Objective: The purpose of this investigation is to test whether a poroelastic model with enhanced structure could capture in vivo interstitial pressure dynamics in a brain undergoing mock surgical loads. Methods: Using interstitial pressure data from a porcine study, we use an inverse model in order to reconstruct these pressures and estimate material properties of the brain tissue. This is done in four distinct reconstruction parameterizations to isolate the influence of the three features studied. These features are the dural septa, the treatment of the ventricles, and treatment of the brain as a saturated media. Results: The approach demonstrates accurate capturing of the interstitial pressure dynamics, pressure gradients, tissue deformation, and the presence of intracranial pressure compartmentalization. Conclusion: This study demonstrates that in order to capture appropriate pressure compartmentalization, interstitial pressure gradients, pressure transient effects, and deformations within the brain, the proposed boundary conditions and structural enhancement coupled with a heterogeneous description invoking partial saturation was needed. Significance: To our knowledge there has not been a systematic study of the influence of anatomical features within brain models. Also, the quality of interstitial pressure fits shown here has not been seen within previous literature. Lastly, the common assumption of saturated tissue is challenged and the noted compliance related to our fits likely reflects remaining anatomical structures not yet captured.

Laparoscopic liver surgery is challenging to perform due to a compromised ability of the surgeon to localize subsurface anatomy in the constrained environment. While image guidance has the potential to address this barrier, intraoperative factors such as insufflation and variable degrees of organ mobilization from supporting ligaments may generate substantial deformation. The severity of laparoscopic deformation in humans has not been characterized, and current laparoscopic correction methods do not account for the mechanics of how intraoperative deformation is applied to the liver. In this work, we first measure the degree of laparoscopic deformation at two insufflation pressures over the course of laparoscopic-to-open conversion in 25 patients. With this clinical data alongside a mock laparoscopic phantom setup, we report a novel biomechanical correction approach that leverages anatomically load-bearing support surfaces including ligament attachments to iteratively reconstruct and account for intraoperative deformations. Laparoscopic deformations were significantly larger than deformations associated with open surgery, and our correction approach yielded subsurface target error of 6.7±1.3 mm and surface error of 0.8±0.4 mm using only sparse surface data with realistic surgical extent. Laparoscopic surface data extents were examined and found to impact registration accuracy. Lastly, we demonstrate viability of the correction method with clinical data.

High field magnetic resonance imaging (MRI) offers several advantages over imaging at low field strengths, namely increased spectral resolution, better contrast due to longer T1 relaxation, higher signal to noise ratio (SNR), and better parallel imaging performance. However, many imaging techniques require strong flip angle uniformity and fast readouts, which are susceptible to trajectory errors. Optimization and machine learning methods are introduced to reduce image artifacts and decrease RF inhomogeneities in high field acquisitions. This is accomplished by employing algorithms that 1) exploit redundancies inherent in parallel imaging and 2) exploit redundant information in multi-subject data to learn characteristic relationships between RF and image parameters. First, an algorithm to reduce trajectory errors--Trajectory Auto-Corrected image Reconstruction (TrACR)-- is presented. TrACR was evaluated with in vivo 7 Tesla (7T) brain data from non-Cartesian acquisitions. TrACR reconstructions reduced blurring and streaking artifacts and bear similar quality to images reconstructed using trajectory measurements. Second, an extension of TrACR is presented for echo planar imaging acquisitions to reduce trajectory and phase errors. EPI-TrACR is validated in vivo at 7T, at multiple acceleration and multishot factors, and in a time series, and consistently reduces image artifacts. Finally, to improve transmit field uniformity, a method is introduced for predicting tailored RF shims. RF-shim Prediction by Iteratively Projected Ridge Regression (PIPRR) was validated in simulation for single-slice shimming for 100 phantom human heads. PIPPR-predicted shims reduced profile inhomogeneity and maintained comparable specific absorption rate (SAR) efficiency and homogeneity to that of directly designed shims. PIPRR predictions for a new patient require just milliseconds, reducing compute time for RF shimming by orders of magnitude.

The identification of patterns of highly correlated low frequency Magnetic Resonance Imaging (MRI) signals in resting states provides a powerful approach to assess brain functional organization. However, functional MRI (fMRI) studies rely on detecting hemodynamic changes as revealed by blood oxygenation level-dependent (BOLD) signals to infer underlying neuronal activity. Precise interpretations of fMRI studies require a deep understanding of the relationships between BOLD signal changes and their corresponding electrophysiological signatures [e.g., local field potentials (LFPs)]. This thesis evaluates whether brain inter-regional correlations in resting state fMRI signals reliably measure functional connectivity, and investigates the dynamic nature of functional connectivity in both fMRI and frequency-specific LFPs. The spatial local correlation profiles and dynamic changes in functional connectivity between LFPs and submillimeter resolution BOLD at 9.4T are compared within primary somatosensory (S1) cortex in squirrel monkeys. This thesis reports high spatial correspondence at a columnar level between BOLD and LFPs, and suggests that resting state fMRI dynamic connectivity is reflective more of low frequency LFP coherence than high frequency LFP coherence in S1 cortex.

Precision medicine is the concept of incorporating patient-specific variability into prevention and treatment strategies. Precision medicine initiatives in oncology have primarily focused on the use of genetics to classify and pharmaceutically target cancers. While the genetic-centric approach to precision cancer therapy has merit in selecting therapy, an expanded effort is required to guide optimal dosing of those therapies. Fundamentally, treatment response is driven by patientâ, tumorâ, and cellâspecific pharmacologic properties. We posit that mathematical models that explicitly incorporate such processes will improve the ability to deliver precision therapy. In this Dissertation, we develop a combined experimental-mathematical modeling framework to establish a mechanistic mathematical model of doxorubicin treatment response in triple negative breast cancer (TNBC). TNBC is a subgroup of invasive cancers that lack significant expression of the estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Lacking specific pharmaceutical targets, the current approach to neoadjuvant therapy for locally advanced disease employs a combination of cytotoxic drugs, including doxorubicin. We present a coupled pharmacokinetic/pharmacodynamic (PK/PD) model that describes how the concentration and duration of doxorubicin therapy shape subsequent cell population dynamics in vitro. The proposed model accurately captures doxorubicin uptake and treatment response dynamics in a panel of cell lines, and the model can be leveraged to predict response to a wide range of doxorubicin treatment timecourses. We propose the equivalent dose metric, a value derived from the mechanistic PK/PD model, to explicitly account for variable cell line pharmacological properties. We demonstrate that the equivalent dose is a more precise means of quantifying combination therapies and comparing cell line response to therapy relative to current approaches. Finally, we extend the model to describe treatment response in heterogeneous populations. We demonstrate that the biological composition of the population significantly impacts treatment response dynamics, and we propose a PK-based mechanism to explain the behavior. By studying various experimental perturbations within a single mechanistic, mathematical framework, this approach provides a means for more efficient discovery of predictive biomarkers and translation of those discoveries into patient care.

<p> Aerobic glycolysis (Warburg effect) is accompanied by significant alterations in cellular redox state and constitutes one of the hallmarks of cancer cell metabolism. Label-free multi-photon microscopy (MPM) methods based on two-photon excited fluorescence (TPEF) have been used extensively to form high-resolution images of redox state in cells and tissues based on intrinsic NADH and FAD+ fluorescence. However, changes in cellular redox alone are insufficient to fully characterize cancer metabolism and predict invasive potential. We demonstrate that label-free MPM measurements of TPEF-derived redox state (optical redox ratio, ORR = FAD+/(FAD + NADH)) combined with coherent Raman imaging of lipid formation can be used to quantitatively characterize cancer cells and their relative invasive potential. In addition, we confirm, using coherent Raman and deuterium labeling methods, that glucose is a significant source for the cellular synthesis of lipid biomass in glycolytic breast cancer cells. Live cell metabolism was imaged in 3D models of primary mammary epithelial cells (PME) and 2 cancer cell lines, T47D and MDA-MB-231. While we observed overlap in the distribution of the optical redox ratio between these different cell lines, the combination of ORR and lipid volume fraction derived from coherent Raman signals provided complementary independent measures and clear separation. Furthermore, we observed an increase in both lipid synthesis and consumption rates in E2-treated T47D cancer cells cultured in deuterated glucose by tracking the formation and disappearance of deuterated lipids. These results suggest that due to the relatively wide range of ORR values that reflect the natural diversity of breast cancer cellular redox states, the addition of lipid signatures obtained from coherent Raman imaging can improve our ability to characterize and understand key metabolic features that are hallmarks of the disease.</p><p>

The goal of this dissertation was to understand the role of age-related changes in muscle mechanical properties in the control of upright posture in humans. First, a methodology for estimating subject-specific muscle properties in healthy young and older individuals was developed. Magnetic resonance and ultrasound imaging were used in conjunction with dynamometer experiments, musculoskeletal modeling, and numerical optimization to estimate the properties of the dorsiflexor and individual plantarflexor (gastrocnemius and soleus) muscles for 12 young and 12 older adults (balanced for gender). With aging there were declines in maximal isometric strength and increases in series-elastic stiffness in the male subjects, but no differences in the female subjects. Regardless of gender, there were age-related changes in the shape of the force-velocity relation, such that the older subjects produced less relative force during both concentric and eccentric muscle contractions. The second study tested the balance abilities of the same subjects under a variety of static (quiet stance, leaning forward/backward) and dynamic (swaying at preferred/imposed frequencies, maximal reaching, external perturbation) conditions. The older adults performed more poorly on most of the balance tasks. While maximal isometric force made a smaller than expected contribution to predicting balancing ability, the force-length, force-velocity and force-extension properties of the muscles were all predictive of the age-related declines in balance control, explaining ∼40% of the variance as independent predictors and ∼50% when these factors were combined. Finally, a feedback-driven inverted pendulum model of postural control was developed, which incorporated realistic representations of young and old dorsiflexor and individual plantarflexor muscles using the previously estimated mechanical properties. A sensitivity analysis was performed by manipulating the properties of the plantarflexor muscles. The balancing ability of the model was most influenced by the optimal length of the contractile component and the slack length of the series elastic component of the plantarflexor muscle models. The quiet stance model highlighted the importance of the force-length relation of muscle to the stabilization of upright posture. This dissertation demonstrated that there are age-related changes in the dorsi- and plantarflexor mechanical properties, and these changes are associated with the declines in postural control that accompany aging.

The current, most widely used method to screen for latent tuberculosis infection is the Mantoux tuberculin skin test, where tuberculin is injected into a patient's arm and may result in a cutaneous induration forming at the site of injection. A diameter measurement of the resultant induration, recorded using a ruler and ball point pen, is currently used to indicate the presence of latent tuberculosis infection. Limitations associated with the tuberculin skin test procedure are the crudeness of the induration measurement method, the follow-up clinical visit required from patients to have their induration measured, and the need for trained clinicians who can perform the induration measurement. These limitations motivated research into a mobile phone-based screening system which can be used to obtain a more accurate measurement of the induration without the need for a second visit to the clinic by patients. The prototype screening tool consists of a user interface for capturing induration images and a backend processing system that produces a threedimensional reconstruction of the induration for measurement. Recommendations from previous studies on the prototype screening tool, which involved evaluation of the mobile application using mock induration images, included improving the accuracy of measuring the induration and evaluating the tool on real induration images. The aim of this study was to evaluate the existing backend system and explore an alternative assessment approach for assessing the induration. This was achieved through the following objectives: (1) applying the current backend system to real induration images, (2) examining the need for three-dimensional reconstruction for delineation of the induration for measurement and (3) exploring an alternative method for the assessment of induration images using deep learning. Results for the first objective showed the three-dimensional reconstruction to be unsuccessful on real images. This was due to the homogeneity between the indurations and the surrounding skin, rendering the algorithm ineffective in delineating the indurations to obtain the diameter measurement required for diagnosis. The second objective involved determining whether the image orientation or induration height affected the diagnostic measurement. It was found that real indurations are much flatter and more subtle compared to the mock indurations used in the previous studies. This motivated an alternative image assessment approach using deep learning. However, deep learning approaches require large databases of annotated images to prevent overfitting on training data. The last objective therefore involved the design and implementation of a generative adversarial network for generation of synthetic images from a limited number of real images, which allowed the generation of an unlimited number of realistic-looking synthetic images from 150 real induration images.

Excessive production of Type I collagen is the hallmark of fibrotic disorders. The production of Type I collagen is mainly regulated at post-transcriptional level by a COLLAGEN mRNAs binding protein La ribonucleoprotein domain family member 6 (LARP6). LARP6 binds the conserved secondary structure of COLLAGEN mRNAs, the 5' stem loop (5'SL), and by recruiting accessory factors regulates translation of COLLAGEN mRNAs. This regulation is the predominant mechanism to maintain the high production of type I collagen in fibrotic disorders. In this dissertation, we studied the two roles of LARP6: the role of LARP6 and nonmuscle myosin in translation of COLLAGEN mRNAs and the function of LARP6 interacting with PIH1D3 protein in embryonic development. The LARP6-nonmuscle myosin interaction was found to be important for partition of COLLAGEN mRNAs to the ER membrane and the LARPs-PIH1D3 interaction maintains normal organ development in Xenopus embryos. In the first part of the dissertation, we report the importance of LARP6 and nonmuscle myosin filaments in regulated delivery of COLLAGEN mRNAs to the ER membrane. We show that COLLAGEN mRNAs are targeted to ER membrane through SRP independent pathway, and that LARP6 and myosin filaments mediate this process. Our conclusions were based on the following lines of evidence. First, inhibition of the translation, which blocks the translation of signal peptide essential for the SRP mediated delivery, did not affect the correct targeting of COLLAGEN mRNAs to ER membrane. These results suggest the COLLAGEN mRNAs are delivered to ER by the SRP independent pathway. The SRP independent delivery of mRNAs to ER usually depends on RNA binding proteins. LARP6 is a RNA binding protein that binds specifically to COLLAGEN mRNAs with high affinity. Therefore, we speculated that LARP6 is involved in COLLAGEN mRNAs trafficking. When COLLAGEN mRNAs distribution was analyzed in LARP6 knock down cells, the mRNAs were retained in the cytosol and were inefficiently targeted to the ER membrane. Rescue of the LARP6 expression restored the proper ER delivery of COLLAGEN mRNAs. This strongly suggests that LARP6 mediates COLLAGEN mRNAs targeting independent of the SRP pathway. Nonmuscle myosin was found to bind COLLAGEN mRNAs by interacting with LARP6. As the SRP independent pathway usually depends on motor proteins, we further analyzed the role of nonmuscle myosin in COLLAGEN mRNAs targeting. Depolimerization of nonmuscle myosin strongly inhibited partitioning of COLLAGEN mRNAs to the ER membrane. Thus, two components of the mechanism that regulates trafficking of COLLAGEN mRNAs to the ER membrane were discovered. The consequences of the blockade of this mechanism are dramatic. When either LARP6 was knocked down or nonmuscle myosin filaments were disrupted, COLLAGEN mRNAs targeting to the ER membrane were impaired, and collagen polypeptides accumulated in the cytosol. Further analysis of the accumulated collagen polypeptides showed that the polypeptides were hyper modified, probably by excessive hydroxylations. This indicated a severe defect in type I collagen synthesis. We proposed a new molecular model of LARP6 and nonmuscle myosin mediated COLLAGEN mRNAs targeting, with profound implications for understanding the pathogenesis of fibrotic disorders. In the second part of the project, we studied the LARP6 -PIH1D3 interaction. We carried out yeast two hybrid screen using LARP6 as a bait to identify the new components of LARP6 network. One protein showed interaction was PIH1D3, which is a new protein with unknown function. We discovered that LARP-PIH1D3 interaction plays an important role in Xenopus embryos development, and this interaction is mediated by La domain of LARPs and PIH1 domain of PIH1 family. We first verified the LARP6-PIH1D3 interaction in vivo by coimmunoprecipitation experiments and further confirmed that the interaction is direct by pull down assay. We identified the domains of LARP6 and PIH1D3 involved in the interaction, as this may be important for understanding the function. We found that the La domain of LARP6 is necessary and sufficient for binding PIH1D3. LARP6 is a member of the LARP superfamily of proteins, composed of five members, all family members share one domain, the La domain. Therefore, we studied if other LARPs can bind PIH1D and found LARP1, LARP3 and LARP6 interact with PIH1D3 through the La domain. PIH1D3 is also a member of PIH1 protein family, which has three members, D1, D2 and D3. We also discovered the PIH1 domain of PIH1D3 is responsible for the interaction with LARP proteins and that two of PIH1 family members PIH1D1 and PIH1D3 can interact with LARP6. Thus, interactions between family members of the two groups of proteins have been discovered. The function of the La domain in LARPs proteins is unknown and this is the first description of its functional role. We next studied the function of PIH1D3. Since the expression of PIH1D3 mRNA was not detectable in the available cell lines and PIH1D3 is a new protein, we investigated the pattern of PIH1D3 expression in tissues. Interestingly, we found that PIH1D3 is exclusively expressed in rat testis but not in other tissues. Other family members PIH1D1, and PIH1D2 were also expressed predominantly in testis, with low expression in liver and kidney. These results suggest the specific function of PIH1D3 in testis and also indicate that PIH1D1 and PIH1D3 may perform similar functions. We surmised that PIH1D3 protein may also have a role in embryonic development, so we used microinjections in Xenopus embryos to study this. Temporal expression of PIH1D3 during the Xenopus development indicated that the gene is expressed from stage 2 to stage 23 throughout the early development, while the spatial expression was restricted to neural tube plate and secreted epithelial cells at the early stages, and to the nerve system at late stages. Knock down of PIH1D3 in Xenopus embryos caused severe defects in kidney with development of a large cyst. This phenotype resembles the PKD(poly cystic kidney disease) [1]. Because it is known that mutation of genes, which encode for the structural components of cilia result in cystic kidney disease [2], we speculated that PIH1D3 may be related to the cilia formation in Xenopus embryos. Since our biochemical data showed a strong interaction of PIH1D3 and members of LARP proteins, we speculated that the both protein families regulate ciliogenesis in Xenopus development. In summary, we mapped the interactions network between LARPs family and PIH1 family, and demonstrated that PIH1D3 plays an important role in Xenopus development. Our work linked PIH1D3 function to the polycystic kidney development and ciliogenesis and laid the foundation for the new research on regulation of ciliogenesis. / A Dissertation submitted to the Department of Biomedical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester, 2015. / February 3, 2015. / Collagen, LARP6, liver fibrosis, mRNA targeting, xenopus development / Includes bibliographical references. / Branko Stefanovic, Professor Directing Dissertation; Hengli Tang, University Representative; Myra Hurt, Committee Member; Yanchang Wang, Committee Member.

Includes bibliographical references (leaves 109-114). / Sulphide as a precipitating agent is effective as it facilitates the removal of heavy metals to very low residual concentrations (ppm - ppb levels) over a wide pH range, owing to the low solubilities (Ksp) of metal sulphides. However, previous work on metal sulphide precipitation has highlighted a number of challenges. The low solubilities of metal sulphides in combination with the rapid kinetics of sulphide precipitation leads to rapid, uncontrolled metal sulphide precipitate formation. The extremely high supersaturations result in high rates of nucleation, leading to the formation of particles with undesirable characteristics. In this thesis, to gain insight on the metal sulphide precipitation of nickel and cobalt from the RES, a simplified model system, consisting of a synthetic NiS04 solution with a concentration of 200ppm Ni2+, was utilised to determine the effect of H2S(g) as a precipitating agent.