VictorJuiz/thesis huggingface dataset:
The impact of III-V and GE devices on circuit performance [electronic resource]
Keywords: Electrical Engineering

Because the performance enhancement from scaling in accordance to Moore's law encounters difficulties, recent research has focused on finding new device materials with higher intrinsic carrier mobility. III-V and Ge MOSFETs have been, especially, studied as potential replacements for Si MOSFETs. This dissertation addresses the building of spice-compatible models for such new devices, the estimation of the delay and energy of digital circuits, and the performance comparison of various digital blocks and SRAM cells with different combinations of Si, III-V, and Ge devices. This work, first, develops spice-compatible III-V nFET and Ge pFET models in order to estimate the actual gain of using these devices in digital circuits. A compact model is employed for modeling the III-V nFET, a modified BSIM library is used for describing the Ge pFET, and a RC model is adopted for counting the effect of wires. With these models, various common digital blocks are explored. This thesis covers the modeling and simulations of the delay and energy of digital logics, including inverters, 32-bit adders, interconnect drivers as well as FPGAs. The driving capability of the nFET and pFET should be matched for optimum noise margin and performance, in typical digital design. Both capacitance and driving current are important for performance. The combination of III-V nFET with a thick barrier layer and Ge pFET achieves the best delay-energy performance for many digital logic circuits. The advantages of small capacitance and high driving capability disappear with long wire interconnect. FPGA design does not benefit from advanced device because the delay-energy performance is dominant by wires. An SRAM cell is also studied. This work addresses the trade-offs between performance specifications including noise tolerance of SRAM cells comprising Si, III-V, and Ge device. The read margin of SRAM is maximized with the Si passgate, the III-V nFET pull-down, and the Ge pFET pull-up transistor. The write margin of SRAM, on the other hand, is maximized with the III-V passgate, III-V nFET pull-down, and Ge pFET pull-up transistor. There is a tradeoff between read and write margin. The modeling and simulation methodology and insights provided in this thesis enable us to determine the actual gain of digital circuits with advanced devices. The results offer suggestions for the direction of future device development.
The impact of traditional textbook and epistemologically transparent text accounts on high school biology students' interest, comprehension, learning, and epistemology [electronic resource]
Keywords: Education.

Textbooks are highly influential in defining both the curriculum and instruction of high school biology classrooms, yet most widely-used textbooks have been criticized for their extensive focus on declarative knowledge that fails to reflect the nature of the discipline. This study compares the impact of traditional textbook accounts and alternative "epistemologically transparent" accounts on students' interest, comprehension, learning, and epistemological perspectives. Unlike traditional textbooks that provide scientific facts and concepts with no justification, these alternative texts incorporate narratives of historical experiments that include authentic research questions, methods, and data that support scientists' claims. This study included two components -- four replications of a randomized experiment involving approximately 235 students and a think aloud/interview protocol with 24 students. Results of the experiment showed that text type did not have a differential impact on student interest or comprehension. Students in the treatment condition did show instances in which they transferred biological concepts and experimental designs to novel situations at a statistically higher rate than students in the control group. Students in the treatment group also exhibited more sophisticated epistemological perspectives than students in the control group. Think alouds and interviews with a small sub-set of students indicated that the epistemic elements embedded in the treatment text positively affected students' interest, comprehension, and trust in the text's claims. These results suggest that epistemologically transparent texts may function as helpful supplements to traditional textbook accounts in order to help students both learn biological concepts and how the discipline justifies these concepts.
Improved quantification of in vivo metabolic kinetics using hyperpolarized 13C magnetic resonance spectroscopic imaging [electronic resource]
Keywords: Electrical Engineering

With signal-to-noise ratio enhancements on the order of 10,000-fold, hyperpolarized 13C MRSI allows the study of both the injected substrate and downstream metabolic products in vivo within the target organ, with the appearance of the 13C labels on the various metabolites resulting from a combination of isotopic exchange and metabolic flux. Although hyperpolarized [1-13C] pyruvate has been extensively researched as an in vivo biomarker for disease diagnosis and response to therapy, efficient and robust quantification still remains important areas of investigation. Recently, a new quantification paradigm called the saturable kinetics of 13C labeling process was proposed. This method utilized a Mechaelis-Menton-like mathematical formulation with the estimated apparent Vmax to directly quantify the dose dependence (i.e., the saturation effects) of lactate and alanine reaction velocities following one hyperpolarized 13C pyruvate injection. However, to obtain the apparent Vmax, the current quantification method repeats the multi-site exchange model fitting with different pyruvate doses and each data point corresponds to one independent pyruvate injection. Therefore, the process needs multiple injections and multiple subjects to obtain one single saturation curve. Such an intense injection pattern is almost impossible for clinical trials. Also, the estimated apparent Vmax inevitably involves the inter-subject variability due to the multi-subject requirement. Therefore, it is necessary to have an efficient quantification method for the saturable kinetics and apparent Vmax measurement. First, we developed an inflow-based single-slice quantification method which can measure saturable kinetics in one slice efficiently. The experiment time can be reduced from multiple injections with multiple animals to one injection. We demonstrated our quantification method on healthy models (rat kidney and liver) and disease models (mouse prostate tumor). Second, we applied our proposed inflow-based single-slice quantification method and demonstrated the relative change of apparent Vmax of the lactate 13C labels was well correlated with the gold-standard ALDH2 enzymatic activity in rat liver. It may serve as a potential noninvasive in vivo indicator for ALDH2 activity and provide an alternative way to research the related diseases including alcoholism and ischemia. Finally, we extended our proposed inflow-based quantification method to the 3D case so that the saturable kinetics in multiple slices can be measured efficiently following one single pyruvate injection. This extension further improved the quantification efficiency and is useful in the case of the heterogeneous in vivo saturable kinetics. We demonstrated our 3D quantification method in healthy rat models.
An in vitro CENP-A assembly assay reveals a role for CENP-C in CENP-A deposition [electronic resource]
Keywords: Biochemistry

Eukaryotic chromosomes segregate by attaching to microtubules of the mitotic spindle through a chromosomal microtubule-binding site called the kinetochore. Kinetochores assemble on a specialized chromosomal locus termed the centromere, characterized by the replacement of histone H3 in centromeric nucleosomes with the essential histone H3 variant centromere protein A (CENP-A). CENP-A nucleosomes are believed to epigenetically specify centromere identity, thus understanding how CENP-A chromatin is assembled and maintained is central to understanding chromosome segregation mechanisms. CENP-A nucleosome assembly requires the Mis18 complex and the CENP-A chaperone HJURP. HJURP binds to pre-nucleosomal CENP-A and facilitates the deposition of new CENP-A nucleosomes into centromeric chromatin. The mechanistic roles of the Mis18 complex in CENP-A assembly and maintenance are not well understood. The Mis18 complex and HJURP localize to centromeres in telophase/G1, when new CENP-A chromatin is assembled. The molecular interactions that control their targeting are unknown. Several constitutive centromere proteins that remain associated with CENP-A chromatin throughout the cell cycle have also been implicated in CENP-A assembly, including CENP-C. Their functions in CENP-A assembly are unknown. The first chapter of this thesis work describes the development of an in vitro system for centromeric chromatin assembly in Xenopus laevis egg extracts. We show that CENP-A assembly in extract recapitulates the cell cycle dependence and HJURP requirement of CENP-A assembly in somatic cells. We then use this in vitro system to identify a novel role for CENP-C in recruiting CENP-A assembly factors to the centromere to promote CENP-A assembly, described in Chapter 2. We show that CENP-C is required to target the Mis18 complex protein M18BP1 to Xenopus sperm centromeres in metaphase. In the absence of CENP-C, M18BP1 and HJURP targeting to centromeres is disrupted and new CENP-A assembly into centromeric chromatin is inhibited. We find that CENP-C interacts directly with M18BP1 through conserved domains in the CENP-C protein. Thus, CENP-C provides a link between existing CENP-A chromatin and the proteins required for new CENP-A nucleosome assembly. Overall, this work extends our mechanistic understanding of how the pre-existing centromere directs the local assembly of new CENP-A nucleosomes to ensure stable propagation of the centromere. Furthermore, the ability to assemble centromeric chromatin in vitro will provide a valuable tool for dissecting the biochemical and cell cycle regulatory mechanisms that control new CENP-A assembly and ensure faithful centromere propagation.
India’s Red Stain: Explaining the Indian Government’s Ineffective Response to the Maoist-­Naxalite Insurgency Since 1967
Keywords: Center for International Security and Cooperation
CISAC
India
Naxalite movement
Communist Party of India
insurgency
policy
Thesis

Since 1967, the Maoist-Naxalite movement has grown from a local peasant rebellion to a violent insurgency that operates in more than 10 of India’s 28 states and is widely considered to be the single biggest threat to India’s internal security. For more than four decades, as Naxalite violence has killed an estimated 15,000 Indians, the government has failed to address the driving motivation of the insurgency, allowing the movement to spread geographically and increase its violent threat. Most of what has been written about the Naxalites offers only partial or murky explanations of India’s failure to effectively address the violence. This thesis examines the nature of the Naxalite movement since its inception and analyzes the response of the government over time to answer the question: What accounts for India’s failure to effectively address Naxalite violence from 1967 to the present? It concludes that India consistently adopted the wrong strategy at the wrong time toward the insurgency, and that it did so due to a combination of three factors: the shifting nature of the movement; inherent inefficiencies in center-state relations; and the presence of other security challenges on the nation’s agenda. India is increasingly the focus of global attention, as its economy today grows at a rate second only to that of China. Yet, its advancement is still constrained by the same socio-­economic grievances that inspired the Naxalites in 1967. The study concludes with the implications relevant for current and future Indian policymakers to consider in adopting a strategy against the threat posed by the Maoist-­Naxalite insurgency.
Inferring the Halo Mass Function from Galaxy Clusters: Accuracy Limits Due to Redshift-Space Distortions
Keywords: Physics
Petrosian, Vahe
dark matter halos
halo mass function
fingers-of-God effect
Thesis

Measuring the abundance of dark matter halos as a function of mass – termed the halo mass function – allows us to constrain cosmological parameters of interest. One way to infer the halo mass function is through measuring the abundance of galaxy clusters as a function of optical richness in redshift surveys. However, redshift-space distortions cause errors in cluster-finding and thus place a fundamental limit on the accuracy of this method. In particular, the velocity dispersion of member galaxies stretches out a galaxy cluster in redshift-space along the line of sight, in what is known as the 'fingers-of-God' effect. The main focus of this thesis is to estimate the contribution of this effect to the accuracy limit of the cluster mass function measured from optically-selected galaxy clusters.
This study uses Monte Carlo experiments to estimate the error rate in cluster-finding due to 'fingers-of-God' confusions in an idealized model. The trade-off between two types of error – fragmentation and overmerging – is studied in detail, and presented as an intermediate result. The model is then applied to a halo catalog from a cosmological simulation. Redshift-space confusions are found to tilt the measured halo mass function towards higher masses. Under the assumptions of our setup, the effects bias the best-fit cosmological parameters by a few percent, within the range that is relevant for inferring these parameters from upcoming surveys.
Infrapolitics [electronic resource] : the social life of water in Mumbai
Keywords: Anthropology

Framed by popular and scholarly anxieties about burgeoning cities on one hand, and disappearing water resources on the other, this dissertation is an account of how urban water is made, moved, and subsequently delivered to settlers and other marginalized residents in one of the world's largest cities- Mumbai, India. Based on twenty-two months of ethnographic fieldwork among settlers, engineers of the city's water department, and various other urban experts (plumbers, city planners, social workers), it explores how cities, citizens and their states are made and differentiated through the incremental and continuous extension of the city's hydraulic infrastructure. In theorizing how cities are claimed, inhabited and made livable, particularly for (and by) politically marginalized groups, this research seeks to make a contribution to the literature in political ecology, state formation and citizenship. Where many settlers are formally and substantively denied access to water from the city's public system, I show how they access water through infrapolitics, by drawing on relations with social workers, laws, politicians, pipes, plumbers and policies. By focusing on these everyday practices of making connections, this dissertation shows why we need to reconsider normative distinctions between rights and commodities, persistent in international debates about urban water supply. The everyday practices of settlers in making water connections effect what I suggest are forms of hydraulic citizenship; forms of belonging to the city that are enabled by effective political and material claims to the city's public water system. I show how settlers mobilize hydraulic citizenship through a diverse articulation of political, social and material relations with the city's water pipes and their various authorities. In showing how Mumbai's hydraulic infrastructure constantly and consistently escapes political control, this research also seeks to make a contribution to the scholarship in Science Studies and Political Ecology. I suggest that the materiality of the city's public water system- made through thousands of miles of pipes and employees- makes it especially conducive to the claims of marginalized groups. As settlers and other residents constantly mobilize their votes, favors and money to evaluate and respond to the dynamic flow of water in the city, their connections both elucidate and differentiate the ways in which they are able to make reliable homes in the city despite the predations of states and markets.
Insights into structural details and energy usage of the group II chaperonin TRiC [electronic resource]
Keywords: Biology.

Chaperonins are a subset of molecular chaperones which assist in the protein folding process. These oligomeric chaperone complexes can be classified into two structurally distinct classes: group I, which are found in prokaryotes and endosymbiotic organelles, or group II, which are present in archaea and eukaryotes. The TCP-1 ring complex (TRiC) or CCT, is an essential, barrel-shaped group II chaperonin complex involved in folding approximately 10% of all proteins within the eukaryotic cytosol. While the general architecture of TRiC is understood, the exact arrangement of the 8 unique TRiC subunits (CCT1-8) within each ring, as well as the stacking between the two rings, has been debated for over a decade. This thesis includes data to support a specific arrangement for the TRiC complex based on results from mass spectrometry from crosslinked yeast and bovine TRiC, yeast ex vivo crosslinking, and probabilistic models. In addition, this work also characterizes the different affinities for ATP among CCT1-8 as well as their functional relevance in vivo. These developments contribute to the understanding of fundamental mechanisms regarding how TRiC mediates the folding of different protein substrates in the chaperonin-assisted folding process.
An integrated approach to robotic navigation under uncertainty [electronic resource]
Keywords: Electrical Engineering

Autonomous robot navigation has been gaining popularity in the field of robotics research due to its important and broad applications. Sequential Monte Carlo methods, also known as particle filters, are a class of sophisticated Bayesian filters for nonlinear/non-Gaussian model estimation, and have been used for the simultaneous localization and mapping (SLAM) problem in robot navigation in lieu of extended Kalman filters. However, the current particle filters, and their derivatives such as the particle-based SLAM filters for robotic navigation, still need further improvement to have better trade-off between performance and complexity in order to be used for online applications. Also, the current robot navigation approaches often focus on one aspect of the problem, lacking an integrated structure. In this work, we designed better sampling proposal distributions for particle filters, and demonstrated their superiority in simulation. Then, we applied our new particle filters to design and implement improved particle-based SLAM filters for the application of the SLAM problem in robot navigation, and tested using both simulation and outdoor experimental datasets. Finally, we incorporated the new particle-based SLAM filters in the design of a new framework for solving robotic navigation problems under uncertainty in a continuous environment. The framework balances between exploration and exploitation, and integrates global planning algorithms, local navigation routines, and exploration procedures in order to achieve the global goal, overcoming many common drawbacks of current approaches.
Integrated plasmonic waveguide photodetectors for optical interconnection of silicon chips [electronic resource]
Keywords: Electrical Engineering

To keep pace with the scaling of semiconductor technology, the amount of energy required to transmit one bit of information needs to be drastically reduced. Optical interconnects may become a key technology in enabling high bandwidth interconnections, provided that its components operate at sufficiently low energies per bit. At the receiver, the capacitance of the photodetector limits the speed and power consumption that can be achieved. Lower capacitance can be achieved by reducing the physical size of the photodetector to nanoscale volumes, an order of magnitude smaller than the optical wavelength. This dissertation focuses on metallic nanostructures that can be used to bridge this size mismatch between the optical mode and the optoelectronic device. They can be used to enhance the interaction between the optical signal and the photodetector, and if designed as a waveguiding structure, they can provide an efficient way of routing optical signals with deep subwavelength mode dimensions and can integrate well with nanoscale photodetectors, providing a route towards highly integrated low capacitance detectors for optical interconnects.
Integration of electronic health records and public biological repositories illuminates human pathophysiology and underlying molecular relationships [electronic resource]
Keywords: Biomedical Informatics.

Secondary use of electronic health record (EHR) data has the potential to unlock novel insight into human pathophysiology. While EHR data has often been used in retrospective studies, management of public health, and to improve patient safety, its use in discovering underlying molecular mechanisms of human disease and pathophysiology has been limited. Much of this can be attributed to the differing priorities between healthcare providers and basic biological researchers. The advent of biobanks that collect physiological measurements as well as tissue samples and molecular measurements promises to address this issue. However, the sheer number of different biological and clinical measurement modalities hinders the generation of a truly complete view of the human organism. The increased adoption of EHRs as well as growing biological data repositories enables researchers to answer biological questions applicable to the human population. The goal is not to treat humans as experimental organisms, but rather to gain as much knowledge as possible from every patient seen. By viewing EHRs as a repository of perturbations and their associated physiological consequences we can begin to design experiments that leverage EHR data to generate hypotheses that can be further evaluated. This thesis aims to describe methods to summarize EHR biomarker data in a systematic way to enable downstream analysis as well as methods for integrating EHR data and disparate biological data. I will describe the creation of the "clinarray" and its application to specific disease populations to differentiate patients by severity and to discover latent physiological factors associated with disease. I will also describe how to aggregate and analyze clinarrays from across the EHR to build models of aging. Finally I will discuss the use of diseases to integrate EHR data with gene expression data from a disparate biological data source to discover genes related to aging and to generate hypotheses for relationships between biomarkers and genes. The integration of readily available clinical and biological data promises to improve our understanding of phenomics without impacting patient care and adding an unnecessary burden to the healthcare system. It is important for biological research to leverage the increased amount of molecular and environmental data stored in EHRs to build a more complete view of the human organism.