VictorJuiz/thesis huggingface dataset:
Probing the ultrafast dynamics of salts in condensed and aqueous phases [electronic resource]

The movement of molecules through a condensed phase is governed by an extremely complex hierarchy of considerations and constraints on motion. This is particularly true when electric fields from ions and hydrogen bonding is involved, let alone heterogeneous structuring of the liquid. This thesis seeks, principally, to quantify the timescales of probe molecule motions and to then improve the understanding of how these motions occur. The ultimate goal is to predict how changes in the environment will affect motion both of the liquid and any dissolved solutes. The nature of molecular motions in the condensed phase was investigated using ultrafast two-dimensional infrared spectroscopy. This enabled non-perturbative interrogation of the systems in question as well as the time resolution necessary to detect changes in motion. Both the reorientation of the molecules and the spectral diffusion (which quantifies structural fluctuations) were used to better understand the motions in a number of chemical systems, focusing on the effect of salts. Both aqueous solutions of salts and room temperature ionic liquids (which are a subset of salts that remain molten at room temperature) with dissolved solutes were investigated. A number of noteworthy results were obtained and some interesting conclusions were drawn about aqueous salt solutions. It was found that, in water, some salts (particularly those with a high charge density) can slow the movement of water molecules considerably. This is primarily dependent on the anion, to which the water is directly hydrogen bonded, but the cation can play a role. However, certain salts (including borohydride) leave the dynamics of water unperturbed even when extremely concentrated. This is facilitated by the formation of hydrogen bonds with water molecules such that the hydrogen bond network remains fairly intact despite the presence of the ions. The structuring of the liquid may also play a role -- ionic liquids, which exist as liquids even without the addition of water and have internal structuring, have different dynamics than typical salts when the same amount of water is added to both. Studies were conducted on ionic liquid solutions to determine the effect of structuring. By changing the alkyl chain length of the cation, the ionic liquid adopts different configurations. This cause the dynamics of solutes to change in ways that would not necessarily be expected given the change in bulk properties like viscosity. The region of the ionic liquid that is solvating the probe molecule is found to determine the dynamics rather than the liquid as a whole. However, as was found with dissolved carbon dioxide as it is of note for carbon capture applications, the long range structuring of the ionic liquid can play a role for a subset of the motions that the probe experiences.

Keywords: Chemistry.
Advisor: Fayer Michael D. primary advisor. Thesis advisor
Dai Hongjie
Moerner W. E. (William Esco)
Productive struggle [electronic resource] : the instructional scaffolds of exemplary reading teachers of middle school emergent bilinguals

This exploratory study examines the instructional scaffolding practice of six highly-regarded teachers working in one large, urban district serving a high percentage of emergent bilinguals (students formally classified as English Language Learners). All six teachers had been nominated as "exemplary" by school and district administrators, who knew their work well. The overarching research questions that guide this dissertation are: During 60 lessons of reading instruction with emergent bilinguals, 1) What is the range and variation of scaffold use by teachers who were nominated as exemplary? 2) How did teachers explain their goals, decisions, and uncertainties about how to use scaffolds? 3) How did students appear to respond to scaffolded instruction? Primary data sources included 10 audiorecorded and videorecorded observations of each teacher's instruction over the course of one academic year (60 total); 3 semi-structured interviews with each teacher (12 total), and students' pre and post-assessment in reading and English language proficiency. Instruction was analyzed for the presence/absence of hard and soft scaffolds, in addition to evidence of additional features of instruction. Sociocultural discourse analysis (Mercer, 2004) of a subset of reading lessons closely examined teachers' turn-by-turn use of soft scaffolds in classroom talk and students' responses to scaffolding. Findings indicated that all six teachers chose from a range of hard and soft scaffolds and used scaffolds in order to provide students access to rigorous, middle school-appropriate, reading instruction. Teachers relied on complex pedagogical content knowledge (Shulman, 1986). Teachers' selection and use of scaffolds varied by the composition of the class as individual teachers assessed the range of possible scaffolds--their effectiveness, availability, familiarity, and ease of enactment. Fine-grained analysis of turns of talk in two English Language Development classes revealed that the two teachers' patterns of scaffolding provided their students with different opportunities for student talk and higher-order thinking. These findings have both theoretical and practical implications for conceptualizing scaffolding as a pedagogical tool and how teachers can effectively reduce scaffolding over time so emergent bilinguals can assume greater independence.

Keywords: Education.
Advisor: Aukerman Maren (Maren Songmy)
Grossman Pamela L. (Pamela Lynn)
Martínez Ramón
Valdés Guadalupe advisor. Thesis advisor
Profiling human immune variation at the systems-level in clinical contexts and at steady-state [electronic resource]

The immune system consists of a multitude of interacting cells that together execute coor- dinated responses against threats. However, most studies thus far have focused on studying single cell types in isolation. Furthermore, much of this research has been performed in mice rather than in humans. The work presented here combines the high-dimensional single-cell technology of mass cytometry with analysis techniques from statistics and machine learning to study the hu- man immune system as a system. We provide the first demonstration of the clinical utility of mass cytometry as an immune monitoring tool. We present a pipeline for using mass cytometry on clinical samples to relate patient immune responses with clinical outcomes, specifically recovery from surgery. We follow up this work with an assay that tests a pa- tient's pre-surgical immune state to predict recovery. We further use our mass cytometry pipeline to identify system-wide differences in maternal and neonatal immune systems. In a finaly study, we present a developed and curated data set of healthy individuals for use as a reference tool for studies of the immune system that use mass cytometry in different clinical contexts. We measured cell type-specific signaling responses to a variety of immune modulators, generating a set of reference ranges of healthy immune variation. Both the raw and analyzed data are available for public use. We further exploited the high- dimensional nature of the dataset to identify sets of coordinated immune features that, when grouped as modules, improve predictive performance in modeling immune differences in our demographic data. This work contributes to the growing efforts in using systems-immunology for human immune monitoring. Future work is needed to apply this framework to other immune perturbations, to integrate this data with the the healthy reference, and to translate these results from the research setting to personalized diagnostics of immune health in the clinic.

Keywords: Microbiology and Immunology.
Advisor: Nolan Garry P. primary advisor. Thesis advisor
Angst Martin S.
Davis Mark advisor. Thesis advisor
Sonnenburg Justin
Tibshirani Robert advisor. Thesis advisor
Proteostatic mechanisms and degree of transcriptional change with age in different neural stem cell populations [electronic resource]

The stem cell pool of most organs contains quiescent and actively dividing (activated) populations. These populations face different challenges over the course of life, raising the question of whether they maintain homeostasis differently and age in different ways. In this work, I perform transcriptomic profiling on multiple populations of the brain's regenerative neural stem cell (NSC) pool from young and old mice to gain an unbiased overview of their differential homeostatic properties and their changes with age. Interestingly, I find that quiescent and activated NSC populations differ in their degree of transcriptome-wide change with age and express different transcriptional signatures for the three primary branches of protein homeostasis (proteostasis)—the proteasome, the lysosome, and molecular chaperones. Additionally, aspects of these divergent modes of proteostasis can be generalized to other organs' stem cells. I functionally validate that quiescent and activated NSC populations differ in their regulation of multiple branches of proteostasis. Intriguingly, the populations with less active proteasomes and lysosomes also have higher levels of protein aggregates and undergo a greater degree of transcriptional change with age. Additionally, I find that the genes most changed with age in each cell type are the genes that constitute that cell type's signature with regard to quiescence and activation. Together, these findings highlight novel differences in the proteostatic strategies used by different stem cell populations that could potentially contribute to their differential aging.

Advisor: Brunet Anne
Palmer Theo advisor. Thesis advisor
Winslow Monte advisor. Thesis advisor
Psychological ecosystem services [electronic resource] : the impacts of nature experience on affect, emotion regulation, and cognitive function

The world is currently undergoing rates of urbanization that are unprecedented in human history. Concurrent with this trend is a marked decrease in the rate of nature exposure for many urbanites. Although urban life provides many benefits, it is also associated with an increased risk for certain anxiety and mood disorders, including depression. As humanity is increasingly concentrated in urban environments, it is necessary that we gain an empirical understanding of the human well-being repercussions resultant from a decline in the frequency and duration of nature experience. This dissertation is focused on the ways in which nature experience benefits cognitive function, mood, and emotion regulation. With this understanding, we can begin to envision the manner in which environmental psychology can be incorporated into the paradigm of ecosystem services. The psychological health of human beings may then be included in this accounting of the potential impacts on well-being of elements of nature, and of changes in their distribution across rural and urban landscapes, and in people's access to them.

Advisor: Daily Gretchen C.
Gross James J.
Kareiva Peter M.
Lambin Eric F. advisor. Thesis advisor
Meyer-Lindenberg Andreas
Satz Debra advisor. Thesis advisor
Public private partnerships in water and wastewater [electronic resource] : case studies on Brownfield leases

Local government finances across the United States are being strained by decisions made over the past several decades. Underfunded pension liabilities and growing debt burdens are forcing governments to make hard choices to resolve them. In addition to broad fiscal pressures, governments are facing acute stress from deteriorating infrastructure. State and local governments are faced with difficult choices about how to resolve these pressures. Public private partnerships (P3s) are seen as a tool for tackling looming liabilities as well as deferred maintenance. When used on existing or brownfield infrastructure, P3s allow governments to lease the asset in exchange for payments which can be used to resolve their fiscal challenges. Between 2012 and 2014, Bayonne, New Jersey; Allentown, Pennsylvania and Middletown, Pennsylvania entered into P3s for their existing water and sewer systems. The three cities faced mounting pension and debt burdens that were resolved in large part by the use of a P3. This thesis develops case studies for each transaction. The case studies for this thesis expand the previous research on P3s for brownfield infrastructure by focusing on smaller transactions in the water sector. In addition, previous case studies have failed to look at how the procurement process impacts the contract structure and risk sharing arrangement. Finally, the case studies for this thesis illustrate how learning and standardization occurs across multiple transactions. This thesis finds that while each city was able to reduce its pressing fiscal challenges, the three transactions have had both positive and negative impacts that stem from the procurement process and goals of each city. In addition, the three transactions provided a benefit beyond the three cities by facilitating learning by various stakeholders that could be applied to future transactions.

Keywords: Civil and Environmental Engineering.
Advisor: Levitt Raymond E. advisor. Thesis advisor
Quantifying the 3D morphology of fin whale (Balaenoptera physalus) and sei whale (Balaenoptera borealis) baleen: implications for filtration hydrodynamics

Baleen whales (Mysticeti) are gigantic filter feeders that exploit large numbers of small-bodied prey suspended in the ocean using a keratinized oral filter called baleen. Although the gross anatomy of baleen has been described for more than a century, the detailed three-dimensional morphology of baleen plates remains unknown. Using CT scans of baleen from a fin whale (Balaenoptera physalus) and a sei whale (Balaenoptera borealis), I quantified the three-dimensional anatomy of baleen plates in order to calculate the area available for flow during filtration. From the flow area for a standardized section of baleen belonging to each species, I calculated what percentage of the total area was taken up by plate material; the remaining area was considered potentially available for flow. Analyses of the flow area through a section of 37 plates indicate that the maximum areas available for flow in the fin whale can be found closer to the lingual edge (17.9% of the way across the baleen rack) than in the sei whale (69.2%). Given the relative size of the whales, the fin whale, a much larger animal, exhibited a greater peak area of 0.08413m^2 at 0.035m from the lingual edge than the peak area of 0.0095m^2 measured 0.045m from the lingual edge in the sei whale. Furthermore, after analyzing three sections (anterior, middle, and posterior) along a sei whale baleen rack, the greatest total area was found in the posterior section at 0.0198m^2.These data provide the first three-dimensional measures of baleen morphology using computed tomography and significantly increase our understanding of this poorly understood yet critical filtering structure.

Keywords:  Department of Biology
Marine Biology
Baleen
Fin whale
Sei whale
Thesis
Advisor: Goldbogen Jeremy
Denny Mark
Quantifying the impact of providing model-based cost visualization on the design of steel frame structures [electronic resource]

Structural engineers are challenged to accurately estimate the cost implications of design decisions, particularly early in the design process. Structural engineers face these challenges because they lack both important data and the multi-disciplinary expertise required to accurately assess the cost of steel structures during early design. This thesis presents a method to visualize the cost implications of design decisions for steel frame structures in the context of the Building Information Model (BIM). The intent is to empower engineers to make more informed design decisions early in the design process when those decisions have the greatest influence. The proposed method enables engineers to accurately assess material, fabrication, and erection costs, and provides actionable guidance on where to focus efforts to improve the design and how to do the same. This is achieved using visualization methods like relative color mapping and notifications that clearly describe cost drivers in the context of decisions that designers have control over. An existing estimation method is used to provide visual cost feedback based on supplier cost data provided by steel mills, fabricators, and erectors. This data is combined with information from the analytical model to automatically detail the structure to produce specific quantities required to estimate fabrication and erection costs. The research goes further to validate the visualization method and to quantify its impact on design decisions and how those decisions affect the overall design outcome. I apply the method to a two-dimensional 1x10 special moment steel frame and illustrate the difference in design outcome, cost and weight between a frame designed using the proposed visual feedback method, and one using conventional methods, without visual cost feedback. The experimental validation showed that the designers who did have access to cost feedback were able to attain 13% cost savings, or about $13,000 for the specific case, but with a 2.7% heavier structure. The results highlight the limitations and challenges of designing to cost using current design practices, and demonstrate the importance of providing visual cost feedback to designers in order to make more informed design decisions that improve overall product economy and quality.

Keywords: Civil and Environmental Engineering.
Advisor: Fischer Martin
Flager Forest
Quantitative brain tissue oxygenation mapping using magnetic resonance spin relaxation [electronic resource]

Oxygenation, as quantified by the parameter of oxygen saturation, is a vital property that reflects the functional status of brain tissues. It enables effective assessment of the health and salvageability of tissues affected by pathology, and allows for better understanding of physiological and neuronal mechanisms in the brain. Magnetic resonance imaging (MRI), a safe, non-invasive and flexible imaging modality, may be utilized for mapping brain tissue oxygenation. This dissertation focuses on the clinical translation and validation of one class of MRI-based techniques, which derives oxygenation information from a transverse relaxation rate of MRI signal denoted R2'. We found that the measurement of R2' is highly dependent on the MRI technique used. Having identified gradient-echo sampling of free induction decay and echo (GESFIDE) as a good candidate for simultaneous quantitation of the three transverse relaxation rates (R2', R2* and R2), we benchmarked their intra-scan reproducibility and assessed their changes during gas challenges in normal subjects, finding strong hypoxia to be the recommended gas challenge for validating oxygenation mapping methods, and tissue R2' change to be the recommended relaxation-based metric for studying brain tissue oxygenation. Finally, we assessed the changes in these three relaxation rates in Moyamoya disease, along with measuring acetazolamide-induced cerebrovascular reactivity, finding regions with limited perfusion augmentation also displayed reduction in R2', suggesting a potential for baseline oxygenation measurement to replace the acetazolamide challenge, and again recommending R2' over R2* and R2 as the preferred tissue oxygenation metric.

Keywords: Electrical Engineering.
Advisor: Zaharchuk Greg primary advisor. Thesis advisor
Moseley Michael E. (Michael Eugene)
Nishimura Dwight George advisor. Thesis advisor
Spielman Daniel (Daniel Mark)
Quantitative measurements and artifact correction methods in body magnetic resonance imaging [electronic resource]

Magnetic Resonance Imaging (MRI), with its flexibility and good soft tissue contrast, is a powerful modality for imaging tissues such as organs, muscle, and cartilage. MRI of cartilage can provide not only morphological images but also quantitative estimates of the tissue, aiding in early detection of diseases such as osteoarthritis, which affects tens of millions of US adults at tremendous societal cost. One of the most promising techniques for this purpose is the Double-Echo in Steady-State (DESS) sequence, a steady-state sequence providing two distortion-free images with high SNR efficiency. However, DESS has complicated signal contrast, can suffer from motion artifacts, and can be sensitive to noise for some quantitative estimates. Another challenging problem in body MRI is imaging close to metallic implants, which distort the magnetic field. Sequences have been developed to overcome this, but they tend to have long scan times. In this thesis, methods are introduced to improve anatomical and quantitative imaging using DESS. This will involve exploring novel signal models for DESS which allow for improved quantification and artifact reduction. Improvements in image quality and quantification are demonstrated. Reduced noise sensitivity of diffusion estimates from DESS by the choice of scan parameters and post processing method is shown as well. A separate method is also presented that greatly accelerates MRI close to metal implants by data undersampling. The resulting aliasing does not corrupt the image due to the pattern of the signal distortion caused by the metal.

Keywords: Electrical Engineering.
Advisor: Hargreaves Brian Andrew primary advisor. Thesis advisor
Gold Garry E.
Nishimura Dwight George advisor. Thesis advisor
Quantitative measures of gait and reaching in toddlers born preterm with very-low birth-weight [electronic resource]

This dissertation aims to quantitatively analyze functional lower- and upper-extremity movement in toddlers born preterm with very-low birth-weight (VLBW). Children born preterm with VLBW have increased risk of motor impairment, and early identification of impairment guides treatment to improve long-term function. Temporal-spatial parameters were quantified and analyzed in the context of neurodevelopment for two functional tasks: gait and reaching. 81 VLBW (≤1500 g) preterm (≤32 weeks) and 43 typically-developing (TD) toddlers successfully completed motor assessments at 18-22 months of age, adjusted for prematurity. Neurodevelopment of VLBW preterm participants was assessed with Bayley Scales of Infant Development-3rd Edition (BSID-III) motor composite, gross motor, and fine motor scores. Differences in temporal-spatial gait were found between lower-scoring preterm toddlers and TD toddlers, and BSID-III motor scores correlated with gait in preterm children. These differences were quantified in the Toddle Temporal-spatial Deviation Index (Toddle TDI), an index quantifying toddler gait deviation from typical. The Toddle TDI demonstrated sensitivity and specificity to gross motor function, and has potential as an easily-administered, revealing clinical and research gait metric. A new method for measuring temporal-spatial reach parameters with inertial sensors showed good agreement with the current gold standard of 3D marker-based motion capture. Using this method, preterm toddlers demonstrated substantial differences in temporal-spatial reach compared to TD toddlers, and evidence indicated several reach parameters were revealing of function and may be useful as a clinical assessment.

Keywords: Bioengineering.
Advisor: Delp Scott primary advisor. Thesis advisor
Rose Jessica
Gold Garry E.