clinical or translational leads were conducted across a focused set of ten "pathway-modifying" cancer drug programs (CDK4/6, MDM2 and P13KP inhibitors) that reflect the biological complexity of future targeted therapies. These interviews provided empirical data as to how biomarkers are being incorporated into current clinical trial decisions. All respondents were planning to use a companion diagnostic for their program, however, the use of biomarkers varied significantly. For those programs with ongoing clinical trials in phase I and II, 54% (n=7/13) were pursuing a biomarker-guided strategy while 46% (n=6/13) were using an initial all-comers strategy. This fairly equal split separated when compared by phase where trials in phase I and 1/11, 60% (n=6/10) were using an all-comers strategy but for those trials in phase II (n=3), all were using biomarker-guided strategies. A key finding of the interviews was that 66.7% (n=4/6) were planning biomarker enrichment as part of expansion plans. Disproving my hypothesis, however, common thresholds for neither biomarker prevalence nor companion diagnostic performance were being used to guide these decisions. Biomarker prevalences of 50-100% were stated as potentially appropriate for an all-comers strategy. Companion diagnostic performance thresholds were even less influential as only a few respondents provided a general range of desired sensitivity and specificity. This study found that actions of drug developers are not necessarily following the emerging recommendations for targeted therapies due to the significant challenges of biomarker and companion diagnostic development. / by Heather Stacey Tomkinson Vital. / S.M.in Health Sciences and Technology

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2003. / Includes bibliographical references (p. 40-44). / There is a clear and present need to improve the quality of diabetes care. Information technology can be used as a means to that end. In this article, we discuss the design and implementation of a web-based diabetes application. We show the role of modeling clinical workflow in the design philosophy of our application, and summarize our application's features and usage. Next, we describe observations made during and after design and implementation, and how they relate to the informatics literature. Finally, we elaborate on the paradigm of feedback control systems, its parallels with the design philosophy of our application, and its use as an organizational framework for the roles of information technology in diabetes care. / by Anil Kumar Dubey. / S.M.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2008. / Includes bibliographical references (leaves 81-86). / Bacterial infections represent a significant source of morbidity and mortality. Biofilms and antibiotic resistance pose challenges to our future ability to treat bacterial diseases with antibiotics (1). Bacteria frequently live in biofilms, which are surface-associated communities encased in a hydrated extracellular polymeric substances (EPS) matrix (2, 3). Biofilms are crucial in the pathogenesis of many clinically-important infections and are difficult to eradicate because they exhibit resistance to antimicrobial agents and removal by host immune systems (4). Antibiotics can even induce biofilm formation (5, 6). The development of antibiotic-resistant bacteria is also a growing medical problem. Antibiotic resistance genes can be acquired by horizontal gene transfer and passed vertically to later generations (7). Antibiotic resistance can also result from persistence, a phenomena in which a subpopulation of cells can withstand antibiotic treatment without containing antibiotic-resistance genes (8). These problems, coupled with decreasing output of new antibiotics, have highlighted the need for new treatments for bacterial infections (1, 9-12). I developed three novel strategies for attacking bacterial biofilms and antibiotic resistance using synthetic biology. To remove biofilms, I engineered bacteriophage to express a biofilm degrading enzyme during infection to simultaneously attack biofilm cells and the biofilm EPS matrix. These enzymatically-active bacteriophage substantially reduced biofilm cell counts by 4.5 orders of magnitude (-99.997% removal), which was about two orders of magnitude better than that of non-enzymatic phage. To address antibiotic-resistant bacteria, I targeted gene networks with synthetic bacteriophage to create antibiotic adjuvants. / (cont.) Suppressing the SOS network with engineered bacteriophage enhanced killing by ofloxacin, a quinolone drug, by over 2.7 and 4.5 orders of magnitude compared with control bacteriophage plus ofloxacin and ofloxacin alone, respectively. I also built phage that targeted multiple gene networks and demonstrated their effectiveness as antibiotic adjuvants. Engineered bacteriophage reduced the number of antibiotic-resistant bacteria and performed as strong adjuvants for other bactericidal antibiotics such as aminoglycosides and P-lactams. Finally, I designed synthetic in vivo sensors for antibiotic-resistance genes that can be coupled with effector components to kill cells carrying resistance genes or to block horizontal transmission of those genes. My work demonstrates the feasibility and benefits of using engineered bacteriophage and synthetic biology constructs to address the dual threats of bacterial biofilms and antibiotic-resistant bacteria. / by Timothy Kuan-Ta Lu. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, June 2005. / Includes bibliographical references. / Chapter 1. An Introduction to Self-Assembled Monolayers & Surface Characterization A brief summary of the formation, structure, and characterization techniques of self assembled monolayers (SAMs) is described. The characterization techniques include contact angle goniometry, ellipsometry, grazing-angle Fourier-transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV), sum-frequency generation spectroscopy (SFG), and atomic force microscopy (AFM). Chapter 2. A Reversibly Switching Surface The design of surfaces that exhibit dynamic changes in interfacial properties such as wettability in response to an electrical potential is described. The change in wetting behavior was caused by surface-confined, single-layered molecules undergoing conformational transitions between a hydrophilic and a moderately hydrophobic state. Reversible conformational transitions were confirmed both at a molecular level using sum-frequency generation spectroscopy and at a macroscopic level using contact angle measurements. This type of surface design enables amplification of conformational transitions at a molecular level to macroscopic changes in surface properties without altering the chemical identity of the surface. Such reversibly switching surfaces may open new opportunities in interfacial engineering.Chapter 3. A Synthetic Chemical Route for the Formation of Homogeneously- Mixed Self-Assembled Monolayers A novel way to produce self-assembled monolayers (SAMs) uniformly mixed on the molecular length scale is described. / (cont.) Initially, a precursor SAM was formed from molecules that are derived from 16-mercaptohexadecanoic acid (MHA) and contain a globular end group. Self-assembly of these molecules resulted in a SAM that is densely packed with respect to the space-filling end groups, but shows low-density packing with respect to the hydrophobic chains. Subsequent cleavage of the space-filling end groups established a low-density SAM of MHA. A mixed monolayer of MHA and n-butanethiol was formed by backfilling the low-density monolayer of MHA with the corresponding alkanethiol. The new "mixed" SAM was characterized by optical ellipsometry, contact angle goniometry, X-ray photoelectron spectroscopy (XPS), Fourier Transform Infrared Spectroscopy (FT-IR), cyclic voltammetry (CV), and reductive desorption voltammetry. The results indicate a uniformly mixed monolayer as compared to a SAM generated by coadsorption of mixtures of the same MHA and n-butanethiol molecules. This approach provides a way to produce SAMs that are uniformly mixed using a synthetic chemical route, which affords considerable flexibility in composition and also in the ratio of the different molecules in the mixed SAM. Chapter 4. / (cont.) Design of Oligonucleotide Arrays Using Homogeneously Mixed Self - Assembled Monolayers We have employed two quantitative techniques, quart-crystal microbalance with dissipation monitoring (QCM-D) and surface plasmon resonance imaging (SPR) to quantify the hybridization efficiency of a 25-mer oligonucleotide probe to two different surfaces: a dense 16-mercaptohexadecanoic acid self-assembled monolayer (MHA SAM) and a homogeneously-mixed (HM) SAM generated from the method described in Chapter 3 that allows for regular spacing of functional -COOH groups. This reduced density of functional groups led to reduced attachment of oligonucleotide probes to the surface, increasing the area per probe, and allowed more space in which complimentary sequence can bind. Reducing the density of immobilized probes led to the improvement in hybridization efficiency as demonstrated in both SPR and QCM-D results, which are comparable to previous reports. Our method paves the way for customizing binding efficiency and target probe density based on the distance between functional groups. By changing the headgroup size of the precursor monolayer, different distances between functional group can be formed, allowing for an ability to tailor distances between molecules. This method may allow for improvement in DNA array technology.Chapter 5. Long-Term Stability of Self-Assembled Monolayers in Biological Media The study of long term stability of self-assembled monolayer (SAM) in biological media is of importance in evaluating its usefulness for applications in implantable biochips, biosensors, or biological microelectromechanical system (bioMEMs) devices for drug delivery. / (cont.) To minimize biofouling effects, researchers have investigated protein/cell adhesion resistant surface-bound materials such as poly(ethylene glycol) or oligo(ethylene glycol) terminated self-assembled monolayers. However, no long term study in biological media has been done. To address the issue of moderate to long-term stability of SAMs for bioMEMS device modification, alkanethiol and oligo(EG) terminated alkanethiol monolayers were prepared and studied after immersion in either phosphate buffer saline (PBS) or calf serum. Here, undecanethiol (CllH23SH) and tri(ethylene glycol) terminated undecanethiol (HO(C2H40)3C H22SH) self-assembled monolayers (SAMs) on clean gold surfaces were prepared and characterized. The SAMs were then immersed into either phosphate buffered saline (PBS) or calf serum. The SAM samples were emmersed and investigated using several analytical techniques at numerous points over the next 35 days. Contact angles and current densities in voltammetry changed dramatically for the PBS samples over the time period, particularly after 21 days. Results indicate substantial loss of the integrity of the SAM. Similar alterations with time were observed for the calf serum samples in both contact angle and voltammetry measurements. X-ray photoelectron spectroscopy indicates that the likely origin is desorption of the alkanethiol moiety as evidenced by appreciable loss of the S 2p signal after 35 days. Additionally, this work may serve as a starting point for further studies of surface chemical modification methods for moderate to long-term minimization of biofouling for in vivo applications. / by Thanh-Nga T. Tran. / Ph.D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references. / Superior semicircular canal dehiscence (SCD) syndrome is a recently defined clinical disorder in which patients present to the clinic with vestibular symptoms, auditory symptoms, or both. Understanding the effect of SCD, a hole in the bony superior canal, on hearing will broaden our understanding of the mechanics of the inner ear and lead to better diagnosis and treatment of SCD syndrome. We evaluate the effect of SCD on cochlear responses to both air- and bone- conducted sound. In chinchilla SCD produces reversible changes in cochlear potential: an increased sensitivity to bone-conducted sound and a decreased sensitivity to air-conducted sound. Such differences in air- and bone-conducted sound (air-bone gaps) are typically associated with a conductive hearing loss due to middle-ear pathology; however, a SCD is an inner-ear pathology. We hypothesize that the SCD acts as a 'third window' into the inner ear, shunting volume velocity away from the cochlea and through the dehiscent canal, altering cochlear responses to sound. To qualitatively evaluate this hypothesis we measured sound-induced fluid motion within the SCD as well as the effect of SCD on sound-induced stapes velocity and middle-ear input admittance. / (cont.) Our results are consistent with the hypothesis that the SCD introduces a low-impedance shunt pathway. To quantitatively evaluate the third-window hypothesis we developed an anatomically and physiologically constrained lumped-element mechano-acoustic model that predicts the effect of SCD on cochlear responses. Our model also predicts the effect of anatomical variations, such as dehiscence size and location, on auditory sensitivity. This work demonstrates that an air-bone gap can be caused by pathological changes in inner-ear mechanics. Additionally, our model provides a framework that will be of direct clinical benefit in understanding the variable effects of SCD among patients. / by Jocelyn E. Songer. / Ph.D.

Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 130-139). / Pharmacological inactivation studies have shown that the frontal eye field (FEF) is critical for executing saccades to remembered locations. FEF neurons increase their firing rate during the three epochs of the memory-guided saccade task: visual stimulus presentation, the delay interval, and motor preparation. It is unclear, though, whether FEF activity during each epoch is necessary for memory-guided saccade execution. To address this question, techniques for millisecond-precise optical inactivation of the primate brain were invented. A red-shifted halorhodopsin (Jaws) and a novel large-volume tissue illuminator were used in two rhesus macaques to inactivate part of the FEF at different times during the memory-guided saccade task. Neuronal recordings showed that the inactivated tissue volume (i.e., the volume where the firing rate of >80% of neurons decreased by >80%) spanned several cubic millimeters, which is consistent with histological findings. When the target was in the inactivated receptive field, error rates (i.e., failures to execute memory-guided saccades to the proper target location) increased in both monkeys with inactivation during either the target, delay, or motor period. This implies that FEF neuronal activity contributes to performance throughout the memory-guided saccade task. / by Leah C. Acker. / Ph. D.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references (leaves 62-68). / Sensory cells and afferent auditory neurons in the cochlea receive efferent feedback via olivocochlear (OC) neurons originating in the brainstem's olivary complex. The OC system comprises 1) medial (M)OC neurons that decrease electromotility in outer hair cells, and 2) lateral (L)OC neurons that elicit slow excitation or inhibition of auditory nerve dendrites that contact inner hair cells. We investigated the organization and function of the LOC system by immunohistochemical and physiological studies in mice with unilateral stereotaxic destruction of LOC cell bodies. Double immunostaining in control cochleas and brainstems revealed two cytochemical subgroups of LOC neurons: a majority cholinergic population and a minority dopaminergic population. The observation of two LOC subgroups is consistent with reports that LOC activation can either excite or inhibit auditory nerve activity. In lesioned mice, we observed two physiological abnormalities. First, ipsilateral ears were more vulnerable to noise-induced auditory nerve dysfunction, consistent with speculation that dopaminergic transmission controls glutamate excitotoxicity of auditory nerve dendrites after acoustic overexposure. / (cont.) Second, ipsilateral auditory nerve responses were increased while contralateral responses were decreased, and the normal tight correlation of neural excitability between the two ears was disrupted. A neural circuit is proposed to explain bilateral effects from unilateral LOC innervation. We suggest that a key LOC function is to bilaterally balance ascending inputs to olivary complex neurons, which are responsible for computing sound location based on the interaural level differences coded in the response rates of auditory nerve fibers. / by Keith N. Darrow. / Ph.D.

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2006. / Includes bibliographical references (leaves 29-30). / Some have argued that the genetic differences between continentally defined groups are relatively small and unlikely to have biomedical significance. In this study, the extent of variation between continentally defined groups was evaluated. Small numbers of randomly selected single nucleotide polymorphisms from the International HapMap Project were used to train classifiers for prediction of ancestral continent of origin. Predictive accuracy was then tested on independent data sets. A high degree of genetic similarity implies that groups will be difficult to distinguish, especially when only a limited amount of genetic information is used. It is shown that the genetic differences between continentally defined groups are sufficiently large that one can accurately predict ancestral continent of origin using only a minute, randomly selected fraction of the genetic variation present in the human genome. Genotype data from only 50 random single nucleotide polymorphisms can be used to predict ancestral continent of origin in the primary test data set with an average accuracy of 95%. / (cont.) Single nucleotide polymorphisms were also characterized as being in introns, coding exons, regulatory regions and regions coding for untranslated mRNA and classifiers constructed using only single nucleotide polymorphisms from a specific category. Predictive accuracy was similar across all of the classifiers created in this manner. Single nucleotide polymorphisms useful for prediction of ancestral continent of origin are common and distributed relatively evenly throughout the genome. These findings demonstrate the extent of variation between continentally defined groups and argue strongly against the contention that genetic differences between groups are too small to have biomedical significance. / by Dominic J. Allocco. / S.M.

Thesis (Ph.D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2000. / Includes bibliographical references (p. 133-137). / This research characterizes the respiratory system dynamics at the initiation and termination of utterances and determines correlations of physiological measures with acoustic cues for these prosodic boundaries. The analysis includes boundaries within a breath as well as boundaries that are aligned with the initiation and termination of exhalation. Simultaneous recordings of the acoustic signal, airflow, esophageal pressure and lung volume were collected during read isolated utterances and short paragraphs. These measures were used to derive estimates of recoil forces of the chest wall, net muscular forces, and the area of the airway constriction. Data are presented from four subjects (two men, two women), all native speakers of American English. Perceptual ratings for initial and final prominent syllables and the locations of pauses within the utterance were also collected. For speech boundaries th.i.t are aligned with breath boundaries, utterance initiation occurs during a rapid transition in muscular effort. Sound begins as soon as conditions permit and these conditions consistently occur during net inspiratory muscular force. Alveolar pressure reaches an initial peak (PpI) that is, in most cases, correlated to the relaxation characteristic of the chest wall. The timing of Pp1 generally coincides with a prominent syllable if that syllable is the first or second syllable in the utterance and precedes later prominences. Pressure at phonation onset is, on average, near 0.3PpI for utterances initiated with a voiced sonorant and is near 0. 8Pp1 for utterances initiated with a voiceless fricative. Phonation termination results from an approximately 3-fold increase in glottal area and a J-3 cm H20 fall in pressure. Irregular fundamental frequency (FO) at the end of voicing, in many cases, does not fit the classical definition of glottalization. Instead, voicing terminates with increasing glottal area, and FO becomes irregular during the increase. In some cases, regular FO resumes as glottal area continues to increase. Distinct respiratory gestures are made at pauses within a breath. The pressure is reduced by 2-3 cm H20, on average, during a period of relatively little volume change. The findings in this research show that the role of the respiratory system in speech production goes beyond a more traditional view of this role as one of simply providing a relatively constant driving pressure during speech. / by Janet Slifka. / Ph.D.

Thesis (Ph. D.)--Harvard--Massachusetts Institute of Technology Division of Health Sciences and Technology, 2000. / Includes bibliographical references (leaves 167-175). / by Christopher Joseph Long. / Ph.D.