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Title: Measurement of the charged current muon neutrino differential cross section on scintillator with zero pions in the final state with the T2K on/off-axis near detectors
Creator: Cudd, Andrew Bruce
Date: 2020
Collection: Electronic Theses & Dissertations
Description: The Tokai to Kamioka (T2K) is a long-baseline neutrino oscillation experiment in Japan producing precise measurements of neutrino oscillations and neutrino interactions with nuclear targets. T2K utilizes a muon (anti-)neutrino beam produced at the J-PARC proton accelerator facility which is measured at a suite of near detectors, ND280 and INGRID, and the far detector, Super-Kamiokande. One of the dominant systematic uncertainties for the oscillation analysis is from the uncertainty in...
Show moreThe Tokai to Kamioka (T2K) is a long-baseline neutrino oscillation experiment in Japan producing precise measurements of neutrino oscillations and neutrino interactions with nuclear targets. T2K utilizes a muon (anti-)neutrino beam produced at the J-PARC proton accelerator facility which is measured at a suite of near detectors, ND280 and INGRID, and the far detector, Super-Kamiokande. One of the dominant systematic uncertainties for the oscillation analysis is from the uncertainty in neutrino interaction modeling with complex nuclei, which will eventually become the limiting uncertainty for the next generation of neutrino oscillation experiments. Therefore measurements of neutrino cross sections on nuclear targets is essential for understanding how to model these complicated nuclear interactions. This thesis presents a novel neutrino cross section measurement utilizing both of the T2K near detectors, ND280 and INGRID, in a joint statistical fit. Because the T2K near detectors are exposed to neutrinos from the same beamline, the uncertainties in the neutrino flux prediction will be correlated. This fact combined with the different neutrino energy spectra seen at each detector will allow for some separation of flux and cross section effects, and presents an opportunity to study the neutrino cross section as a function of energy using the same neutrino beam. This analysis is the first cross section measurement on T2K to use samples from multiple detectors in the same beamline. This thesis presents a description of the statistical analysis framework, the event selection, the treatment of systematic uncertainties, and the extracted muon neutrino CC0pi double differential cross section in bins of muon kinematics for ND280 and INGRID, including the correlations between the detectors.
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Title: Use of administative claims data to design and emulate a clinical trial in acute stroke patients comparing rehabilitation at inpatient rehabilitation facilities to skilled nursing facilities
Creator: Simmonds, Kent P.
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Stroke affects nearly 800,000 people every year in the United States and is a leading cause of adult disability. After hospitalization half of stroke patients continue to require medical and rehabilitation services provided at inpatient rehabilitation facilities (IRFs) or skilled nursing facilities (SNFs). In general, IRFs provide time-intensive therapy for two to three weeks, while SNFs provide moderately intensive therapy for four- to five-weeks. There is substantial variation in the...
Show moreStroke affects nearly 800,000 people every year in the United States and is a leading cause of adult disability. After hospitalization half of stroke patients continue to require medical and rehabilitation services provided at inpatient rehabilitation facilities (IRFs) or skilled nursing facilities (SNFs). In general, IRFs provide time-intensive therapy for two to three weeks, while SNFs provide moderately intensive therapy for four- to five-weeks. There is substantial variation in the utilization of these alternative rehabilitation settings, but their relative comparative effectiveness remains uncertain. A randomized controlled trial (RCT) would provide an unbiased comparative effectiveness estimate, but the design of such a trial is complicated by several practical and ethical issues. The overarching purpose of this dissertation was to use Medicare claims data to inform the design and to emulate such a trial. In the first aim, we sought to identify patient and hospital level factors that were associated with IRF or SNF discharge and characterize the heterogeneity of hospital effects that influenced discharge to an IRF (vs. SNF). From a retrospective cohort of 145,894 stroke patients, we used multi-level multivariable models to identify several patient- and hospital- level factors that were independently associated with discharge setting. We also showed that hospitals contributed around a third of the variation in IRF (vs. SNF) discharge, but there was substantial variation in the effect that specific hospitals had on influencing IRF discharge. The second aim, was to identify a target trial population that optimized the explanatory-pragmatic balance of a subsequent RCT. To identify this population, we profiled hospitals based on their propensity to discharge stroke patients to IRFs (vs. SNFs) and inferred IRF and SNF referral networks for each hospital. The final target trial population included 44,950 patients (30.8% of the starting sample) who were treated at 441 hospitals (14.5%) and subsequently discharged to 745 IRFs (64.8%) and 5,974 SNFs (48.2%).The third aim was to emulate three alternate RCTs that compared patient outcomes at IRFs vs. SNFs. Trial #1 used the target trial population identified in Aim 2, while trials #2 and 3 excluded increasingly infrequently used IRFs and SNFs. Comparative effectiveness was estimated using a matched propensity score analysis. Overall, on a relative basis, patients treated at IRFs were between 18-35% more likely to be successfully discharged home (i.e., alive and at home for >30 days) and were between 11-15% less likely to die within one year of acute care discharge. The variation in the effect size estimates across the trials was driven by poorer outcomes among patients treated at infrequently used SNFs. Finally, we identified that a moderate sized unmeasured confounder would nullify the observed differences.In conclusion, we identified that referring hospitals are a major driver of IRF or SNF use, and that patients treated at IRFs had better outcomes (relative to SNF patients). However, our results were limited by the inability to adjust for potentially important unmeasured confounders. A pragmatic RCT would eliminate such biases and provide a more valid comparative effectiveness estimate of these two alternative rehabilitation settings.
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Title: Understanding free-carrier accumulation in semiconductor nanomaterials : plasmonic behavior, charge storage energetics, and quantum confinement resilience of colloidal indium nitride nanocrystals
Creator: Liu, Zhihui
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Heavily doped semiconductor nanocrystals (NCs) are promising materials that can reversibly and substantially store electrical charges. Indium nitride (InN) is a particularly interesting semiconductor material for studying charge storage processes. Colloidal InN NCs are spontaneously degenerately doped with carrier densities large enough to lead to strong localized surface plasmon resonances (LSPR) in the infrared (IR) part of the spectrum. Unfortunately, many fundamental quantities that...
Show moreHeavily doped semiconductor nanocrystals (NCs) are promising materials that can reversibly and substantially store electrical charges. Indium nitride (InN) is a particularly interesting semiconductor material for studying charge storage processes. Colloidal InN NCs are spontaneously degenerately doped with carrier densities large enough to lead to strong localized surface plasmon resonances (LSPR) in the infrared (IR) part of the spectrum. Unfortunately, many fundamental quantities that ultimately control the behavior of colloidal InN NCs are currently unknown. In this thesis, we focused on advancing our current understanding of the properties of colloidal InN NCs, with special emphasis on the quantification of free electron density, the LSPR behavior, the charge storage ability, the screening effect on phonon behaviors and few other important fundamental quantities such as the electron effective mass, Fermi level, conduction band (CB) edge potential and IR transition oscillator strength.To understand the LSPR behavior of InN NCs, we first evaluated the free carrier density with a direct, model-independent quantification. We found that the number of free electrons per as-prepared InN NC is directly proportional to the NC volume, such that the free electron density is a size-independent quantity. Furthermore, we demonstrated that free electrons in InN NCs can be reversibly extracted with redox species, which leads to a direct way to manipulate the LSPR. Importantly, the LSPR energy in InN NCs barely shifts with free electron density, a behavior strikingly at odds with what is typically observed in other semiconductor plasmonic systems. These unusual plasmonic signatures are shown to arise from the nonparabolicity of the CB dispersion, which leads to a change in the electron effective mass with the number of free electrons per NC, thus mitigating the shift of LSPR in InN NCs.Consequently, we estimated the charge storage capability of InN NCs by pinning the chemical potential of InN NCs to redox-active molecular species. These studies directly yielded precise information on the Fermi level and on the chemical capacitance of InN NCs, which allowed the CB edge potential of InN NCs to be quantitatively determined for the first time. Surprisingly, the CB edge in InN NCs hardly showed any sign of quantum confinement effects, even for NCs sizes that were clearly smaller than the excitonic Bohr radius of InN. This "resilience to quantum confinement" effect was shown to also arise from the same nonparabolic dispersion effects described above.In addition, the light harvesting ability of free electrons in InN NCs was evaluated by calculating the molar absorptivity per free electron. This value directly yielded the optical oscillator strength of LSPR. We found that optical oscillator strength (per free electron) is independent of NC.Finally, the effects of free electrons on lattice vibrations were also explored. We demonstrated that free electrons weakened the A1(LO) phonon mode by screening the Coulombic restoring force induced by the lattice distortion. The A1(LO) mode frequency red-shifted linearly with the increasing free electron density. This relationship provided a fast way to estimate free electron density of InN NCs by measuring Raman spectroscopy.
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Title: Interfacial challenges of all-solid-state Li-ion batteries : multi-scale computational approach
Creator: Tian, Hong-Kang
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "All-solid-state Li-ion batteries (ASSLB) with solid electrolytes (SEs) have enhanced safety and higher volumetric/gravimetric energy density than conventional Li-ion batteries with liquid electrolytes. However, the applications of ASSLB are still limited by the interfacial issues, such as Li dendrite growth through the SEs and the high SE/electrode interfacial resistance. This thesis developed a multi-scale computational approach, combining Density Functional Theory (DFT) calculation and...
Show more"All-solid-state Li-ion batteries (ASSLB) with solid electrolytes (SEs) have enhanced safety and higher volumetric/gravimetric energy density than conventional Li-ion batteries with liquid electrolytes. However, the applications of ASSLB are still limited by the interfacial issues, such as Li dendrite growth through the SEs and the high SE/electrode interfacial resistance. This thesis developed a multi-scale computational approach, combining Density Functional Theory (DFT) calculation and Finite Element Method (FEM), to investigate the interfacial challenges in ASSLB. The Li dendrite growth through pores in SEs and the resulting short-circuit limit the highest current density in ASSLB. The underlining mechanism of Li dendrite nucleation and growth in SEs is still unclear. A DFT model was developed to evaluate the electronic properties of the bulk and surface structures of different SEs. It was revealed that the reduced bandgap and trapped electrons on the pore and crack surfaces are the main reasons for Li dendrite to form. The DFT computed material properties were compared for different SEs, and it was found that the ranked Li dendrite resistance in these SEs, based on the surface electronic properties instead of mechanical properties, is consistent with a broad range of experimental observations. The DFT results also served as the input to a phase-field model, which predicted the formation of isolated Li dendrite that matched with experimental observations. Furthermore, materials design strategies were proposed based on the critical material properties that can resist Li dendrite growth in SEs.The physically imperfect contact at interfaces is formed during the fabrication process of ASSLB and gets worse during cycling, resulting in high interfacial resistance and damaging to the battery performance. A 1D FEM battery model was constructed to investigate the relationship between the contact area and the discharging performance. Furthermore, the multi-scale Persson's contact theory was applied to predict the necessary pressure to prevent ASSLB capacity degradation due to contact area loss during the cycling of ASSLB. Cracked SE and SE/electrode interfaces also increase the impedance in ASSLB. The mechanical degradation of ASSLB is expected to be more severe than that in traditional Li-ion batteries with liquid electrolytes, as the solid-electrolyte also imposes mechanical constraints on the deformation of electrodes. A coupled electrochemical-mechanical FEM model was developed to evaluate the stress development in ASSLB. Two sources of volume change, namely the expansion/shrinkage of electrodes due to lithium concentration change and the interphase formation at the SE/electrode interface due to the decomposition of SEs, were considered. The favorable SE decomposition reactions and the associated volume change were predicted by DFT calculations. It was found that the SE-decomposition induced stress can be much larger than the electrodes volume changes due to Li concentration change, up to tens of GPa, if there are no voids in ASSLB to release some induced-stress. This model can also be used to design 3D ASSLB architectures to minimize the stress generation in ASSLB."--Pages ii-iii.
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Title: Signal processing and machine learning approaches to enabling advanced sensing and networking capabilities in everyday infrastructure and electronics
Creator: Ali, Kamran (Scientist)
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Mainstream commercial off-the-shelf (COTS) electronic devices of daily use are usually designed and manufactured to serve a very specific purpose. For example, the WiFi routers and network interface cards (NICs) are designed for high speed wireless communication, RFID readers and tags are designed to identify and track items in supply chain, and smartphone vibrator motors are designed to provide haptic feedback (e.g. notifications in silent mode) to the users. This dissertation focuses on...
Show moreMainstream commercial off-the-shelf (COTS) electronic devices of daily use are usually designed and manufactured to serve a very specific purpose. For example, the WiFi routers and network interface cards (NICs) are designed for high speed wireless communication, RFID readers and tags are designed to identify and track items in supply chain, and smartphone vibrator motors are designed to provide haptic feedback (e.g. notifications in silent mode) to the users. This dissertation focuses on revisiting the physical-layer of various such everyday COTS electronic devices, either to leverage the signals obtained from their physical layers to develop novel sensing applications, or to modify/improve their PHY/MAC layer protocols to enable even more useful deployment scenarios and networking applications - while keeping their original purpose intact - by introducing mere software/firmware level changes and completely avoiding any hardware level changes. Adding such new usefulness and functionalities to existing everyday infrastructure and electronics has advantages both in terms of cost and convenience of use/deployment, as those devices (and their protocols) are already mainstream, easily available, and often already purchased and in use/deployed to serve their mainstream purpose of use.In our works on WiFi signals based sensing, we propose signal processing and machine learning approaches to enable fine-grained gesture recognition and sleep monitoring using COTS WiFi devices. In our work on gesture recognition, we show for the first time thatWiFi signals can be used to recognize small gestures with high accuracy. In our work on sleep monitoring, we propose for the first time aWiFi CSI based sleep quality monitoring scheme which can robustly track breathing and body/limb activity related vital signs during sleep throughout a night in an individual and environment independent manner.In our work on RFID signals based sensing, we propose signal processing and machine learning approaches to effectively image customer activity in front of display items in places such as retail stores using commercial off-the-shelf (COTS) monostatic RFID devices (i.e. which use a single antenna at a time for both transmitting and receiving RFID signals to and from the tags). The key novelty of this work is on achieving multi-person activity tracking in front of display items by constructing coarse grained images via robust, analytical model-driven deep learning based, RFID imaging. We implemented our scheme using a COTS RFID reader and tags.In our work on smartphone's vibration based sensing, we propose a robust and practical vibration based sensing scheme that works with smartphones with different hardware, can extract fine-grained vibration signatures of different surfaces, and is robust to environmental noise and hardware based irregularities. A useful application of this sensing is symbolic localization/tagging, e.g. figuring out whether a user's device is in their hand, pocket, or at their bedroom table, etc. Such symbolic tagging of locations can provide us with indirect information about user activities and intentions without any dedicated infrastructure, based on which we can enable useful services such as context aware notifications/alarms. To make our scheme easily scalable and compatible with COTS smartphones, we design our signal processing and machine learning pipeline such that it relies only on builtin vibration motors and microphone for sensing, and it is robust to hardware irregularities and background environmental noises. We tested our scheme on two different Android smartphones.In our work on powerline communications (PLCs), we propose a distributed spectrum sharing scheme for enterprise level PLC mesh networks. This work is a major step towards using existing COTS PLC devices to connect different types of Internet of Things (IoT) devices for sensing and control related applications in large campuses such as enterprises. Our work is based on identification of a key weakness of the existing HomePlug AV (HPAV) PLC protocol that it does not support spectrum sharing, i.e., currently each link operates over the whole available spectrum, and therefore, only one link can operate at a time. Our proposed spectrum sharing scheme significantly boosts both aggregated and per-link throughputs, by allowing multiple links to communicate concurrently, while requiring a few modifications to the existing HPAV protocol.
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Title: Development of a fast and cost-effective asphalt mixture fatigue test system
Creator: Seitllari, Aksel
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Fatigue cracking is one of the critical distress modes in asphalt pavements. Accurate prediction and evaluation of fatigue performance are crucial to extending the service life of asphalt mixtures. Naturally, laboratory testing methods for fatigue characterization are time-consuming and require sophisticated procedures. Any effort to improve the speed and quality of the information gained from laboratory fatigue tests is valuable. This research work presents the results of a study...
Show moreFatigue cracking is one of the critical distress modes in asphalt pavements. Accurate prediction and evaluation of fatigue performance are crucial to extending the service life of asphalt mixtures. Naturally, laboratory testing methods for fatigue characterization are time-consuming and require sophisticated procedures. Any effort to improve the speed and quality of the information gained from laboratory fatigue tests is valuable. This research work presents the results of a study investigating the possibility of implementing a new approach to characterize asphalt mixture fatigue behavior. This new approach includes cyclic tests run on cylindrical asphalt specimens in three-point beam mode (herein referred to as three-point bending cylinder (3PBC) geometry). Timoshenko beam theory along with the viscoelastic continuum damage (VECD) theory was implemented to model the mechanical response of the specimens. An excellent correlation between the results of 3PBC tests and uniaxial push-pull fatigue tests were observed. The 3PBC setup possesses the most advantages of uniaxial push-pull tests and includes more advantages such as not requiring a saw to cut the ends of the sample, not requiring gluing operation (and the gluing jig) and the possibility of estimating Poisson's ratio from the data. The proposed 3PBC approach was evaluated through laboratory tests conducted on various asphalt mixtures with varying binder types, mix components, and volumetric properties. The approach proposed herein was validated through finite element analysis. In addition, ruggedness evaluation of the 3PBC testing approach through varying factors and their levels were investigated and presented.
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Title: Investigation of students' causal mechanistic reasoning in undergraduate organic chemistry
Creator: Crandell, Olivia Marie
Date: 2020
Collection: Electronic Theses & Dissertations
Description: The undergraduate organic chemistry course is a prerequisite course for many students who plan to pursue careers in chemistry and chemical engineering. It also serves those students who wish to pursue professional careers in medicine, dentistry, and veterinary sciences. Previous research on student learning in organic chemistry shows that students struggle to understand ideas such as acid-base reactions and structure-property relationships which are foundational concepts on which more complex...
Show moreThe undergraduate organic chemistry course is a prerequisite course for many students who plan to pursue careers in chemistry and chemical engineering. It also serves those students who wish to pursue professional careers in medicine, dentistry, and veterinary sciences. Previous research on student learning in organic chemistry shows that students struggle to understand ideas such as acid-base reactions and structure-property relationships which are foundational concepts on which more complex concepts are built. Furthermore, the typical organic chemistry course emphasizes students use of the electron-pushing formalism to represent how bonds are formed and broken in chemical reactions. Expert organic chemists use this formalism to represent predicted reaction mechanisms that explain the formation of products. Numerous studies have characterized student difficulties using electron-pushing mechanisms in an expert-like way as well as associating underlying chemical principle with the representations. We suggest that deep understanding of chemical reactions and their underlying chemical principles can be developed by engaging students in causal mechanistic explanation as part of a transformed organic chemistry course that emphasizes students using their knowledge of electrostatics, structure-property relationships, and energy to engage in explanation of chemical phenomena. Our goal is to engage students in as specific type of explanation called in casual mechanistic explanation which includes reasoning about the underlying causal factors in conjunction with the underlying entities and their activities that bring the phenomenon about. The studies reported here use a qualitative approach to elicit student' written explanations and drawn reaction mechanisms for various chemical reactions. Students were sampled at multiple time points over the course of their two-semester organic course to investigate how student reasoning changes overtime. Students participants were enrolled in either the beforementioned transformed organic chemistry course or were enrolled in an untransformed course that we refer to as the traditional context. This traditional context served as a control group for which to compare possible changes in reasoning for students enrolled in the transformed course sequence. Findings suggest that student engagement in causal mechanistic reasoning varies depending on students' general chemistry and organic chemistry course experience as well as the nature of the prompt eliciting the reasoning. Findings also suggest that students are generally capable of drawing mechanistic arrows that would generally be considered correct, however triangulating student reasoning with a detailed analysis of students' drawings, we found that typical organic chemistry assessment items that lack a reasoning component may overestimate student understanding. Our investigations also revealed student difficulties invoking the correct nucleophilic substitution process for a given reaction. Students often invoked an SN1 mechanistic process incorrectly, despite their engagement in casual mechanistic reasoning. Implications of these findings for organic chemistry instruction and assessment are discussed along with implications for future research.
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Title: Cross-disciplinary integration : through argumentation and for sustainability
Creator: Laursen, Bethany
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Today's sustainability problems require wisdom that can only come by integrating different ways of knowing for each situation. When academic researchers undertake sustainability work, many of these ways of knowing come from different disciplines. However, years of cross-disciplinary research and practice have yielded only metaphorical or abstract understandings of what researchers actually do to integrate disciplinary contributions. Without a clear understanding of the actions researchers...
Show moreToday's sustainability problems require wisdom that can only come by integrating different ways of knowing for each situation. When academic researchers undertake sustainability work, many of these ways of knowing come from different disciplines. However, years of cross-disciplinary research and practice have yielded only metaphorical or abstract understandings of what researchers actually do to integrate disciplinary contributions. Without a clear understanding of the actions researchers take to accomplish integration, we have been left with confusion, inconsistent proxy measures, or lengthy learning by trial and error. This has left sustainability and other wicked problems either in the hands of veterans with decades of experience or subject to unreliable integrative attempts by newer investigators. To aid practice through clearer understanding, I open the black box of cross-disciplinary integration, explicating one the main processes that investigators use to integrate disciplinary contributions into cross-disciplinary insights: reasoning together.Through three articles, the dissertation shows that (1) as a field, argumentation studies provides valuable, actionable insights into cross-disciplinary integration, (2) one of the main processes of cross-disciplinary integration is reasoning together, and (3) the details of cross-disciplinary reasoning specify and clarify two existing, more abstract models of cross-disciplinary integration. Thus, overall, the dissertation clarifies what has been an urgent but confusing process in sustainability investigations, and, in doing so, it points the way to practical improvements in sustainability research policies, norms, and education.
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Title: Systematic analysis of the signal responsive gene regulatory network governing Myxococcus xanthus development
Creator: Saha, Shreya
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Studies of signal-induced gene expression in bacteria have contributed to understanding of how bacteria cope with environmental stress. As an extensively studied model, Myxococcus xanthus provides fascinating insights into how changes at the level of gene expression enable which bacteria to survive environmental insults such as nutrient limitation. Upon starvation M. xanthus cells glide into aggregates and form mounds that mature into fruiting bodies as some cells form spores. Previously, our...
Show moreStudies of signal-induced gene expression in bacteria have contributed to understanding of how bacteria cope with environmental stress. As an extensively studied model, Myxococcus xanthus provides fascinating insights into how changes at the level of gene expression enable which bacteria to survive environmental insults such as nutrient limitation. Upon starvation M. xanthus cells glide into aggregates and form mounds that mature into fruiting bodies as some cells form spores. Previously, our group defined 24-30 h poststarvation as the critical period for commitment to spore formation, when cells commit to form spores despite perturbation of the starvation signal by nutrient addition. The process of multicellular development that culminates in sporulation is governed by a network of signal-responsive transcription factors that integrate signals for starvation and cellular alignment. In this dissertation I present the first systematic approach to elucidate the network dynamics during the commitment period.In the network, MrpC is a starvation-responsive transcription factor, whereas FruA is a transcription factor that responds to cellular alignment conveyed by C-signaling. Transcription of fruA is dependent on MrpC binding, and FruA activity is proposed to be posttranslationally regulated by C-signaling, although the mechanism is unknown. FruA and MrpC cooperatively regulate transcription of the dev operon. My systematic analysis of the network dynamics supported a model in which posttranslational activation of FruA by C-signaling is critical for dev transcription and for commitment to spore formation. Similar to dev, MrpC and C-signal-activated FruA combinatorially controlled transcription of the late-acting fadIJ operon involved in spore metabolism. Regulation of late-acting operons implicated in spore coat biogenesis (exoA-I, nfsA-H, MXAN_3259-MXAN_3263) was discovered to be under complex control by MrpC and FruA. My evidence suggests that transcription of these operons depends at least in part on a C-signal-dependent switch from negative regulation by unactivated FruA to positive regulation by activated FruA during the period leading up to and including commitment to sporulation. MrpC negatively regulated exo and MXAN_3259 during mound formation, but positively regulated nfs. During commitment to sporulation, MrpC continued to positively regulate nfs, switched to positive regulation of MXAN_3259, and continued to negatively regulate exo. A third transcription factor, Nla6, appeared to be a positive regulator of all the late genes. We propose that in combination with regulation by Nla6, differential regulation by FruA in response to C-signaling and by MrpC controls late gene expression to ensure that spore resistance and surface characteristics meet environmental demands.
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Title: Dynamic behavior of liquid nanofoam and its functionalized materials and structures
Creator: Li, Mingzhe (Of Michigan State University)
Date: 2019
Collection: Electronic Theses & Dissertations
Description: The use of energy absorption materials and structures for protection in collision, explosion, and impact attacks has long been recognized as one of the most effective approaches to reduce and prevent personnel injuries and infrastructure damages. These systems have been widely used in many industrial, medical, and military applications. Recently, an advanced energy absorption material, liquid nanofoam (LN), has been developed with high energy absorption capacity as well as high energy...
Show moreThe use of energy absorption materials and structures for protection in collision, explosion, and impact attacks has long been recognized as one of the most effective approaches to reduce and prevent personnel injuries and infrastructure damages. These systems have been widely used in many industrial, medical, and military applications. Recently, an advanced energy absorption material, liquid nanofoam (LN), has been developed with high energy absorption capacity as well as high energy mitigation rate. The LN system, composed of a liquid phase and a hydrophobic nanoporous media, employs the pressurized liquid flow in nano-channels as its energy absorption mechanism. However, previous studies of the LN mainly focused on the quasi-static behaviors. Only limited effort had been made to understand the working mechanism of the LN under dynamic impacts which are the practical loading condition in scenarios such as auto collisions, blunt impacts and blasts. This dissertation presents the first systematic experimental study on the dynamic behavior of the LN system and reveals the deformation mechanism of LN under high strain rates. These scientific findings open up new applications of the LN functionalized materials and structures.The intermediate and high strain rate responses of LN systems have been characterized by a lab-customized drop tower apparatus. The competition between liquid infiltration and porous structure deformation at high strain rates has been elucidated at nanoscale. Results show that liquid infiltration into nanopores is independent of the axial buckling stress of the nanopore, and thus is the dominating deformation mechanism of the LN. More importantly, the activation of liquid infiltration as well as liquid flow in nanopores are much faster than the nanoscale porous structure deformation. This much-enhanced liquid flow speed in nano-environment is experimentally quantified for the first time. It has been demonstrated that the liquid infiltration speed is adaptive to the impact energy level, which provides mechanistic explanation for the high energy absorption efficiency of LN at high strain rates. Results also suggest that LN in the liquid marble form performs better than the liquid form upon high strain rate impact due to the macroscopically homogenous structure in the liquid marble form.Based on the fundamental understanding of the deformation mechanism and the adaptive nanoscale liquid flow, LN has been integrated into other materials and structures to generate multifunctional materials and structures, e.g. LN-filled tube (LNFT), hybrid hydrogel, and advanced seat belt retractor system. In LNFT, LN is utilized as a novel filling material in thin-walled tube. The resulted LNFTs possess enhanced average post-buckling strength and energy absorption capacity due to the "perfect bonding" between the LN and the tube wall. Also, based on the adaptive nanoscale liquid flow, the LNFT is more efficient for energy mitigation at elevated strain rates. In LN-based hybrid hydrogels, LN is formulated and encapsulated in hydrogel by integrating nanoporous particles into the 3D polymer network. Liquid infiltration mechanism, combined with the chemical and physical cross-linking effects, leads to the improvement of both strength and toughness of the hybrid hydrogel, which is not seen in current hydrogels. In LN-based seat belt retractor system, LN is employed as the load-bearing component, which allows additional payout tunability, adaptability, and reusability in the system.The knowledge gained in this study will facilitate the design of next generation of advanced LN-functionalized materials and structures for extreme working conditions.
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Title: Determinants of eating behaviors of us army ROTC cadets in Midwestern universities
Creator: George, Beatriz G.
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Young adults 18-25 years of age, the largest demographic of the military, experience a high burden of obesity and eating disorders (ED) despite an emphasis on physical fitness, body composition, and operational readiness. Etiologic models for obesity and ED suggest body dissatisfaction (BD), dieting, negative affect (NA), and affect regulation represent potentially shared pathways. However, no studies have examined these factors and their shared pathways in military personnel, including ROTC...
Show moreYoung adults 18-25 years of age, the largest demographic of the military, experience a high burden of obesity and eating disorders (ED) despite an emphasis on physical fitness, body composition, and operational readiness. Etiologic models for obesity and ED suggest body dissatisfaction (BD), dieting, negative affect (NA), and affect regulation represent potentially shared pathways. However, no studies have examined these factors and their shared pathways in military personnel, including ROTC cadets. The overarching aim of this dissertation research was to investigate if ED symptoms were associated with body mass index (BMI), an indicator of obesity, and to describe potential correlates of their development. Three specific aims of this research focus on: 1) the prevalence and correlates of ED risk classification and symptoms in ROTC cadets, 2) the association between ED symptoms and BMI, and their potentially shared mechanisms, psychological inflexibility related to BD and dieting, and 3) the gaps in knowledge about eating behaviors and mediators of eating behaviors within the ROTC context and from perspective of ROTC cadets.In 2018, US Army ROTC cadets (n = 205) were recruited from two Midwestern universities and completed questionnaires about demographics, military-specific eating behaviors and mediators of eating behaviors, ED symptoms, and anthropometric measures. Chi-square, multivariable logistic regression, and multiple linear regression were performed in determining the rate of ED risk classification and correlates of ED risk classification and symptoms (Aim 1). Two measures of psychological inflexibility related to BD and dieting, in addition to the data for Aim 1, were used in mediation path analysis to examine the association of ED symptoms to BMI, and the indirect effects as mediated by psychological inflexibility related to BD and dieting (Aim 2). A purposively selected sample of eighteen cadets participated in one-on-one, semi-structured telephone interviews on eating behaviors and their mediators in the context of ROTC (Aim 3). Interviews were analyzed using thematic analysis to identify the most important themes and determinants related to eating behaviors in ROTC cadets.We found that ED symptoms and ED risk classification are prevalent in a sample of US Army ROTC cadets (10.1% of sample). Correlates associated with greater likelihood of ED risk classification and elevated ED symptoms were: sex, dieting, and military contextual factors such as attempting dieting and weight loss to meet body composition standards, and peers' comments on weight. Total ED symptoms scores were positively associated with BMI and partially mediated by psychological inflexibility related to BD and dieting. Cadets discussed perceived determinants of eating behaviors which included traditional determinants (e.g. time, money, nutrition knowledge) and ROTC-context specific determinants (e.g. preparation for body composition assessments and body image perceptions), which contributed to unhealthy weight control behaviors (dieting) and negative body image perceptions (BD) for some cadets. In conclusion, the prevalent correlates for eating disorder symptoms and risk in the sample of US Army ROTC cadets in this study were factors related to the enforcement of body composition standards and body image perceptions in the military context which may contribute to the development of dieting, BD, and NA. Longitudinal and/or intervention studies on this important topic may benefit our understanding of how ED symptoms and obesity develop over time and how targeting dieting, BD, NA, and affect regulation may be leveraged to mitigate ED and obesity to promote physical fitness, operational readiness and health in military personnel.
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Title: Non-equilibrium phase transformations in charge-density wave and strongly correlated systems studied by coherent femtosecond electron diffraction
Creator: Zhou, Faran
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "By photo-exciting electrons in a material causing subsequent electron-electron and electron-phonon interactions, an energy landscape is created that is very different from that in thermal equilibrium. This distinction sets the baseline that photo-induced phase transitions (PIPT) could go through very different pathways compared with the thermally-induced phase transitions in equilibrium. This opens up a new dimension for complex materials research in non-equilibrium with ultrafast tools. In...
Show more"By photo-exciting electrons in a material causing subsequent electron-electron and electron-phonon interactions, an energy landscape is created that is very different from that in thermal equilibrium. This distinction sets the baseline that photo-induced phase transitions (PIPT) could go through very different pathways compared with the thermally-induced phase transitions in equilibrium. This opens up a new dimension for complex materials research in non-equilibrium with ultrafast tools. In recent years, with the discovery of photo-induced superconductivity (SC) and other hidden quantum states, the study of these metastable and hidden phases in quantum materials has drawn intense interest in the ultrafast community.With femtosecond electron diffraction, we have observed intriguing phenomena in a few charge-density wave (CDW) materials (CeTe3, ErTe3 and 1T-TaS2) and iron chalcogenide systems (FeTe, FeSe0.44Te0.56 and FeSe). We explore the metastable hidden phases and observe universal dynamics in these materials far from equilibrium.CeTe3 exhibits uni-directional stripe CDW order in thermal equilibrium. Bi-directional CDW is thermodynamically forbidden. After femtosecond laser pulse excitation, the system is driven to a bi-directional order as it crosses a nonthermal fixed point. The new state is formed through associated symmetry changes that cause softening/hardening of CDW-related phonons. The CDW wavevector change proves that Fermi surface nesting (FSN)-enhanced electron-phonon coupling plays a central role in driving the CDW instabilities. Based on these results, we propose a nonthermal phase transition pathway in the non-equilibrium phase diagram.The work in ErTe3 is one step further based on the CeTe3 results. ErTe3 is on the opposite side of the rare-earth tritelluride (RETe3) series to host two orthogonal CDW orders at low temperature. Together with CeTe3 data, the ultrafast results at various temperatures in ErTe3 indicate that the system becomes more symmetric after laser excitation. Given the robustness of the data, the conclusion here may be extended to similar systems as well.The generic features of CDW dynamics in 1T-TaS2 are very similar to those in the quench dynamics of isolated quantum systems (e.g. cold atoms). After laser excitation, the system goes to the prethermalization plateau region before the thermalization stage. We find that both regimes follow universal scalings due to the existence of two nonthermal fixed points. Microscopically, we propose a chiral-symmetry-breaking mechanism that mediates the phase transformation. With a 2500 nm excitation laser, we emphasize the photo-doping, instead of the photo-thermal effect, in driving the phase transition. Due to the lack of thermal energy, the phase transition induced by the 2500 nm laser is more first order-like with faster switching speeds than 800 nm excitation. This high-speed switching with little thermal energy deposition holds promise for better future optoelectronic applications.In FeTe, we directly observed the ultrafast structural transition by ultrafast electron diffraction (UED) for the first time. In the studies of optimally-doped compound FeSe0.44Te0.56, we observed the large-amplitude acoustic phonon excitations at right above the transition temperature Tc. While experiments with better spatial-temporal resolutions are needed, the acoustic phonon observed here might be important for SC in iron chalcogenide. In FeSe, we observed the laser-enhanced local stress that is known to be coupled to the nematic phase and superconductivity. Future UED experiments targeted for understanding the local stress would be very helpful."--Pages ii-iii.
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Title: Measuring the half-life of O-26
Creator: Redpath, Thomas
Date: 2019
Collection: Electronic Theses & Dissertations
Description: An interesting property of some neutron-unbound systems is true two-neutron emission where the neutrons are emitted simultaneously as opposed to a sequential decay through an intermediate state. Since neutrons are only affected by the angular momentum barrier, the timescale for this process is much shorter than for two proton emission which is dominated by the Coulomb barrier. One such case is ²2076O where a very low decay energy was measured and the two valence neutrons are expected to...
Show moreAn interesting property of some neutron-unbound systems is true two-neutron emission where the neutrons are emitted simultaneously as opposed to a sequential decay through an intermediate state. Since neutrons are only affected by the angular momentum barrier, the timescale for this process is much shorter than for two proton emission which is dominated by the Coulomb barrier. One such case is ²2076O where a very low decay energy was measured and the two valence neutrons are expected to occupy d-wave orbitals. Also, the ground state of ²2075O is located 700 keV higher. Using the data from a previous measurement of the decay energy, the MoNA collaboration extracted a lifetime of 4:5+1:1-1:5(stat) ± 3(syst) ps with a confidence level of 82% (1). Results from a recent measurement give T1/2 = 5:0+2:0-1:6 (stat) ±1:7 (syst) ps and support the previous finding.Measurements of neutron-unbound systems using invariant mass spectroscopy are often performed using low-intensity radioactive ion beams. Low reaction yields can be countered by using a thicker target but at the expense of larger uncertainties in the reconstructed invariant mass. A new segmented target was designed to address this trade-off, and it was first used in this experiment to re-measure the ground state half-life of ²2076O.
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Title: Analysis of drinking water quality and sanitation in a peri-urban area of Dar es Salaam, Tanzania
Creator: Ngasala, Tulakemelwa Mhamilawa
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "While the Sustainable Development Goal 6 called for universal access to water and sanitation by 2030, the challenge of achieving this goal seems daunting in the context of the bourgeoning peri- urban communities of the developing world. These areas are often in a regulatory grey area, receiving municipal water on an irregular basis and lacking sanitation and other basic services. And yet, SDG 6 recognizes that improving global health and wellbeing is critically linked to addressing this...
Show more"While the Sustainable Development Goal 6 called for universal access to water and sanitation by 2030, the challenge of achieving this goal seems daunting in the context of the bourgeoning peri- urban communities of the developing world. These areas are often in a regulatory grey area, receiving municipal water on an irregular basis and lacking sanitation and other basic services. And yet, SDG 6 recognizes that improving global health and wellbeing is critically linked to addressing this problem. A multi-method study of the peri-urban area of Dar es Salaam was conducted to determine the extent of the problem and to make recommendations for system-wide approaches to alleviate the risk of waterborne disease. Existing water sources in the area were identified. Water collection and storage practices were assessed at the household level to determine how water from relatively clean sources becomes contaminated. Escherichia coli (E. coli), nitrate, and total dissolved solid (TDS) were analyzed as indicators for the sewage contamination. Bivariate correlation and univariate regression analyses were used to identify the sources of contamination. The assessment focused on the relationship and association of water contamination with site-specific variables. The variable that had the highest negative impact to the water source was analyzed by using a groundwater flow and contaminant transport model as a tool to make recommendations for proper site-specific sanitation practices. Of the three water sources identified (city water, vendors, and domestic wells), water quality analysis showed that city water at the point of collection (POC) was deemed excellent, whereas it diminished at the point of use (POU) for all three water sources. Reasons for change in water quality at POU and POC were due to mixing of water from different water sources at homes during storage. Using a multinomial regression model, the main reason for mixing water was determined to be the dilution of the salty taste of well water (p < 0.05) and insufficient storage containers (p < 0.05). Of the three water sources identified, domestic wells were found to be the most contaminated. Further analysis on the domestic wells showed a significant contamination, where 80% of wells tested contained E. coli. Also, 58% and 81% of wells tested had concentrations of nitrate and TDS, respectively, that exceeded the WHO guidelines. Univariate regression analysis confirmed the association of contaminants with distance of a well from a sanitation system and well depth (p < 0.05). Groundwater transport modeling showed a strong correlation between the tracer and contaminants and the tracer and distance and helped identify the safe well setback distance that is specific to site conditions, soil type, and aquifer properties. Groundwater modeling was shown to be a good assessment tool for contamination within an aquifer system in urban overpopulated areas of developing countries. Our findings also indicate that the risk of exposure to waterborne disease comes from a combination of factors that involve multiple actors, from improved awareness and sanitation practices to improved regulatory oversight, supply practices, and sanitation technologies."--Pages ii-iii.
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Title: Development and validation of risk stratification models in a cohort of community-living homebound older adults, comparison of three methods : logistic regression, random forest, and Cox proportional hazard regression
Creator: Nasiriahmadabadi, Mojdeh
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Risk stratification (RS) models make predictions of an outcome based on the observed information from predictor variables. Classification of a population into different groups based on their risk of an outcome provides the opportunity for delivering targeted services to each group based on their needs and priorities. Different RS tools have been developed for older adults, but there is a limited number of RS studies developed for use in community-living older adults. This dissertation aims to...
Show moreRisk stratification (RS) models make predictions of an outcome based on the observed information from predictor variables. Classification of a population into different groups based on their risk of an outcome provides the opportunity for delivering targeted services to each group based on their needs and priorities. Different RS tools have been developed for older adults, but there is a limited number of RS studies developed for use in community-living older adults. This dissertation aims to develop and validate risk stratification models in a cohort of community-living homebound older adults. The study population consisted of older homebound adults who received home-based medical services from the Visiting Physician Association (VPA), which is a part of the United States Medical Management (USMM) Corporation. USMM provides a range of services, including home-based primary care and medical visits, senior home care, palliative care, and hospice services. The cohort had several features indicative of high risk: the average age was 82 years, 50% had 2265 5 comorbidities, and 45% had a severe disability (defined by a Karnofsky Performance Score KPS 226440). The population had very high rates of mortality and hospice admission (1-year rates were 32% and 10%, respectively). Given the unique and high-risk nature of this population, a RS approach was developed to help to provide USMM patients with appropriate services aligned with their priorities, as guided by a recent conceptual framework for the care of older adults with multiple comorbidities (Table 1.2). We developed and validated prediction models for two outcomes (death and hospice admission) by using three alternate statistical approaches: logistic regression (LR), random forest (RF), and Cox regression. The performance of these models was compared using the discrimination ability measured by area under the receiver operating curve (AUC). When developing the LR model we applied different variable selection methods (stepwise, backward, forward, adaptive lasso, elastic net, and manual). We developed a prediction model using a RF algorithm and used Cox regression to model time-to-event for each outcome separately (using the same variable selection methods as used in Logistic regression). All three models were developed in a derivation dataset (consisting of a random 50% of the cohort) and validated by applying to the validation dataset. Because of the large amount of missing data among predictor variables we applied multiple imputation (MI) procedures and compared the performance of LR and RF models in the original data and imputed data. For the prediction of mortality, all of the variable selection methods used in the LR model showed similar predictive performance (AUC 0.762- 0.769). Random forest had the best discrimination ability (AUC=0.83), whereas the LR and Cox models had comparable AUCs (0.76 and 0.74 respectively). We determined that the higher AUC of the RF model was mainly due to its ability to include subjects with missing data because when the subjects with missing data were excluded from the RF cohort, the UAC of the model was similar to the LR model. Also when the RF model was applied to imputed data it has similar predictive performance as the LR model which indicated the basic assumption of multiple imputation (i.e., missing at random) was not met in this data. For hospice admission, all three models had a similar discriminative ability (AUC for RF, LR, and Cox, were 0.70, 0.73, and 0.72, respectively). The variables age, race, KPS, serum albumin, surprise question (SQ), and hyperlipidemia were consistently selected as the important predictors of both outcomes in all three approaches. WE concluded that the RF approach can significantly improve the predictive performance of the RS model but this advantage comes from its ability for the inclusion of observation with missing data. When data are missing not at random use of MI had a limited effect on improving the prediction of models because the basic assumption in MI procedure is missing at random. The quality of data from large electronic health record datasets remains a limitation of developing RS models.
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Title: Environmental determination and dynamic regulation of the carbon concentrating mechanism in Fremyella diplosiphon
Creator: Rohnke, Brandon
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "Cyanobacteria are single-celled photoautotrophic organisms that are major contributors to global carbon fixation. Since the accumulation of significant amounts of oxygen (O2) in the atmosphere, they have contended with decreased amounts of available inorganic carbon (Ci) with which to supply photosynthesis. This has led to the evolution of a carbon concentrating mechanism (CCM) that involves increasing the Ci uptake into the cell and utilizing a specialized bacterial microcompartment (BMC)...
Show more"Cyanobacteria are single-celled photoautotrophic organisms that are major contributors to global carbon fixation. Since the accumulation of significant amounts of oxygen (O2) in the atmosphere, they have contended with decreased amounts of available inorganic carbon (Ci) with which to supply photosynthesis. This has led to the evolution of a carbon concentrating mechanism (CCM) that involves increasing the Ci uptake into the cell and utilizing a specialized bacterial microcompartment (BMC) called the carboxysome to trap carbon dioxide (CO2) around the carbon-fixing enzyme, rubisco. Since the CCM is an integral part of cyanobacterial photosynthesis, it is expected to be regulated by many environmental factors that affect photosynthesis. Here, I present findings from studies on Fremyella diplosiphon, a model cyanobacterium that exhibits complementary chromatic acclimation (CCA), wherein photosynthetic pigmentation and efficiency are tuned in response to environmental light cues. A photoreceptor, RcaE, that controls CCA was shown to be important for determining the abundance and stoichiometry of CCM components. The size and abundance of carboxysomes were found to correlate with the ratio of carboxysomal cargo:shell in a Delta-rcaE mutant strain, suggesting a role for RcaE in regulating carboxysome morphology. Additionally, F. diplosiphon is one of many cyanobacteria that express an activase-like cyanobacterial (ALC) protein, a homologue to rubisco activase that is an essential protein in plants for rubisco activity. The ALC protein is not coded for in the genomes of many model cyanobacteria but was predicted to be targeted to the carboxysome when present, thus representing an important factor in the nuanced regulation of the CCM. Through contributions to a study highlighting the carboxysomal localization and enzymatic activity of the ALC protein, I provide evidence that ALC is involved in the cellular response to Ci availability. Additionally, computational modeling of the interaction between ALC and rubisco contrasted two potential binding sites and suggested that the interaction could depend on species of origin and post-transcriptional modification. Given the myriad of factors impacting carboxysome regulation, I then analyzed the carbon fixation capabilities of F. diplosiphon strains under variations in light quality, light quantity, and Ci availability. Assessment of carbon fixation behavior utilizing a novel application of carbon response curves to cyanobacteria was consistent with expectations and provided additional insight into which components of the CCM respond to environmental cues. The Delta-rcaE mutant exhibited a noteworthy green-light-dependent limitation in carbon fixation, and further analyses suggested that this depended on rubisco levels and the expression of Ci-uptake genes. These findings, alongside the behavior of other cultivation conditions and F. diplosiphon strains, were used to distinguish at a preliminary level the components of carbon response curves in cyanobacteria as a method to assess carbon fixation behavior and the functional impacts of CCM regulation."--Pages ii-iii.
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Title: Pedagogies of black agrarianism : a cultural process of recovery
Creator: Tyler, Shakara
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "Black agrarianism is a pedagogical thought, praxis, and social movement. Black agrarian pedagogies are the processes by which we teach and learn with one another through the exchange of knowledges that range from basic survival necessities on how to feed, shelter, and cloth ourselves to cultural stories that affirm our identities and value as dignified human beings. The abundant literature citing black agrarianism as a form of social, economic and political liberation skims the surface of...
Show more"Black agrarianism is a pedagogical thought, praxis, and social movement. Black agrarian pedagogies are the processes by which we teach and learn with one another through the exchange of knowledges that range from basic survival necessities on how to feed, shelter, and cloth ourselves to cultural stories that affirm our identities and value as dignified human beings. The abundant literature citing black agrarianism as a form of social, economic and political liberation skims the surface of educational processes in black agrarian spaces. In response, this inquiry explores the historical, contemporary and self-reflective pedagogies of black agrarianism.The historical pedagogies of black agrarianism are interrogated through a two-part historiography: a historiographical essay and an oral history theatrical representation. The historiographical essay illuminates the mothering of black agrarian pedagogies that creatively crafted black agrarian educational environments through the late 19th and 20th centuries in institutions such as Tuskegee University and the Black Panther Party. In the tradition of African storytelling, the oral history theatrical representation performs the life history of Wendell Paris, a black agrarian organizer and educator, in dialogue with historical black agrarians such as Booker T. Washington, George Washington Carver and Fannie Lou Hamer to portray the importance of culture as the first and most important teacher where every day acts of shelling peas, organizing for black voting rights and learning how to survive were some of the primordial lessons that captured the Black Freedom Movement of the mid-to-late 20th century. Relatedly, the ethnographic case study of D-Town Farm of the Detroit Black Community Food Security Network (DBCFSN) explores the contemporary contours of black agrarian pedagogies. Through participant observation, semi-structured interviews with 12 farm volunteers and 7 D-Town farmers and interns and content analysis via internal documents and social media postings, I interpret D-Town Farm pedagogy as a spiritually-driven praxis that exists in a culturally-representative community village striving toward self-reliance. By bringing everything full circle, the farm facilitates a culture of belonging (hooks, 2009) through African-centered culture as a pedagogical agent. Lastly, the self-reflective pedagogies of Black agrarianism are contextualized via an autoethnography where I reflect on my understandings of how black agrarian pedagogies has impacted me as a researcher."--Pages ii-ii.
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Title: On designing biological nanoscale organization
Creator: Young, Eric J.
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "Life at the nanoscale creates a dazzling array machines and structures. Studying these nanoscale creations often requires inter-disciplinary efforts of scientists, along with the support of other personnel. This thesis serves to communicate some personal insights and data captured in studying nanoscale organization of biologically-driven components, as part of such a team. The first chapter addresses spatiotemporal organization of material inside cells, with a focus on scaffolding-type...
Show more"Life at the nanoscale creates a dazzling array machines and structures. Studying these nanoscale creations often requires inter-disciplinary efforts of scientists, along with the support of other personnel. This thesis serves to communicate some personal insights and data captured in studying nanoscale organization of biologically-driven components, as part of such a team. The first chapter addresses spatiotemporal organization of material inside cells, with a focus on scaffolding-type strategies. The second chapter offers a literature perspective on constructing scaffolds with a structurally-characterized protein-domain. The third chapter surveyed functionality of an in vivo designer nanoscaffolding system. The fourth chapter, alongside the appendix materials, forms a collection of future-steps and comments on projects I have encountered while working on my thesis project."--Page ii.
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Title: Deciphering the genetic basis for complex trait variation : utilizing alternative genome-wide association metrics and molecular phenotypes
Creator: Funkhouser, Scott A.
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Within any population, complex trait variation can be attributed to an impressive number of genetic factors. Identification of such factors has been made possible, in part, by large biomedical datasets comprised of genotypes and phenotypes for hundreds of thousands of individuals. Furthermore, understanding the biological mechanisms through which genetic variation creates complex trait variation has been facilitated by high-throughput sequencing technology, used to quantify molecular,...
Show moreWithin any population, complex trait variation can be attributed to an impressive number of genetic factors. Identification of such factors has been made possible, in part, by large biomedical datasets comprised of genotypes and phenotypes for hundreds of thousands of individuals. Furthermore, understanding the biological mechanisms through which genetic variation creates complex trait variation has been facilitated by high-throughput sequencing technology, used to quantify molecular, intermediate phenotypes. Despite such datasets being widely available, we lack understanding of the full spectrum of genetic effects, including gene-by-sex (GxS) interactions. We also have yet to uncover various molecular phenotypes that may "link" genetic variation to complex trait variation. To address these gaps in knowledge, the following chapters will 1) develop and utilize statistical methodology for mapping GxS interactions among human traits, and 2) utilize a pig model to characterize RNA editing-a relatively understudied form of transcriptional regulation- and evaluate its potential to link genetic variation with complex trait variation.Growing evidence from genome-wide parameter estimates suggest males and females from human populations possess differing genetic architectures. Despite this, mapping GxS interactions remains challenging, suggesting that the magnitude of a typical GxS interaction is exceedingly small. We have developed a local Bayesian regression (LBR) approach to estimate sex-specific single nucleotide polymorphism (SNP) marker effects after fully accounting for local linkage-disequilibrium (LD) patterns. This provided means to infer GxS interactions either at the SNP level, or by aggregating multiple sex-specific SNP effects to make inferences at the level of small, LD-based regions. In simulations, LBR provided greater power and resolution to detect GxS interactions than the traditional approach to genome-wide association (GWA), single-marker regression (SMR).When using LBR to analyze human traits from the UK Biobank (N 223C 250,000) including height, BMI, bone-mineral density, and waist-to-hip ratio, we find evidence of novel GxS interactions where sex-specific effects explain a very small proportion of phenotypic variance (R2 < 1x10-4) but are enriched in expression quantitative trait loci (eQTL). By leveraging large datasets and powerful metrics, we are providing evidence that GxS interactions may influence phenotypic variance for a variety of human complex traits.Adenosine to inosine (A-to-I) RNA editing impacts gene function by converting adenosine to inosine molecules within specific regions of the transcriptome and is catalyzed by adenosine deaminase acting on RNA (ADAR). High-throughput sequencing studies, most of which utilizing human models, have found thousands of A-to-I edited loci commonly located within repetitive elements such as the primate-specific Alu element. Here, we utilized matched whole-genome sequencing and RNA sequencing from the same animal to demonstrate that widespread RNA editing occurs within pig transcriptomes, largely within pig-specific repetitive elements known as PRE-1.The degree that sites in the transcriptome are edited by ADAR-the "editing level"-has been observed to vary within populations but it is largely unknown how genetic variation as whole influences editing level variation. Using 168 F2 pigs with SNP genotyping data and RNA sequencing from skeletal muscle, we identified five RNA editing sites across four genes whose editing level variation was significantly attributed to the additive effects of all observed SNP markers (estimated genomic heritability = 0.31-0.56; p-value = 8.2E-5-8.8E-4). We then used bivariate models to estimate how genetics influences covariance between site-specific RNA editing levels and complex traits in pigs. We found modest evidence that SNPs near ADAR contribute to covariance in RNA editing activity and numerous growth traits such as average daily gain (local genetic correlation [SE] = -0.87 [0.16]; p-value = 0.029). These results suggest potential pleiotropic effects between RNA editing activity and complex traits and encourages further use of multi-variate mixed models determine if RNA editing can "link" genetic variation with complex trait variation.
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Title: Guilt, empathy, and compliance in a naturalistic moral scenario : predicting prosocial and externalizing behavior in 3-7-year-old children
Creator: Listro, Caitlin J.
Date: 2017
Collection: Electronic Theses & Dissertations
Description: Current science offers only limited answers concerning the development of empathy disturbances. Indeed, few studies have attempted to empirically identify the developmental trajectory of empathy to define either normal or aberrant developmental patterns. The present study aimed to use an observational approach to assess empathy, guilt, and obedience in children, and to validate this approach by exploring how these observational measures of child moral behavior associated with characteristics...
Show moreCurrent science offers only limited answers concerning the development of empathy disturbances. Indeed, few studies have attempted to empirically identify the developmental trajectory of empathy to define either normal or aberrant developmental patterns. The present study aimed to use an observational approach to assess empathy, guilt, and obedience in children, and to validate this approach by exploring how these observational measures of child moral behavior associated with characteristics theoretically linked to moral development and antisocial behavior. We utilized a videotaped Picture Tearing task in which the child is presented with a moral dilemma. Trained coders rated the tasks for several child behaviors (e.g. guilt, gaze avoidance, defiance) using a coding scheme adapted from the Lab-TAB (Goldsmith et al., 1993). Variations in moral behavior were investigated using person-centered (cluster analysis) and variable-centered (factor analysis) methods, then associations between resulting behaviors and other relevant child characteristics (temperament, externalizing behaviors) were examined concurrently and over time. In general, results indicated that empathic verbalizations and defiance were consistently associated with externalizing pathology. This association was observed concurrently; empathy did not predict externalizing over time. Overall, these results suggest that compliant without complaint is the most adaptive response at this age. Furthermore, the Picture Tearing task does provide useful data about empathic behavior and its associations in young children. Recommendations are made for adaptations to the task and coding scheme to improve the measurement of moral behavior in future research.
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