VictorJuiz/thesis huggingface dataset:
A Geometric Morphometric and Histological Study of the Role of Development in Avialan Evolution

In order to fully understand the processes that influence phenotypic evolution, it is necessary to explore the role that developmental channeling plays in shaping morphology. In my doctoral research, I have investigated how an increased understanding of ontogenetic patterns gives insight into the evolution of birds. Here, I present the results of an integrative study combining material from multiple levels of the biological hierarchy (clade, individual organism, and cell), using both paleontological and neontological data. Specifically, I studied post-natal gross morphological change and cellular growth in a phylogenetically broad sampling of Cretaceous and modern avians, using ontogenetic series when available./nA three-dimensional geometric morphometric analysis of ontogenetic cranial shape change indicates that a relatively high level of developmental constraint governs the evolution of the skull, although shape at onset of growth is a more variable characteristic, in large part because hatchling chicks already have cranial morphology very similar to that of adults. Histological study of extant bird skeletons also indicates high variability in onset of growth among taxa and reveals a common pattern of greater skeletal maturity of the femur relative to the humerus at the time of hatching. This is interpreted as an example of a ‘spandrel,’ later exapted by semi-precocial taxa in which pelvic limbs appear to achieve functional maturity before pectoral limbs for adaptive reasons. Histological analysis of Cretaceous avians indicates this trait of differential maturity between limb elements may have a very deep evolutionary origin, and could explain substantial microstructural differences that persist into adulthood in some extinct taxa. I focused in particular on growth in members of the Enantiornithes, and further conclude that this group exhibits a greater diversity of growth strategies than originally hypothesized, although with no apparent relationship to body size or geological age, and that this clade had a unique developmental mode not directly comparable that of to any crown-group birds. Finally, phylogenetic and functional constraints appear to have a much greater influence on cellular growth of long bones than on cranial shape change, for which developmental channeling is a primary influence.

Advisor: Wake, Marvalee H
Lindberg, David R
Modeling and simulation of particle doped composites for electromagnetic applications

Most modern electromagnetic devices consist of dielectric and magnetic particulate composites, which are designed with specific properties for delivering optimal performance. Predicting the effective electric permittivity and effective magnetic permeability of the envisioned composite is of great importance in validating the design for such applications. Analytical bounds to estimate these effective properties can be found in literature. However, they often yield large solution ranges and do not account for the microstructure of the composite. We present here a numerical method to estimate these effective electromagnetic properties for any given composite microstructure. It consists of solving Maxwell’s equations numerically using a particular Finite Difference Time Domain (FTDT) method, known as Yee’s scheme, over a representative volume element of the composite of interest. It allows capturing its electromagnetic response, and subsequently computing its effective electromagnetic properties. Results obtained with this method show good agreement with analytical bounds and experimental data. We also observe more accurate estimations than analytical bounds. The method is then used to assess thermal influence on these effective electromagnetic properties. A numerical design tool, that combines the optimization technique known as genetic algorithm with the proposed numerical method for estimating effective electromagnetic properties, is also presented. It allows determining the required composition and microstructure parameters for a particle doped composite in order to achieve the desired effective electromagnetic properties.

Advisor: Zohdi, Tarek I
The Power in Being Yourself: The Experience of Authenticity Enhances Power

Recent research indicates that power breeds authenticity, suggesting that people associate power with behaving authentically. Extending this notion, we hypothesized that the converse is also true—that the experience of authenticity enhances power. Five experiments (total N = 703) yielded support for this hypothesis. Specifically, participants who recalled an authentic, versus inauthentic, experience reported greater state power (Studies 1-3). Studies 2 and 3 showed further that this authenticity-to-power link was mediated by a reduced fear of rejection for expressing one’s true self. Fear of rejection was manipulated in Study 4 to document the causal impact of a reduced fear of rejection on feelings of power. Finally, Study 5 extended the prior studies into the realm of social perception, demonstrating that people infer others’ power from their acts of authenticity. Our findings could not be explained by pre-existing power differences that may have led to the authentic or inauthentic behavior in the first place (Studies 1, 2, & 5), nor by authenticity eliciting positive affect (Studies 3 & 5). Implications for the maintenance of power hierarchies, and the use of authenticity as a strategic means through which power can be obtained, are discussed.

Advisor: Chen, Serena
Conceiving Earths: Imagining Nature and Society in a Global Environment

The following chapters are the culminating product of a sustained investigation into the entangled relationships between humans and land in the context of global capitalism. Looking specifically at the role of ideas in contests over territory, these pieces address this question via a number of different contexts: the cultivation of a chemicals-based understanding of soils to accompany the spatial expansion of industrial agriculture; new formulations of race in Latin America in relation to anti-imperialist land claims; emergent “land epistemologies” in revolutionary Mexico; and the National Federal of Colombian Coffee Growers' simultaneous investigations of coffee soils and coffee growers in a new science of the nation's biggest export sector. Together, these stories form a meditation on the ways that struggles between social actors for access to land are also about changing relationships between human and non-humans, between society and nature. They also address a foundational geographic theme- the social production of space- with particular attention to the critical role of the production of knowledge in that process.

Advisor: Kosek, Jake
Watts, Michael
Control without Coercion: Public Service Provision for Migrant Workers and Social Control in China

This project focuses on the following puzzle: Why have local authorities in China engaged in a distinctive pattern of expanding and restricting public services at the same time? What explains the particular pattern of expansion and restriction?/nWhile local officials primarily enact social policy to provide services, they have engaged in a distinctive pattern of expansion and restriction of services to also enhance social stability and control migrant workers. These governments face the daunting challenge of the world’s most rapid urbanization: they seek to attract migrant workers and to preserve social stability at the same time. Therefore, they devise an approach to the provision of social services that sometimes gives preference to the state’s goals of stability over the migrant workers’ actual welfare needs. I define social control as the state’s means, both formal and informal, of influencing members of society to make decisions and act in ways that are desired by the state. As local governments channel and contain migrant demands, collective claims of exclusion and discrimination are supplanted by individual bureaucratic battles over eligibility and documentation. At the same time, service provider discretion and migrant agency counter the effects of social control and enable some migrants to gain access to education and healthcare./nMy research challenges existing scholarship on authoritarian durability, public service provision, and citizenship in China. Regulation of migrants provides a window into state control and day-to-day authoritarian governance. The literature on authoritarian durability focuses on the institutionalization of elite power transitions and harbingers of regime change, but sometimes forgets that stability maintenance is a pressing daily task never far from rulers’ minds. Contrary to some scholars of authoritarian durability who find governments give concessions to avert immediate or visible instability from restive groups, Chinese officials sometimes do the opposite and restrict benefits. Unlike other studies that focus on only whether services are provided (often to maximize efficiency or buy loyalty), I find that how public services are provided is itself a tool of social control. In contrast to the clear bifurcation between rural migrants and urban residents in the past, gradations in second-class citizenship among migrant workers have emerged. My dissertation expands our understanding of how non-democratic states hone their methods of social control.

Advisor: O'Brien, Kevin
Cyclotron-Cavity Mode Resonant Cooling in Single Component Electron Plasmas

Generating cold single component electron plasmas, below 20K, is of interest to many experiments that require low temperatures for optimizing recombination rates or producing monoenergetic beams. Here, we report on the demonstration of a technique that allows for rapid cooling of a single-component electron plasma confined in a Penning trap. Electrons are confined in an electromagnetic cavity, allowing use of the Purcell effect to enhance spontaneous emission of cyclotron radiation in the cavity. This allows for faster passive thermalization of the confined plasma to the temperature of electrodes that constitute the cavity.

Advisor: Fajans, Joel
A Journey to the Center of a Bacterial Organelle

Cellular compartmentalization is a fundamental strategy through which complex tasks can be carried out, where each compartment carries out a specialized function. Compartmentalization strategies in the bacteria have (relatively) recently been discovered and are not present across the entire domain; they instead seem to be tied to niche specialization of the host species. For example, carboxysomes are necessary for all cyanobacteria to fix carbon dioxide in present-day atmospheric conditions. Carboxysomes are part of a larger family of bacterial organelles termed bacterial microcompartments (BMCs), which are all related by the proteinaceous shell that bounds the compartment./nMany different metabolic functions have been attributed to BMCs, such as carbon fixation, propanediol metabolism, and ethanolamine metabolism, and cursory genome gazing had hinted that there may be several more functional types of these organelles in a vast number of bacteria. In order to survey the functional and phylogenetic diversity of BMCs, a bioinformatic algorithm was developed to predict and categorize genetic loci that encode genes that can construct a complete organelle. Our analyses result in a taxonomy of BMCs that identifies several candidate loci and individual genes for further investigation./nWe predicted many of these loci to encode for BMCs with novel functions, and examined one locus apparently isolated to the Planctomycetes and Verrucomicrobia phyla. By genetically manipulating Planctomyces limnophilus, we identified that this locus encodes a fully-functional organelle that is involved in degrading fucose and rhamnose, which is likely critical to the niche specialization of many Planctomycetes that associate with algae./nWe also found the widespread usage of a novel phosphotransacetylase enzyme in the BMCs. By analyzing the primary, secondary, and quaternary structures of this novel protein, we identify well-conserved motifs within distinct domains of the protein and identify a peptide that is involved in modulating the quaternary structure./nOne of the many uses of fundamental research is to provide the foundation for engineering synthetic constructs. Finally, we describe two bioengineering strategies geared towards the goal of improving the efficiency of the carbon fixation step of photosynthesis that are based on our knowledge of the cyanobacterial carbon concentrating mechanism, including the carboxysome. The first strategy focuses on the input for the carboxysome, where inorganic carbon must be transported into the cytosol. The second strategy utilizes a carboxysome assembly factor as a scaffolding mechanism.

Advisor: Kerfeld, Cheryl A
Statistical Models for Genome Assembly and Analysis

Genome assembly is the process of merging fragments of DNA sequences produced by shotgun sequencing in order to reconstruct the original genome. It is complicated by repeated regions in genomes, sequencing errors, and experimental biases. Here we focus on our efforts to confront some of the challenges in genome assembly and analysis of genomes to find regions associated with phenotypes using statistical models./nAssembly algorithms have been extensively benchmarked using simulated data so that results can be compared to ground truth. However, in de novo assembly, only crude metrics such as contig number and size are typically used to evaluate assembly quality./nWe present CGAL, a novel likelihood-based approach to assembly assessment in the absence of a ground truth. We show that likelihood is more accurate than other metrics currently used for evaluating assemblies, and describe its application to the/noptimization and comparison of assembly algorithms./nWe then extend this to develop a method for ''scaffolding'' i.e. linking contigs using read pairs based on optimizing assembly likelihood. It uses generative models to approximate whether joining contigs would result in an increase in assembly likelihood. The methods are grounded in a rigorous statistical model yet proper approximations make the implementation named SWALO efficient and applicable to practical datasets. We analyze SWALO on real and simulated datasets used previously to evaluate other scaffolding methods and find that it consistently outperforms all other scaffolders./nFinally, we focus on the problem of analyzing genomic data to associate regions in the genome to traits or diseases. We present an alignment free method for association studies that is based on counting k-mers in sequencing read, testing for associations directly between k-mers and the trait of interest, and local assembly of the statistically significant/nk-mers to identify sequence differences. Results with simulated data and an analysis of the 1000 genomes data provide a proof of principle for the approach. In a pairwise comparison of the Toscani in Italia (TSI) and the Yoruba in Ibadan, Nigeria (YRI) populations we find that sequences identified by our method largely agree with results obtained using standard GWAS based on variant calling from mapped reads. However unlike standard GWAS, we find that our method identifies associations with structural variations and sites not present in the reference genome./nWe also analyze the data from the Bengali from Bangladesh (BEB) population to explore possible genetic basis of high rate of mortality due to cardiovascular diseases (CVD) among South Asians and find significant differences in frequencies of a number of non-synonymous variants in genes linked to CVDs between BEB and TSI samples, including the site rs1042034, which has been associated with higher risk of CVDs previously and the nearby rs676210 in the Apolipoprotein B (ApoB) gene.

Advisor: Pachter, Lior
Modeling and Selection for Real-time Wafer-to-Wafer Fault Detection Applications

The semiconductor manufacturing industry currently faces many challenges in terms of metrology and process control. With the delay of EUV and the advent of high aspect-ratio 3D structures, there is an increase both the number of complex processing steps and systematic/random errors, and optical resolution for metrology has now reached its limit for sub-14nm devices. The industry now requires real-time wafer-to-wafer control and in-line metrology, such as scatterometry or virtual metrology, for effective process monitoring./nData models provide a quick and flexible way for integrating different forms of information. For example, in metrology, often times it is useful to combine sensor data, previous measurements, and other types of signals to extract the best possible measurement. Moreover, as the number of process steps continues to increase, explicit physical modeling of each step becomes extremely time-consuming and empirical data models will quickly become an effective alternative. In this dissertation, we discuss the application and usefulness of empirical data inference models in the context of W2W advanced process control, especially/nfocusing on wafer fault detection./nWe first use virtual metrology, a type of in-line metrology technique, to determine whether the introduction of such data inference models is actually useful for the fab. Moreover, results show that the effective cost is determined by not only the model type and accuracy, but also the resulting false and missed alarm patterns. In the next chapter, we demonstrate an application of data models to fault detection by constructing a support vector machine classifier (SVM) and using only the diffraction signatures from scatterometry measurements to detect alarms. In the last chapter, we develop an algorithm for the SVM that allows one to choose the optimal false and missed alarm combination based on an asymmetric cost function. Moreover, our algorithm can be generalized for optimal hyperparameter selection/nfor any SVM problem.

Advisor: Spanos, Costas J
Evaluating the Impact of Two Cognitive Behavioral Therapy Programs on Recidivism in Chronic Juvenile Offenders

The goal of the present study was to examine the effect of two cognitive behavioral therapy programs on recidivism in a sample of chronic youthful offenders (N = 156) and to evaluate the relationship between commonly identified recidivism risk factors (i.e., prior criminal charges, parental history of criminal behavior, gang involvement, mental health diagnoses, and number of probation violations) and re-offending. All participants were male, 19 to 23 years of age, and were currently, or had been, under the supervision of a Western state’s county probation department. Participants were court-mandated to take either Aggression Replacement Training (ART, n = 90) or ART and Thinking for Change (T4C, n = 66). Survival analyses controlling for different custody release dates indicated that ART+T4C participants demonstrated lower recidivism rates than ART-only participants. The difference was first clearly depicted around Day 300 post-release when approximately 45% of ART-only participants had been arrested compared to 35% of ART+T4C participants. The difference became more apparent by day 500 when 80% of ART-only participants had been arrested compared to 40% of ART+T4C participants. The data provide a statistically significant defense that ART+T4C treatment participants are likely to remain in the community longer without re-arrest than ART-only participants. Regarding recidivism risk factors, a Kaplan Meier survival curve indicated that mental health diagnoses, history of parental arrest, gang involvement, felony, violent and weapons charges, and probation violations did not predict faster time to arrest. Interestingly, the Kaplan Meier analysis indicated that non-violent charges pre-treatment predicted post-treatment re-offending.

Advisor: Worrell, Frank C
First-Principles Approach to Materials Discovery, Design and Optimization: Applications to Transition-Metal Alloys and Functional Materials

This dissertation broadly describes efforts related to materials discovery, design and optimization/nusing a first-principles approach based on density functional theory (DFT)./nThe two main application areas comprise transition-metal alloys and functional materials./nThe research involving transition-metal alloys aims at finding cost-effective replacement/nstrategies for rhenium (Re). Elemental Re exhibits profuse deformation twinning under/nmechanical loads and has a high ductility. It is shown that the twinning characteristics of/nRe and its ductility are correlated with its anomalously low (11-21) twin-boundary energy./nThe origin of this twin-energy anomaly is related to the presence of icosahedral structural/nunits on the (11-21) twin boundary. These structural units are stabilized near d-band fillings/ncorresponding to Re. The (11-21) twin-boundary energy can be lowered further by/ndecreasing the d-band filling with respect to elemental Re. This increases the intrinsic/nductility according to three independent ductility parameters employed in this work: i)/nPugh's ratio of bulk to shear modulus, ii) Yoo's ratio of surface to twin energy and iii) an/nideal-strength criterion. Based on new insights in the relation between d-band filling, defect/nenergies and intrinsic ductility, several candidate alloys for Re replacement are proposed./nRu-based alloys with additions of Ta, W and Re are shown to be potential replacement/ncandidates. The last part of this dissertation describes high-throughput calculations that/nhave culminated in the two largest databases of elastic and piezoelectric tensor properties/navailable to-date. The workflow for doing such calculations is described, along with various/nchecks to ensure the accuracy of the calculated physical properties. The database with/nelastic-tensor properties is expected to be of use in a number of fields where discovery of/nnew materials with desired values of elastic stiffness or (lattice) thermal conductivity are of/ninterest. Further, data mining and machine learning can be applied to better understand/nelastic properties and their physical descriptors. Several novel piezoelectric materials are/ndiscovered as part of this work. Some of these exhibit a high intrinsic piezoelectric response/nand may serve as a starting point for a process in which the piezoelectric response is optimized/nby alloying and microstructure engineering. As such, this database can support a search for future/nreplacement candidates of the widely used piezoelectric materials such as Pb(ZrxTi1?-x)O3 (PZT) that contain lead.

Advisor: Asta, Mark