Quantifying tissue volumes in pediatric brains from magnetic resonance (MR) images can provide insight into etiology and onset of neurological disease. Unbiased volumetric analysis can be applied to large population studies when automated image processing is possible. Standard segmentation strategies using adult atlases fail to account for varying tissue contrasts and types associated with the rapid growth and maturational changes seen in early neurodevelopment. The goal of this project was to develop an automated pipeline and two age-specific atlases capable of providing accurate tissue classification despite these challenges. The automated pipeline consisted of a stepwise initial atlas-to-subject registration, expectation maximization (EM) atlas based segmentation, and a post-processing level set segmentation for improved white/gray matter separation. This level set segmentation is a 3D and multiphase adaptation of a 2D method intended for use on images with the types of intensity Inhomogeneities found in MR images. The initial tissue maps required to determine spatial priors for the one-year-old atlas were created by manually cleaning the results of an adult atlas and the automated pipeline. Additional tissue maps were incrementally added until the spatial priors were sufficiently representative. The neonate atlas was similarly created, starting with the one-year-old atlas.

This dissertation contributes to an ongoing debate on the types of linguistic features which can be acquired in a second language by looking at the multiple learning challenges related to the ergative case system (the appearance of –ne with the subject) in Hindi-Urdu by classroom learners. Some hypotheses in second language research hold that interpretable features (features which contribute semantic information) can be acquired in a second language, whereas uninterpretable features (features which express grammatical information) cannot be easily acquired, if ever. Additionally, hypotheses in second language processing hold that the second language learners are able to process semantic information but not grammatical information. This dissertation investigates at the acquisition process of second language learners of Hindi-Urdu acquiring the uninterpretable ergative case. In Hindi-Urdu, the subject of a sentence appears with the ergative case marker –ne, when the verb is transitive and in the perfective aspect. In my dissertation, I test the validity of the aforementioned hypotheses and investigate the acquisition and acquisitional process of ergative case in L2 Hindi-Urdu by L1 English speakers by analyzing data collected by using an acceptability/grammaticality judgement task, a self-paced reading task and a production task from Hindi-Urdu learners and native speakers.

The blood system consists of two main lineages: myeloid and lymphoid. The myeloid system consists of cells that are part of the innate immune response while the lymphoid system consist of cells that are part of humoral response. These responses protect our bodies from foreign pathogens. Thus, malignancies in these systems often cause complications and mortality. Scientists world wide have been researching alternatives to treat hematologic disorders and have explored induced pluripotent stem cells (iPSCs) and the conversion of one cell type to another. First, iPS cells were generated by overexpression of four transcription factors: Oct4, Sox2, Klf4 an cMyc. These cells closely resemble embryonic stem cells (ESCs) at the molecular and cellular level. However, the efficiency of cell conversion is less than 0.1%. In addition, many iPS colonies can arise from the same culture, but each has a different molecular signature and potential. Identifying the appropriate iPS cell lines to use for patient specific therapy is crucial. Here we demonstrate that our system is highly efficient in generating iPS cell lines, and cell lines with silent transgenes are most efficient in differentiating to different cell types . Second, we are interested in generating hematopoietic stem cells (HSCs) from fibroblasts directly, without going through the pluripotent state, to increase efficiency and to avoid complications associated with a stem cell intermediate. However, a robust hematopoietic reporter system remains elusive. There are multiple hematopoietic reporter candidates, but we demonstrate that the CD45 gene was the most promising. CD45 is expressed early during hematopoiesis on the surface of HSCs; and as HSCs differentiate CD45 levels increase. Furthermore, the CD45 reporter is only active in hematopoietic cells. We were able to confirm the utility of the CD45 reporter using an in vitro and an in vivo murine model. In conclusion, The goal of this research was to expand the knowledge of stem cell reprogramming, specifically the reprogramming of iPS cells. Furthermore, it is our desire that the CD45 reporter system will undergo further validation and find utility in clinical and cell therapy environments.

The ways in which teachers and students speak to each other in middle and secondary English language arts classrooms is integral to the type of learning that occurs there. Ways of engaging in “classroom talk” can be characterized as teacher-centered or student-centered. Teacher-centered classroom talk typically unfolds as a sequence of three steps – a teacher asks a question with a predetermined answer, a student responds, and the teacher evaluates the response. In contrast, student-centered classroom talk is engaging, collaborative, and reciprocal – in these scenarios, teachers and students both ask questions that have multiple answers, students talk to other students, and the discussions grow organically. Working with students in the student-centered way is called dialogic teaching, and while we know dialogic teaching is beneficial to student learning, we also know engaging in this type of teaching is fraught with difficulties. This study sought to explore these difficulties by examining the lived experience of dialogic teaching through the perspectives of six middle and secondary English language arts teachers. The study offers portraits of each teacher’s respective experiences as well as themes that cut across all the teachers’ experiences. Insights are offered about dialogic teaching in terms of lesson planning and attitudes toward students; these insights are termed dialogic by design and dialogic by disposition, respectively.

Memory CD8 T cells offer increased protection to immune hosts by rapidly eliminating pathogen-infected cells during re-infection. Generating and sustaining a protective memory CD8 T cell response is considered a hallmark of adaptive immunity. Extensive research has been devoted to understanding the parameters affecting memory CD8 T cell generation after infection or immunization in order to design the most effective vaccines. An accepted notion in the field is that increased protection from re-infection is afforded by the generation of a large number of memory CD8 T cells. Consecutive prime-boost immunization strategies that elicit secondary responses are often used to increase the absolute numbers of memory CD8 T cells. While parameters affecting the generation of primary memory CD8 T cells are well known, the factors influencing the development of re-stimulated secondary CD8 T cell responses remain understudied. Here, I addressed the mechanisms involved in the generation and development of secondary memory CD8 T cells. I found that the time at which primary memory CD8 T cells enter into an immune response during re-infection impacts their fate and differentiation into secondary memory CD8 T cells. Late-entry of primary memory CD8 T cells into an immune response (relative to the initiation of infection) not only facilitates expression of transcription factors associated with memory formation in secondary effector CD8 T cells, but also influences the ability of secondary memory CD8 T cells to localize within the lymph nodes, produce interleukin-2 cytokine (IL-2), and undergo robust antigen-driven proliferation. The timing of stimulation of primary memory CD8 T cells also impacts the duration of expression of the high-affinity IL-2 receptor (CD25) on secondary effector CD8 T cells and their sensitivity to IL-2 signaling. Importantly, by blocking or enhancing IL-2 signaling in developing secondary CD8 T cells, I verify the role of IL-2 in controlling the differentiation of secondary CD8 T cell responses. The data I present herein suggest that the process of primary memory-to-secondary memory CD8 T cell differentiation is not fixed and can be manipulated, a notion with implications in the design of future prime-boost vaccination approaches. Although vaccines are designed and intended to benefit a range of individuals, at times the efficacy of a vaccination regime depends on the overall health status of a host. Thus, in another portion of my thesis work I explored the extent to which obesity compromises the differentiation and maintenance of protective memory CD8 T cell responses. I found that diet-induced obesity did not impact the maintenance of pre-existing memory CD8 T cells, including their acquisition of a long-term memory phenotype (i.e., CD27hi, CD62Lhi, KLRG1low) and function (i.e., cytokine production, antigen-driven secondary expansion, and memory CD8 T cell-mediated protection). Additionally, diet-induced obesity did not influence the differentiation and maintenance of newly evoked memory CD8 T cell responses, in inbred and outbred hosts, that were generated in response to different types of systemic (LCMV, L. monocytogenes) and/or localized (influenza virus) infections. Interestingly, I found that the rate of naïve-to-memory CD8 T cell differentiation after a peptide-coated dendritic cell immunization was similar in lean and obese hosts. This suggests that obesity-associated inflammation is unlike pathogen- or adjuvant-induced inflammation, and does not influence the development of an endogenous memory CD8 T cell response. My studies reveal that the obese environment does not influence the development or maintenance of memory CD8 T cell responses that are either primed before or after obesity is established. This is a surprising notion with implications for future studies aiming to elucidate the role of obesity in susceptibility to infection and vaccine efficacy. Collectively, the data presented here further the understanding of memory CD8 T cell responses in contexts of health and disease.

Many physiological and pathological processes, such as wound healing and tissue remodeling, are heavily influenced by continuous mechanical cell-cell and cell-ECM communication. Abnormalities that may compromise the biomechanical communication between the cells and the ECM can have significant repercussions on these physiological and pathological processes. The state of the mechanical environment and the reciprocal communication of mechanical signals between the ECM and the cell during wound healing and aged dermal tissue regeneration may be key in controlling the quality of the structure and physical properties of regenerated tissue. This dissertation encompasses a series of studies developed for characterizing the effects of mechanical cues on altering and controlling tissue remodeling, and regeneration in the context of controlling scar formation during wound healing, and the maintenance and regeneration of the dermal extracellular matrix (ECM) during aging. In order to achieve this goal, in vitro models that contained some features of the provisional ECM, and the ECM of the dermis were developed and subjected to an array of quantifiable mechanical cues. Wound models were studied with different mechanical boundary conditions, and found to exhibit differences in initial short-term structural remodeling that lead to significant differences in the long-term synthesis of collagen after four weeks in culture. Dermal models seeded with fibroblasts from individuals of different ages were treated with a hyaluronic acid (HA)-based dermal filler. Changes in the mechanical environment of the dermal models caused by swelling of the hydrophilc HA, resulted in changes in the expression of mechanosensitive, and ECM remodeling genes, essential for the maintenance and regeneration of dermal tissue. Taken together, these data provide new insights on the role of mechanical signals in directing tissue remodeling.

The Patient-Centered Medical Home (PCMH) is a new model for primary care delivery intended to improve the care experience for both patients and providers, improve the health of populations, and reduce health care costs. Adopting the PCMH model into practice requires considerable investment of time and resources which often act as barriers for many small primary care practices; especially in rural areas. Few studies have examined performance of the PCMH model in rural clinics that have successfully implemented the model. It is important to obtain a comprehensive understanding of how context from the surrounding environment relates to implementation and performance of the model and whether there are differences between rural and urban primary care clinics. This study used a sequential explanatory mixed methods approach to assess differences in performance of the Patient Aligned Care Team (PACT) model between rural and urban primary care clinics within the Veterans Health Administration (VHA). Generalized Estimating Equations with repeated measures were used to estimate associations between rurality and five process-oriented endpoints among a national sample of 891 VHA primary care clinics. Results indicate that, after adjusting for patient characteristics and clinic structural capacity, clinics located in large rural or small/isolated rural areas demonstrated difficulty with enhancing access through use of non-traditional encounters (i.e. telephone visits, group visits, or secured messaging) and facilitating care coordination through post-discharge follow-up compared to urban clinics. Findings also suggest that rural clinics were more likely to struggle to meet system-wide performance standards for these same two PACT-related processes than their urban counterparts. A multiple-case study of five VHA primary care clinics was conducted to obtain a contextual understanding of the relationships between rurality and performance of PACT processes from the perspective of primary care staff engaged in PACT implementation. A comparison of the experiences of staff across the five cases revealed cross-cutting themes that are important to understanding the implementation and performance of PACT-related processes within these clinics. These themes included: both rural and urban clinics experience distance-related barriers; patient preferences and behavior impact performance of PACT-related processes; and primary care clinics experience frequent change. Findings from this qualitative assessment highlight the importance of understanding the unique context and circumstances experienced by each clinic and how they relate to performance and implementation of the PACT model. Insights gained through the qualitative assessment revealed that performance of PACT is influenced by complex relationships with both internal and external context. Combination of both quantitative and qualitative methods provided a more comprehensive understanding of these relationships beyond what could have been learned from a solitary assessment of standardized metrics by gaining additional context directly from the voices of those engaged in PACT care delivery. Identifying differences in PACT performance between rural and urban clinics calls attention to the possibility of unique advantages and challenges for PACTs delivering care to rural patients which need further exploration. Findings from this study contribute to the current understanding of PCMH implementation in rural settings by moving beyond the barriers related to structural capacity to performance of processes aligned with PCMH principles. More widespread implementation of PCMH will require additional attention to the complex relationships between the PCMH and surrounding context in order for primary care practices to successfully implement the model.

Polychlorinated Biphenyls (PCBs) are persistent organic pollutants known for their toxicological effects. Though industrial production of legacy PCBs was banned in 1977, they can still be measured in nearly all environmental matrices. The Chicago Sanitary and Ship Canal (CSSC) is lined with industry and the receiving waters to the Stickney Water Reclamation Plant, the World's largest waste water treatment plant and was therefore speculated to be a potential source of PCBs to the Greater Chicago Area. Surficial sediment samples were acquired along a 45 km stretch of the CSSC, from Kedzie Ave. to Lockport. PCBs in the bulk sediment were extracted using accelerated solvent extraction while PCBs in the porewater were extracted using solid phase micro extraction. The PCBs were identified and quantified using a variation on EPA method 1668C. A total of 176 individual and coeluting PCBs were identified and quantified in this study. The sum of PCB concentrations in the bulk sediment was found to range from 70 to 4970 ng/g dry wt. The sum of PCB concentrations in the freely dissolved sediment-porewater was found to range from 2 to 366 ng/L. The bulk and porewater concentrations were used to estimate an average mass flow rate of PCBs through the CSSC of 368 kg/y. The large mass flow rate of PCBs passing through the CSSC and the fact that the CSSC connects Lake Michigan to the Mississippi River suggest that continued monitoring of PCB concentrations are necessary to better understand the transport and fate of PCBs in and out of the Great Chicago Area.

The objectives of this study are (1) to develop an accurate and efficient fatigue analysis procedure that can be used in reliability analysis and reliability-based design optimization (RBDO) of composite wind turbine blades; (2) to develop a wind load uncertainty model that provides realistic uncertain wind load for the reliability analysis and the RBDO process; and (3) to obtain an optimal composite wind turbine blade that satisfies target reliability for durability under the uncertain wind load. The current research effort involves: (1) developing an aerodynamic analysis method that can effectively calculate detailed wind pressure on the blade surface for stress analysis; (2) developing a fatigue failure criterion that can cope with non-proportional multi-axial stress states in composite wind turbine blades; (3) developing a wind load uncertainty model that represents realistic uncertain wind load for fatigue reliability of wind turbine systems; (4) applying the wind load uncertainty model into a composite wind turbine blade and obtaining an RBDO optimum design that satisfies a target probability of failure for a lifespan of 20 years under wind load uncertainty. In blade fatigue analysis, resultant aerodynamic forces are usually applied at the aerodynamic centers of the airfoils of a blade to calculate stress/strain. However, in reality the wind pressures are applied on the blade surface. A wind turbine blade is often treated as a typical beam-like structure for which fatigue life calculations are limited in the edge-wise and/or flap-wise direction(s). Using the beam-like structure, existing fatigue analysis methods for composite wind turbine blades cannot cope with the non-proportional multi-axial stress states that are endured by wind turbine blades during operation. Therefore, it is desirable to develop a fatigue analysis procedure that utilizes detailed wind pressures as wind loads and considers non-proportional multi-axial stress states in fatigue damage calculation. In this study, a 10-minute wind field realization, determined by a 10-minute mean wind speed V10 and a 10-minute turbulence intensity I10, is first simulated using Veers’ method. The simulated wind field is used for aerodynamic analysis. An aerodynamic analysis method, which could efficiently generate detailed quasi-physical blade surface pressures, has been developed. The generated pressures are then applied on a high-fidelity 3-D finite element blade model for stress and fatigue analysis. The fatigue damage calculation considers the non-proportional multi-axial complex stress states. A detailed fatigue damage contour, which indicates the fatigue failure locally, can be obtained using the developed fatigue analysis procedure. As the 10-minute fatigue analysis procedure is deterministic in this study, the calculated 10-minute fatigue damage is determined by V10 and I10. It is necessary to clarify that the rotational speed of the wind turbine blade is assumed to be constant (12.1 rpm) and the pitch angle is fixed to be 0 degree for different wind conditions, since the rotational speed control and pitch angle control have not been considered in this study. For predicting the fatigue life of a wind turbine, a fixed Weibull distribution is widely used to determine the percentage of time the wind turbine experiences different mean wind speeds during its life-cycle. Meanwhile, fixed turbulence intensities are often used based on the designed wind turbine types. These simplifications, i.e., fixed Weibull distribution and fixed turbulence intensities, ignore the realistic uncertain wind load when designing a reliable wind turbine system. In the real world, both the mean wind speed and turbulence intensity vary constantly over one year, and their annual distributions are different at different locations and in different years. Thus, it is necessary to develop a wind load uncertainty model that can provide a realistic uncertain wind load for designing reliable wind turbine systems. In this study, 249 groups of measured wind data, collected at different locations and in different years, are used to develop a dynamic wind load uncertainty model. The dynamic wind load uncertainty model consists of annual wind load variation and wind load variation in a large spatiotemporal range, i.e., at different locations and in different years. The annual wind load variation is represented by the joint probability density function of V10 and I10. The wind load variation in a large spatiotemporal range is represented by the probability density functions of five parameters, C, k, a, b, and τ, which determine the joint probability density function of V10 and I10. In order to obtain the RBDO optimum design efficiently, a deterministic design optimization (DDO) procedure of a composite wind turbine blade has been first carried out using averaged percentage of time (probability) for each wind condition. A wind condition is specified by two terms: 10-minute mean wind speed and 10-minute turbulence intensity. In this research, a probability table, which consists of averaged probabilities corresponding to different wind conditions, is referred as a mean wind load. The mean wind load is generated using the dynamic wind load uncertainty model. During the DDO process, the laminate thickness design variables are tailored to minimize the total cost of composite materials while satisfying the target fatigue lifespan of 20 years. It is found that, under the mean wind load condition, the fatigue life of the initial design is only 0.0004 year. After the DDO process, even though the cost at the DDO optimum design is increased by 31.5% compared to that at the initial design, the predicted fatigue life at the DDO optimum design is significantly increased to 19.9995 years. Reliability analyses of the initial design and the DDO optimum design have been carried out using the wind load uncertainty model and Monte Carlo simulation. The reliability analysis results show that the DDO procedure reduces the probability of failure from 100% at the initial design to 49.9% at the DDO optimum design considering only wind load uncertainty. In order to satisfy the target 2.275% probability of failure, it is necessary to further improve the fatigue reliability of the composite wind turbine blade by RBDO. Reliability-based design optimization of the composite wind turbine blade has been carried out starting at the DDO optimum design. Fatigue hotspots for RBDO are identified among the laminate section points, which are selected from the DDO optimum design. Local surrogate models for 10-minute fatigue damage have been created at the selected hotspots. Using the local surrogate models, both the wind load uncertainty and manufacturing variability has been included in the RBDO process. It is found that the probability of failure is 50.06% at the RBDO initial design (DDO optimum design) considering both wind load uncertainty and manufacturing variability. During the RBDO process, the normalized laminate thickness design variables are tailored to minimize the total cost of composite materials while satisfying the target 2.275% probability of failure. The obtained RBDO optimum design reduces the probability of failure from 50.06% at the DDO optimum design to 2.28%, while increasing the cost by 3.01%.

The purpose of this study was to investigate how design changes in Cochlear Nucleus cochlear implants (CIs) (CI24M, CI24R, CI24RE and CI422) affected electrode impedance and ECAP measures, and to determine if these design changes affected post-lingually deafened adults and children with congenital hearing loss in a similar way. Results of this study showed that electrode impedance was inversely related to the area of the electrode contacts in the array: lowest for the full-banded CI24M CI and highest for adults who used the CI422 device which has the smallest electrode contacts of all four devices. The noise floor of the NRT system likely plays a significant role in the finding that CI users with older devices (the CI24M, and CI24R CIs) had higher ECAP thresholds than individuals with the CI24RE electrode array. The position of the electrode array in the cochlea was also found to have a significant effect on ECAP measures. CI users with modiolar hugging (the CI24R and CI24RE CIs) electrode arrays were found to have lower ECAP thresholds than CI users whose electrode arrays were seated more laterally in the cochlear duct (e.g. the CI24M and CI422 implants). The position of the electrode contacts relative to the modiolus of the cochlea was found to be related to slope of the ECAP growth functions. The lowest slopes were found in CI24RE users. It also had a significant impact on the width of the channel interaction function. Electrode arrays seated further from the modiolus have significantly more channel interaction than electrode arrays that hug the modiolus of the cochlea. Differences between results recorded from post-lingually deafened adults and children with congenital hearing loss were minimal. The difference only reflected on the ECAP slopes. Slopes in children with congenital hearing loss were significantly steeper than those recorded from adults. This may indicate that children with congenital hearing loss may have better neural survival than adults with acquired hearing loss. In conclusion, the results of the current study show evidence of the effects of variations in design and function of the implanted components of the Nucleus CI. Perhaps the most significant finding from the current data set is that electrode arrays located closer to the modiolus of the cochlea have lower thresholds and exhibit less channel interaction than electrode arrays that are positioned more laterally. An argument could be made that lower stimulation levels and less channel interaction may result in better outcomes and/or longer battery life. For CI candidates who do not have significant residual acoustic hearing, the CI24RE implant might be a better choice than the more recently introduced CI422 electrode array.