VictorJuiz/thesis huggingface dataset:
"Living Cadavers" in Bangladesh: Ethics of the Human Organ Bazaar
Keywords: Organ Trafficking
Kidney Seller
Ethics of Kidney Trade
Medical Tourism
Medical Anthropology
Bangladesh

The “miracle” success of transplant technology, alongside the commercialization of health care, and the increasing polarization between rich and poor have created the conditions for an illegal but thriving trade in human body parts. Based on 15 months of challenging fieldwork, my research examines the ethics of the organ bazaar, particularly the experiences of 33 kidney sellers living in Bangladesh. On the underground bazaar, not only human kidneys but also livers and corneas are advertised for sale. Recipients, sellers, and brokers regularly post newspaper advertisements to buy and sell organs. The average price for a kidney is US $1,500 in Bangladesh, a country where 78% of people live on less than $2 a day. My research examines serious ethical questions, such as these: Is it right to purchase an organ, even if the organ sought provides longevity? Is the sale of one’s organ a justifiable means of fighting poverty? These questions allow me to examine the ethics of harvesting organs, particularly from the bodies of impoverished people. Narrating the victims’ deeply moving testimonies, my ethnography reveals how organ buyers (both recipients and brokers) tricked and pressured Bangladeshi poor into selling their kidneys. In the end, these sellers were brutally deprived and deceived, and their suffering was extreme. In the post-vending period, sellers’ health, economic, and social conditions significantly deteriorated, yet none of them received the promised post-operative care—not even one appointment. My research therefore concludes that organ commodification is serious structural violence against the poor, at the terrible cost of harm and suffering to them. Examining the organ market proposition, I argue that the resulting violence and injustice against the poor provide a hefty reason to rebut this trade. Bangladeshi kidney sellers also stood up against organ commodification, speaking out about their suffering, and about various detrimental and unethical outcomes incurred in this deal. My research aims to offer insights to bioethics and to broaden the debate on human rights by exposing how technological advancement, structural violence, and grinding poverty intersect in the violation of justice to the poor, turning them into “living cadavers.”
Mental Health Issues and Work: Institutional Practices of Silence in a Mental Healthcare Organization
Keywords: Mental health
Employment
Healthcare
Institutional ethnography
Qualitative research

Over the past decade, mental illness in the workplace has become a key issue in the health and business communities, fueled in part by recognition of the high prevalence rates and significant costs for individuals and organizations. Although research in the field is starting to emerge, there are significant gaps in what is known, particularly with respect to the workplace context and its impact on workers. The overall objective of this study was to characterize, from a sociological perspective, the experiences of healthcare workers with mental health issues, and to account for how their experiences were shaped by the social relations of work. A qualitative approach, based on principles of institutional ethnography, guided exploration of the interactional, structural and discursive dimensions of work within a large mental health and addictions treatment facility. Data collection included in-depth interviews with twenty employees regarding their personal experiences with mental health issues, interviews with twelve workplace stakeholders regarding their interactions with workers, and a review of organizational texts related to health, illness and productivity. Analysis of the transcripts and texts was based on an institutional ethnography approach to mapping social processes; examining connections between local sites of experience and the social organization of work. The study findings revealed a critical disjuncture between the public mandate of advocacy, open dialogue, and support regarding mental health issues, and the private experience of workers which was characterized by silence, secrecy and inaction. Practices of silence were adopted by workers and workplace stakeholders across the organization, and were shaped by discursive forces related to stigma, staff-client boundaries, and responsibility to act. The silence had both positive and negative implications for the mental health of workers, as well as for relationships and productivity in the workplace. In accounting for the practices and production of silence, I argue that silence is complex, multi-dimensional, and embedded within the social relations of healthcare work. It serves to maintain institutional order. This conceptualization of silence challenges current beliefs and practices related to stigma, disclosure, early identification, support, and return to work for employees with mental health issues.
Characterization of the Cu-Si System and Utilization of Metallurgical Techniques in Silicon Refining for Solar Cell Applications
Keywords: Silicon
Refining
Impurity removal
Solar Si
Cu-Si alloy

Two methods for refining metallurgical grade silicon to solar grade silicon have been investigated. The first method involved the reduction of impurities from metallurgical grade silicon by high temperature vacuum refining. The concentrations of analyzed elements were reduced several times. The main steps in the second refining method include alloying with copper, solidification, grinding and heavy media separation. A metallographic study of the Si-Cu alloy showed the presence of only two microconstituents, mainly pure silicon dendrites and the Cu3Si intermetallic. SEM analysis showed a distinct boundary between the silicon and the Cu3Si phases, with a large concentration of microcracks along the boundary, which allowed for efficient separation. After alloying and grinding, a heavy media liquid was used to separate the light silicon phase from the heavier Cu3Si phase. Cu3Si residues together with the remaining impurities were found to be located at the surface of the pure silicon particles, and should be efficiently removed by acid leaching. Thirty elements were analyzed by the Inductively Coupled Plasma Mass Spectrometry (ICP) chemical analysis technique. ICP revealed a several times higher impurity level in the Cu3Si intermetallic than in the pure silicon; furthermore, the amounts of 22 elements in the refined silicon were reduced below the detection limit where the concentrations of 7 elements were below 1ppmw and 6 elements were below 2ppmw. The results showed that the suggested method is efficient in removing impurities from metallurgical grade silicon with great potential for further development.
Machine Learning Approaches to Biological Sequence and Phenotype Data Analysis
Keywords: Machine Learning
Bioinformatics
Computational Biology

To understand biology at a system level, I presented novel machine learning algorithms to reveal the underlying mechanisms of how genes and their products function in different biological levels in this thesis. Specifically, at sequence level, based on Kernel Support Vector Machines (SVMs), I proposed learned random-walk kernel and learned empirical-map kernel to identify protein remote homology solely based on sequence data, and I proposed a discriminative motif discovery algorithm to identify sequence motifs that characterize protein sequences' remote homology membership. The proposed approaches significantly outperform previous methods, especially on some challenging protein families. At expression and protein level, using hierarchical Bayesian graphical models, I developed the first high-throughput computational predictive model to filter sequence-based predictions of microRNA targets by incorporating the proteomic data of putative microRNA target genes, and I proposed another probabilistic model to explore the underlying mechanisms of microRNA regulation by combining the expression profile data of messenger RNAs and microRNAs. At cellular level, I further investigated how yeast genes manifest their functions in cell morphology by performing gene function prediction from the morphology data of yeast temperature-sensitive alleles. The developed prediction models enable biologists to choose some interesting yeast essential genes and study their predicted novel functions.
Liberalitas in Late Republican and Early Augustan Roman Poetry
Keywords: Latin
Poetry
Catullus
Virgil
Horace
Tibullus
Propertius
Gift Exchange

Liberalitas forms one of the central frameworks for defining social bonds within Roman society, and was part of how Roman poets constructed the world. This is most explicitly evident in the poets’ references to “patrons” and benefactors, but it extends much further. The poets worked within a broad framework of social conventions and expectations which must be understood in order to see how their poetry uses and responds to the concepts associated with liberalitas. Cicero’s de officiis and Seneca’s de beneficiis are therefore useful, as they offer idealised, prescriptive views of liberalitas in Roman society. Many scholars have investigated the relationships between poets and their patrons, including Peter White, Barbara Gold, James Zetzel, and Phebe Lowell Bowditch. I argue that any true understanding of the role of liberalitas in Roman poetry must also comprehend its importance in other areas. This dissertation focuses on the poetry of Catullus, Horace, Propertius, Tibullus, and Virgil in the Eclogues. The introduction addresses traditional liberalitas as defined by Cicero and Seneca in their works on benefits and duties. Chapter one illustrates how Catullus, Horace, and Tibullus display ideals similar to those of Cicero and Seneca and use the conventions of liberalitas for praising and blaming members of their social groups. Chapter two addresses the problems of status raised by liberalitas and investigates the strategies used by Catullus, Horace, Propertius, and Tibullus to mitigate these problems and further their social, literary, and aesthetic aims. Chapter three demonstrates how the love poets used and redefined the terminology and ideology of liberalitas to construct an obligation on the part of their beloveds to reciprocate the gifts given by the poets but reject the gifts given by rival lovers. Finally, Chapter four examines the role of liberalitas in formulating and expressing a poetic program in Virgil’s Eclogues, which points to its function in mediating the connection between ‘real-life’ political and social concerns and the literary preoccupations of Roman poets. The various applications of this concept demonstrated in these four chapters present the study of liberalitas as a useful and productive tool in the investigation of the poetry of this period.
Non-Abelian Localization and U(1) Chern-Simons Theory
Keywords: Chern-Simons Gauge Theory
Sasakian Geometry
Quantum Field Theory
Symplectic Geometry

This thesis studies U(1) Chern-Simons theory and its relation to the results of Chris Beasley and Edward Witten (2005). Using the partition function formalism, we are led to compare U(1) Chern-Simons theory as constructed by Manoliu (1998) to the results of Beasley and Witten (2005). This leads to an explicit calculation of the U(1) Chern Simons partition function on a closed Sasakian three-manifold and opens the door to studying rigorous extensions of this theory to more general gauge groups and three-manifold geometries.
Secure Wavelet-based Coding of Images, and Application to Privacy Protected Video Surveillance
Keywords: wavelet
image coding
encryption
security
privacy
video coding
secure image coding
secure object coding

The protection of digital images and video from unauthorized access is important for a number of applications, including privacy protection in video surveillance and digital rights management for consumer applications. However, traditional cryptographic methods are not well suited to digital visual content. Applying standard encryption approaches to the entire content can require significant computational resources due to the large size of the data. Furthermore, digital images and video often need to be manipulated,such as by resizing or transcoding, which traditional encryption would hinder. A number of image and video-specific encryption approaches have been proposed in the literature, but many of the them have significant negative impact on the ability to compress the data, which is a necessary requirement of most imaging systems. In this work, a secure image coder, called Secure Set Partitioning in Hierarchical Trees (SecSPIHT), is proposed. It combines wavelet-based image coding (compression) with efficient encryption. The encryption is applied to a small number of selected bits in the code domain, to achieve complete confidentiality of all the content while having no negative impact on compression performance. The output of the system is a secure code that cannot be decrypted and decoded without the provision of a secret key. It has superior rate-distortion performance compared to JPEG and JPEG2000, and the bit-rate can be easily scaled via a simple truncation operation. The computational overhead of the encryption operation is very low, typically requiring less than 1% of the coded image data to be encrypted. A related secure object-based coding approach is also presented. Called Secure Shape and Texture Set Partitioning in Hierarchical Trees (SecST-SPIHT), it codes and encrypts arbitrarily-shaped visual objects. A privacy protection system for video surveillance is proposed, using SecST-SPIHT to protect private data, such as face and body images appearing in surveillance footage. During normal operation of the system, the private data objects are protected via SecST-SPIHT. If an incident occurs that requires access to the data (e.g., for investigation), a designated authority must release the key. This is superior to other methods of privacy protection which irreversibly blur or mask the private data.
Biochemical Studies of the CTCF Insulator Protein: Determination of Protein Interactions with CTCF using Tandem Affinity Purification, Characterization of its Post-translational Modification by the Small Ubiquitin-like Modifier Proteins and Studies of CTCF DNA Looping Ability
Keywords: CTCF
Epigenetics

The CTCF protein is involved in several important aspects of gene regulation including transcriptional activation, transcriptional repression and insulator ability. It is also involved in the regulation of epigenetic processes including X-chromosome inactivation and the maintenance of genomic imprinting. CTCF has been shown to bind to approximately 15 000 sites in the mammalian genome and has been implicated in nuclear organization. The CTCF protein mediates long-range chromatin interactions and is believed to form DNA loops. It also acts to block the communication of an enhancer with a promoter by acting as an insulator. Despite its importance in gene regulation, the molecular mechanisms that govern CTCF’s ability to perform its myriad functions remain enigmatic. In this thesis, I add insight into our understanding of the mechanisms behind CTCF’s function. I show that CTCF is post-translationally modified by the Small Ubiquitin-like Modifier proteins and that this post-translational modification contributes to its repressive ability at the c-myc P2 promoter. I also show that CTCF is localized to the sub-nuclear compartment called the Polycomb bodies. The Polycomb protein Pc2 acts as an E3 ligase to enhance the SUMOylation of CTCF by SUMOs 2 and 3. These findings help to explain CTCF’s ability to act as a transcriptional repressor. I also report biochemical evidence to support the role for CTCF in forming an unusual DNA structure, possibly a loop. I hypothesize that a single CTCF binding site is able to form DNA loops. These findings suggest mechanisms by which CTCF is able to organize the mammalian genome and to function as an insulator protein. In addition to these findings I have also purified CTCF interacting proteins through the use of the tandem affinity purification technique. The interacting proteins contain many chromatin and DNA binding proteins further suggesting a role for CTCF in chromatin organization. The results in this thesis enhance our knowledge of the molecular mechanisms of CTCF function and provide a basis for the improved understanding of CTCF mediated gene expression.
MRI Based Imaging of Current Densities and Tissue Conductivities
Keywords: Current Density Imaging
Electrical properties
Magnetic Resonance Imaging
Current Density Impedance Imaging

Magnetic resonance imaging (MRI) is an imaging modality that noninvasively measures magnetic fields by selectively exciting the magnetization of protons inside the body. When combined with an understanding of electromagnetic theory, MRI can be used in a novel way to provide a powerful tool for measuring the electromagnetic fields and electrical properties of biological tissues. This thesis presents the analytical, numerical, processing and experimental components of a successful implementation of Low-Frequency Current Density Impedance Imaging (LF-CDII), an impedance imaging method based on MRI measurements. The accuracy, stability and noise tolerance of this technique are examined. The first in-vivo LF-CDII experiment was conducted with a clinical MRI scanner, and the conductivity distribution of the heart of a live piglet was obtained. Both the simulation and experimental results show that LF-CDII can be used as a reliable tool for accurate noninvasive, quantitative imaging of tissue conductivities. This thesis also presents new data processing algorithms, imaging procedures and hardware development for the measurement of electromagnetic fields at radio frequencies, based on Polar Decomposition Radio Frequency Current Density Imaging (PD-RFCDI). The method was tested on both numerical models and experiments on phantoms. The results show that the techniques presented here are able to successfully image current density fields without the strict restrictions on the direction and magnitude of the currents required in previous versions of RFCDI.
Low and Mid-level Shape Priors for Image Segmentation
Keywords: Perceptual Grouping
Image Segmentation
Superpixels
Symmetry
Closure

Perceptual grouping is essential to manage the complexity of real world scenes. We explore bottom-up grouping at three different levels. Starting from low-level grouping, we propose a novel method for oversegmenting an image into compact superpixels, reducing the complexity of many high-level tasks. Unlike most low-level segmentation techniques, our geometric flow formulation enables us to impose additional compactness constraints, resulting in a fast method with minimal undersegmentation. Our subsequent work utilizes compact superpixels to detect two important mid-level shape regularities, closure and symmetry. Unlike the majority of closure detection approaches, we transform the closure detection problem into one of finding a subset of superpixels whose collective boundary has strong edge support in the image. Building on superpixels, we define a closure cost which is a ratio of a novel learned boundary gap measure to area, and show how it can be globally minimized to recover a small set of promising shape hypotheses. In our final contribution, motivated by the success of shape skeletons, we recover and group symmetric parts without assuming prior figure-ground segmentation. Further exploiting superpixel compactness, superpixels are this time used as an approximation to deformable maximal discs that comprise a medial axis. A learned measure of affinity between neighboring superpixels and between symmetric parts enables the purely bottom-up recovery of a skeleton-like structure, facilitating indexing and generic object recognition in complex real images.
Singularity Formation in Nonlinear Heat and Mean Curvature Flow Equations
Keywords: nonlinear heat equation
mean curvature flow

In this thesis we study singularity formation in two basic nonlinear equations in n dimensions: nonlinear heat equation (also known as reaction-diffusion equation) and mean curvature flow equation. For the nonlinear heat equation, we show that for an important or natural open set of initial conditions the solution will blowup in finite time. We also characterize the blowup profile near blowup time. For the mean curvature flow we show that for an initial surface sufficiently close, in the Sobolev norm with the index greater than [special characters omitted] + 1, to the standard n-dimensional sphere, the solution collapses in a finite time t∗, to a point. We also show that as t → t∗, it looks like a sphere of radius
The Production of Racial Logic In Cuban Education: An Anti-colonial Approach
Keywords: Cuban studies
anti-racism
anti-colonialism
education
teachers
race relations

This work brings an anti-colonial reading to the production and maintenance of racial logic in Cuban schooling, through conversations with, and surveys of Cuban teachers, as well as through analysis of secondary and primary documents. The study undertaken seeks to contribute to the limited existent research on race relations in Cuba, with a research focus on the Cuban educational context. Teasing and staking out a middle ground between the blinding and often hollow pro-Cuba fanaticism and the deafening anti -Cuban rhetoric from the left and right respectively, this project seeks a more nuanced, complete and dialogical understanding of race and race relations in Cuba, with a specific focus on the educational context. With this in mind, the learning objectives of this study are to investigate the following: 1) What role does racism play in Cuba currently and historically? 2) What is the role of education in the life of race and racism on the island? 3) What new questions and insights emerge from the Cuban example that might be of use to integrated anti-racism, anti-colonialism and class-oriented scholarship and activism? On a more specific level, the guiding research objectives of the study are to investigate the following: 1) How do teachers support and/or challenge dominant ideas of race and racism, and to what degree to do they construct their own meanings on these topics? 2) How do teachers understand the relevance of race and racism for teaching and learning? 3) How and why do teachers address race and racism in the classroom? The data reveal a complex process of meaning making by teachers who are at once produced by and producers of dominant race discourse on the island. Teachers are the front line race workers of the racial project, doing much of the heavy lifting in the ongoing struggle against racism, but are at the same time custodians of an approach to race relations which has on the whole failed to eliminate racism. This work investigates and explicates this apparent contradiction inherent in teachers’ work and discourse on the island, revealing a flawed and complex form of Cuban anti-racism.