VictorJuiz/thesis huggingface dataset:
Methods for Measurement and Interpretation of Gene Expression

For the last 15 years, the world's sequencing capacity has increased at a staggering rate. While the focus of much of this has been on the sequencing of genomic DNA, the sequencing of transcribed RNAs as a proxy for the expression of genes has also taken a starring role. In this thesis, we consider three themes related to these RNA-seq experiments, operating at three different levels./nWe begin by considering the quantification of a single RNA-seq experiment. Here the blessing of cheap sequencing has become something of a curse as data is being generated at such a rate that analyzing that it can end up being an onerous task. To address this, we attempt to do as much as we can with very little: without aligning our sequencing data to a genome and foregoing much of the information usually utilized in RNA-seq analyses, we manage to produce quantifications of expression that are close in accuracy to those produced by state of the art, sophisticated models while using a very small fraction of their computational resources./nNext, we consider the quantification of RNA-seq datasets with many samples. While generating such datasets was previously a difficult and expensive undertaking, it is becoming increasingly routine and so the question of whether they should have their own specialized form of analysis should be addressed. In such datasets, the different samples are almost always related in some sense which creates the possibility that, rather than analyzing each sample independently, information could be shared between the analyses thereby improving the accuracy of all. To that end, we propose a method of regularizing the analysis of many sample RNA-seq inspired by techniques in machine learning and provide evidence that it may improve the accuracy many sample RNA-seq experiments which are shallowly sequenced and therefore would most likely benefit from such information sharing./nFinally, we consider some aspects of the analyzing the results of many sample RNA-seq experiments. Specifically, we consider experiments in which expression has been measured in many individuals and ask: do we see the signature of population structure in expression data, as we do in genotype data? While the question has been answered in the negative in the past, we show that more sensitive analysis reveals that population signals do indeed leave their mark on expression.

Advisor: Pachter, Lior
Identification and characterization of genes involved in Arabidopsis thaliana cell wall acetylation

Most non-cellulosic plant cell wall polysaccharides including the hemicellulose xyloglucan and the pectic polysaccharides can be O-acetylated. This feature has direct significance in the use of these polymers in the food and biofuel industry. For example, increased pectin acetylation can reduce its gelling abilities and is hence detrimental in its application as a food thickener or emulsifier. In general, plant biomass with wall polymers with high acetate content can negatively influence biomass hydrolysis by fungal enzymes and interfere with downstream fermentation by yeasts./nGenetic and biochemical approaches were used to identify genes involved in wall polymer acetylation in the model species Arabidopsis. A forward genetics approach was able to identify wall acetylation differences within a population of Arabidopsis ecotypes in both total wall acetate and xyloglucan O-acetylation. One of these naturally occurring mutant alleles of a recently identified putative xyloglucan acetyltransferase (AXY4) was found in the Ty-0 ecotype. Ty-0 completely lacks xyloglucan acetyl-substituents in roots and leaves, suggesting that the lack of XyG acetylation does not compromise the fitness of the ecotype in its ecological niche. In an attempt to further characterize the AXY4 protein, and characterize peptide domains involved in cell wall polymer recognition, a functional domain swap approach was utilized without success. A biochemical approach to identify and purify a putative xyloglucan acetylesterase was attempted also without success. Another way to modulate wall acetylation is by apoplastic plant acetylesterases, which naturally remove acetyl-substituents on polymers. To characterize genes in the Pectin acetyl esterase gene family in Arabidopsis thaliana, reverse genetics was used and lead to the identification of two genes responsible for altering wall acetate levels of pectins. Further pectin fractionation experiments suggest that PAE8 and PAE9 act predominantly but distinctively on pectic rhamnogalacturonan I. Pectin acetylesterase activity was demonstrated in vitro for the proteins encoded by PAE8 and PAE9. Through genetic means it is possible to increase wall acetate content, but this modification lead to a reduction in Arabidopsis inflorescence size giving insights about the function of acetylation of pectins.

Advisor: Pauly, Markus
Essays on Incentives and Measurement of Online Marketing Efforts

This dissertation contains three essays that examine different aspects of online marketing activities, the ability of marketers to measure the effectiveness of such activities, and the design of experiments to aid in this measurement./nChapter 2 examines the impact of search engine optimization (SEO) on the competition between advertisers for organic and sponsored search results. The results show that a positive level of search engine optimization may improve the search engine's ranking quality and thus the satisfaction of its visitors. In the absence of sponsored links, the organic ranking is improved by SEO if and only if the quality provided by a website is sufficiently positively correlated with its valuation for consumers. In the presence of sponsored links, the results are accentuated and hold regardless of the correlation./nChapter 3 examines the attribution problem faced by advertisers utilizing multiple advertising channels. In these campaigns advertisers predominantly compensate publishers based on effort (CPM) or performance (CPA) and a process known as Last-Touch attribution. Using an analytical model of an online campaign we show that CPA schemes cause moral-hazard while existence of a baseline conversion rate by consumers may create adverse selection. The analysis identifies two strategies publishers may use in equilibrium - free-riding on other publishers and exploitation of the baseline conversion rate of consumers./nOur results show that when no attribution is being used CPM compensation is more beneficial to the advertiser than CPA payment as a result of free-riding on other's efforts. When an attribution process is added to the campaign, it creates a contest between the publishers and as a result has potential to improve the advertiser's profits when no baseline exists. Specifically, we show that last-touch attribution can be beneficial for CPA campaigns when the process is not too accurate or when advertising exhibits concavity in its effects on consumers. As the process breaks down for lower noise, however, we develop an attribution method based on the Shapley value that can be beneficial under flexible campaign specifications. To resolve adverse selection created by the baseline we propose that the advertiser will require publishers to run an experiment as proof of effectiveness./nChapter 4 discusses the type of experiments an advertiser can run online and their required sample sizes. We identify several shortcomings of the current prevailing experimental design that may result in longer experiments due to overestimation of the required sample sizes./nWe discuss the use of sequential analysis in online experiments and the different goals of the experiments to make experiments more efficient. Using these techniques we show that a significant lowering of required sample sizes is achievable online.

Advisor: Katona, Zsolt
A Ring Expansion Strategy Toward the Synthesis of Hetisine-Type C20-Diterpenoid Alkaloids

A benzyne insertion ring expansion strategy toward the synthesis of hetisine-type C20-diterpenoid alkaloids has been developed. The first chapter of this manuscript presents an introduction to C20-diterpenoid alkaloids and previous synthetic work toward selected target core structures. The second and third chapters outline our ring expansion strategy for the synthesis of the core of the natural product cossonidine and efforts to complete its total synthesis./nAn overview of the structural and biological properties of C20-diterpenoid alkaloids is provided, as well as a survey of the synthetic studies that have been carried out thus far toward natural products containing the hetidine and hetisine-type framework. The two existing syntheses of a hetisine-type diterpenoid alkaloid are also described. This review outlines some of the salient structural challenges associated with the synthesis of these compounds, as well as the strategies applied to their construction./nAn approach involving a ring expansion was developed to access a tricyclic motif conserved in the hetidine and hetisine frameworks. The acyl-alkylation of aryne intermediates by insertion into C-C sigma bonds was applied to several β-ketoesters and aryne precursors to investigate the efficacy of this transformation on complex systems. Three tricyclic intermediates were synthesized that contain functional handles at the appropriate positions for C-N bond formation to construct the hetisine core./nWith a sequence in place to arrive as several desired tricyclic intermediates, they were then employed to investigate C-N bond formation. A range of conditions was explored, and the desired azabicycle was accessed in 3 steps from the tricyclic scaffold. The requisite [2.2.2] bicycle was then formed in 2 steps to complete the hetisine core. Finally, the synthetic sequence was modified in order to introduce a methyl group necessary for completion of the natural product target. This methylation pathway has been successful in providing the full hetisine core en route to the synthesis of the natural product cossonidine.

Advisor: Sarpong, Richmond
An investigation of roots in forested ecosystems

The root systems of forest ecosystem are both important and understudied. Roots function as the critical organs of nutrient uptake and anchor tree stems against wind throw and aboveground disturbance. Roots are also an important terrestrial reservoir of carbon and play an important role in global climate. Conversion or disturbance of forest lands can result in an emission of carbon dioxide to the atmosphere, and so quantifying the amount of carbon in root biomass is of interest for forest scientists and the climate policy their research informs./nThis dissertation contributes to the science of root biomass measurement and modeling, providing techniques and approaches to improve those estimates, and models for leaf area that can be used to estimate root biomass. It focuses on techniques to improve measurement of root biomass using ground penetrating radar, an emergent method to measure root biomass. First, I investigate what above-ground metrics might best be used to model and predict root biomass and distribution and I develop new models relating basal area to leaf area for quaking aspen (Populus tremuloides) in the Sierra Nevada. Second, I investigate root biomass and distribution in coast redwood (Sequoia sempervirens), and how water acquisition may drive the allocation to roots in redwoods./nGround penetrating radar is shown to have considerable utility for the measurement of coarse root biomass. Above ground biomass is shown to be an excellent predictor of coarse root biomass in Sierran ecosystems. Leaf area, which is predicted by pipe model theory to have a tight relationship with fine root biomass, is shown to have some predictive power for root biomass, and my model represents an improvement over other reported metrics. Finally, I conclude that global root biomass estimates have not been based on reliable or unbiased data to date and I contribute A plan to correct this gap in future global estimates.

Advisor: O'Hara, Kevin
Adolescent Motherhood and the Child Welfare System: Incidence and Prevalence of Early Childbearing among Maltreated Girls Exposed to Foster Care

Although research has suggested that girls in foster care are at high risk of early childbirth, limited data have been available from which rates could be calculated and characterized. Using probabilistically linked vital birth records and administrative child welfare service data for the state of California, this study involved two separate analyses that measured the incidence and prevalence of early childbearing among maltreated adolescent girls who received child welfare services or were in foster care./nThe study generated cross-sectional birth rates among adolescent girls in foster care and compared those rates to similarly aged girls in the general population. Results indicated that a relatively small number of 15- to 17-year-old girls in foster care gave birth each year but on average, birth rates were 60% higher among the foster care population than they were in the general population. Black and Latina adolescents in foster care were more likely to give birth than their White counterparts. Girls who were in foster care for less time or experienced greater placement instability also had higher rates of adolescent childbirth./nThe study also prospectively assessed the cumulative rate of a first birth among a cohort of girls who experienced their first known substantiated allegation of maltreatment after their 10th birthday. Extended Cox proportional hazards models were specified to assess whether or not placement in foster care was associated with a higher rate of early childbirth. Among the full population, just under 18% gave birth for the first time before their 20th birthday. After adjusting for race/ethnicity and maltreatment-related experiences, adolescent girls who spent time in foster care gave birth at a rate that was 12% higher than those who remained at home./nAdolescent mothers with a history of maltreatment and foster care placement may be particularly vulnerable to social, economic and emotional challenges across a number of domains, including a heightened risk for maltreating their own children. The child welfare system has a unique opportunity to provide targeted services and supports to adolescent girls in foster care before, during, and after pregnancy, which can promote their well-being and prevent intergenerational abuse and neglect.

Advisor: Duerr Berrick, Jill
Solid-state NMR Investigations of Proton Conducting Membranes

This thesis applies magnetic resonance techniques to novel and traditional proton conducting/nmaterials in order to gain a better understanding of the molecular aspects of their/nperformance. An array of experiments and techniques are used. One material is a morphologically/ndesigned block copolymer/ionic liquid system. Simple 1-D variable temperature/n(VT) 1H magic angle spinning (MAS) NMR is used to catalogue the dynamic chemical/nshifts, which relates to the prevalence of hydrogen bonding. Relaxation data are used/nto measure the relative mobilities of conduction protons, and these data are related to/npolymer physics phenomena. The effect of morphology is investigated by comparing block/ncopolymer data to a series of homopolymer analogues with no morphological structure./nThe role of entropy in these systems is discussed as well as the effect of a non-symmetric/nionic liquids./nNMR techniques were also applied to more traditional materials, namely perfluorosulfonic/nacid membranes modified with amphoteric imidazole compounds. The chemical/nenvironments of the imidazole as well as the dynamics of proton transfer are measured/nwith Solid-state 1H NMR. The effect of imidazole concentration is also considered. 1H/n-13C cross polarization (CP) MAS NMR is used to reveal the presence of both fast and/nslow moving imidazole in the membranes. Pulsed field gradient (PFG) NMR is used to/nquantify the diffusion of protons and methanol through the material./nThe goal of replacing gaseous hydrogen with organic virtual carrier molecules as a/nproton source for proton exchange membranes (PEM) fuel cells is investigate by testing/nthe effect of model organic liquids in contact with typical membrane materials. A suite/nof data, including 19F NMR relaxation data of the polymer backbone and sidechains, are/nused to explain bulk phenomena and membrane performance.

Advisor: Reimer, Jeffrey A
Developmental Programming and Experience-Dependent Plasticity of Brain and Behavior in the Rodent

Experiences, both in early life and adulthood, can profoundly modify brain and behavior in mammals. In the Long-Evans rat, two salient components of early life experiences are i) the quality of maternal care received and ii) environmental housing parameters/conditions, both of which are capable of modifying numerous components of the developing CNS, including stress or hypothalamic pituitary adrenal axis (HPA) functioning. The following studies address modifications to both brain and behavior (i.e. stress physiology and behavior, executive function, and reproduction) in Long-Evans rat offspring due to variation in the aforementioned parameters. Understanding how basic environmental variables are capable of influencing brain and behavior is important not just in the study of basic neurobiology but also for the exploration of potential sources of psychopathology. Section 2 of this dissertation provides a review of HPA axis regulation, while Sections 3 and 4 discuss relevant primate and rodent models of early life stress axis calibration. Section 6 addresses how early life maternal care is capable of differentially programing sexual behavior and the underlying hypothalamic pituitary gonadal axis (HPG). Section 7 focuses on early life maternal care and developmental programming of stress physiology and executive function. Finally, Section 8 investigates the role of housing parameters, specifically the role of animal bedding, in regulating stress sensitive behaviors. All the studies demonstrate the powerful effect of early life experience and developmental programming of brain and behavior in the rodent.

Advisor: Francis, Darlene D
Musical Materialities in Milan and Liberal Italy at the fine secolo

This dissertation examines musical culture in Milan from the 1870s to 1890s, with particular attention to the ways the material conditions of musical production and consumption were enmeshed with liberal values. The urban center in these decades was known as the capitale morale--the economic, cultural and moral seat of the new nation--in contrast with Rome, the nominal capital. I show that the development of the urban center and that of Milan's preeminent theater, the Teatro alla Scala, were intimately linked. Milanese liberal imperatives of hard work and innovation in these immediate post-unification decades were played out in and around the theater./nSuch imperatives implied breaks with tradition, as in the establishment of the baton conductor and the introduction of electric illumination at the Teatro alla Scala. Chapter 1 concentrates on Franco Faccio, La Scala's first baton conductor. Critics loved the sturdiness of a man measured no less in moral than musical terms. Faccio's reliability and exacting standards of instrumental execution resonated with a new Bismarck-inspired pragmatism in Milan, and the sound Faccio brought forth from the orchestra at La Scala adumbrates the much more famous house sound under his successor, Arturo Toscanini./nChapter 2 centers on the Società Edison Italiana's 1882 installation of electric lighting at La Scala, one of the earliest incandescent installations in the world-- and by far the most ambitious. The innovation was made possible by the economic bullishness and inventiveness of these liberal decades. La Scala became a crucial promotional forum for Edison, where unusual measures were taken to ensure the venture's success, including the unprecedented darkening of the auditorium planned in order to focus audience attention on the novel stage illumination./nMilanese liberal imperatives also implied continual renewal. Chapter 3 investigates the contemporaneous operatic voice: in response to a perceived decline in vocal production, the Milan Conservatory promoted "bel canto" vocal methods in treatises by Lamperti (1864) and Delle Sedie (1874). In fact, however, the latter method set vocal instruction on a controversial new course, one that, because it was alleged to cause extreme vocal strain, stimulated debate about the limits of human productivity./nFinally, Chapter 4 turns to Giuseppe Verdi's Falstaff, which premiered at La Scala in 1893. It is a commonplace of Verdi criticism that the opera was perplexing in its newness. I show that several critics at the premiere chose to promote the idea of Falstaff as a civic innovation par excellence, thereby downplaying its links with other "less groundbreaking" repertory. The more innovative the opera seemed, after all, the more it had in common with the capitale morale, that center of continual work and progress.

Advisor: Smart, Mary Ann
Towards Autonomous Situation Awareness

Technological advances in communication and computing coupled with low costs of sensors have enabled large-scale deployment of video camera networks in our environment nowadays. They are increasingly being used by decision-makers for perceiving elements of an environment in real-time, comprehending their meaning and predicting their status in the near future. Such situational awareness is crucial in dynamic scenarios that arise in military command and control, facility security and emergency services such as policing and fire-fighting. While human perception driven situation awareness has worked well in constrained settings, it is unfortunately not scalable. Furthermore, scenarios such as security and surveillance commonly involve highly complex cognitive tasks that can quickly become monotonous and mentally taxing for human operators. In this thesis, we present new frameworks for automating the perception stage of situation awareness./nWe begin this thesis with the development of a system that is capable of categorizing objects and landmarks in an efficient and distributed manner. Our system is designed to operate with net- works of wireless smart cameras for local perception, and a central station for global inference. We demonstrate that this decoupling of the algorithm pipeline can drastically minimize the power and bandwidth consumed by the wireless cameras. Further, we experimentally validate that our multiple-view inference framework can significantly improve the performance of object and land- mark categorization over traditional single-view settings./nIn the second part of the thesis we extend our distributed object categorization framework to address the problem of automatic human activity detection and categorization. We are particularly interested in the development of rich representations for human motion that are invariant to perspective, scale and the speed at which actions are performed. We propose a generalized framework to perform spatiotemporal fusion of dynamic imagery from multiple wireless smart cameras, and validate the efficacy of our fusion framework on both publicly available, and novel datasets./nIn most realistic scenarios that require situation awareness, objects and people occur in cluttered scenes and exhibit immense variability in their appearance, shape and pose. In the final part of this thesis, we analyze the interplay between computer vision tasks such as segmentation and categorization and present joint frameworks that significantly improve the performance of each task. Our experimental analysis demonstrates that detection and categorization hypotheses help provide good segmentation results, and that segmentation can be used to prune errors in the hypothesis.

Advisor: Sastry, Shankar S