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Cytogps: A Web-Enabled Karyotype Analysis Tool For Cytogenetics, Zachary B Abrams, Lin Zhang, Lynne V Abruzzo, Nyla A Heerema, Suli Li, Tom Dillon, Ricky Rodriguez, Kevin R Coombes, Philip R O Payne

Open Access Publications

SUMMARY: Karyotype data are the most common form of genetic data that is regularly used clinically. They are collected as part of the standard of care in many diseases, particularly in pediatric and cancer medicine contexts. Karyotypes are represented in a unique text-based format, with a syntax defined by the International System for human Cytogenetic Nomenclature (ISCN). While human-readable, ISCN is not intrinsically machine-readable. This limitation has prevented the full use of complex karyotype data in discovery science use cases. To enhance the utility and value of karyotype data, we developed a tool named CytoGPS. CytoGPS first parses ISCN karyotypes …

Graph Deep Learning: Methods And Applications, Muhan Zhang

McKelvey School of Engineering Graduate Student Theses & Dissertations

The past few years have seen the growing prevalence of deep neural networks on various application domains including image processing, computer vision, speech recognition, machine translation, self-driving cars, game playing, social networks, bioinformatics, and healthcare etc. Due to the broad applications and strong performance, deep learning, a subfield of machine learning and artificial intelligence, is changing everyone's life.Graph learning has been another hot field among the machine learning and data mining communities, which learns knowledge from graph-structured data. Examples of graph learning range from social network analysis such as community detection and link prediction, to relational machine learning such as …

Instrumentation For Dynamic Nuclear Polarization And Application Of Electron Decoupling For Electron Relaxation Measurement, Nicholas Howard Alaniva

Arts & Sciences Graduate Student Theses and Dissertations

Dynamic nuclear polarization nuclear magnetic resonance (DNP NMR) exploits internal electron spin and nuclear spin interactions to increase sensitivity and uncover valuable information regarding structure and dynamics of a system. To manipulate these interactions, instrumentation is developed to combine high-power microwave and radiofrequency irradiation with the ability to spin samples at the magic angle (MAS) at temperatures from 90 K to 4.2 K. Electron decoupling uses frequency-modulated microwaves to mitigate the electron-nuclear dipolar interaction, improving signal intensity and resolution in DNP NMR experiments. Electron decoupling is combined with short DNP periods to encode electron spin information in polarized nuclear signal. …

A Noncanonical Function Of The Telomerase Rna Component In Human Embryonic Stem Cells, Kirsten Ann Brenner

Arts & Sciences Graduate Student Theses and Dissertations

Telomeres are stretches of TTAGGG nucleotide repeats located at the ends of linear chromosomes that shorten with progressive cell division and prevent genomic instability at the cost of limiting a cell’s capacity to proliferate. This limitation can be overcome by telomerase, a ribonucleoprotein complex that elongates telomeres via reverse-transcription of the template telomerase RNA component (TERC). Recent studies have reported potential functions of TERC outside of its role in telomere maintenance. These noncanonical functions of TERC are however poorly defined, and the molecular mechanisms and biological relevance behind such functions remain elusive. Here, we generated conditional TERC knock-out human embryonic …

The Tortured Pre-History Of Urban Blight: African American St. Louis And The Politics Of Public Health, 1877-1940, Taylor Desloge

Arts & Sciences Graduate Student Theses and Dissertations

This dissertation is a long history of the contested legal and environmental category of blight, especially in its racialized dimensions, in tandem with the African American experience of living in blighted urban spaces and forging a black politics of public health and welfare. Rethinking the conventional view that identifies blight as simply a preoccupation of post-World War II planners, this dissertation relocates its roots in a politics of public health that emerged a hundred years earlier, in the Post-Reconstruction Era, when black migration to the city and the rise of industrial capitalism raised new questions over both the social needs …

The Transcription Factor Bhlhe40 Regulates Tissue-Resident Macrophages And Type 2 Immunity, Nicholas N. Jarjour

Arts & Sciences Graduate Student Theses and Dissertations

Transcriptional control of gene expression is essential for life, tailoring protein production to development and environment to maintain organismal homeostasis. A limited set of proteins termed transcription factors are critical to this process. As our understanding of these central regulators has improved, new aspects of cell and organismal biology have been revealed. Herein, we demonstrate the importance of the transcription factor Bhlhe40 to tissue-resident macrophages, T helper type 2 cells, and type 2 immune responses, revealing novel transcriptional control of macrophages and unexpected cytokine regulation of helminth infection. We find that Bhlhe40 is cell-intrinsically required for normal proliferation of large …

Elucidating Enhancer Function In Epidermal Development And Filaggrin Loss-Of-Function Variants In African American Atopic Dermatitis, Mary Elizabeth Mathyer

Arts & Sciences Graduate Student Theses and Dissertations

The epidermis is the outermost tissue of the skin and provides the body’s first line of defense against external assaults. The epidermis is primarily composed of keratinocytes that terminally differentiate and rise apically toward the surface to form the semipermeable barrier of the skin. A hallmark of keratinocyte terminal differentiation is the expression of genes from the Epidermal Differentiation Complex (EDC) locus. Many of the EDC protein products contribute to the structural integrity of the skin barrier, evidenced by several gene knockouts such as loricrin, and even genetic variation within gene coding sequences, that modulate the integrity of the skin …

Perceptual Precedence Or Increased Effort?: On The Mechanism Of The Small-Picture-Size Advantage In Category Learning, Toshiya Miyatsu

Arts & Sciences Graduate Student Theses and Dissertations

I have previously identified a novel perceptual manipulation that enhances learning of some complex natural categories, and the current dissertation aims to uncover its mechanism. Specifically, learning of categories of tropical fish was enhanced when learned through small pictures (about 2º) compared to large pictures (about 19º). Through analyzing the previous results and extant theories in various domains, I identified two potential mechanisms through which this small-picture-size advantage manifested. The perceptual precedence hypothesis postulates that the processing of local dimensions is prioritized in large pictures and the processing of global dimensions is prioritized in small pictures. Therefore, small picture size …

Devising A Scalable Synthesis To Probe The G-Protein Cell Receptor Signaling Pathway, Matthew Robert Medcalf

Arts & Sciences Graduate Student Theses and Dissertations

The G-protein coupled cell receptor signaling pathway is amongst the largest and most diverse class of cell-surface receptors in the body. Nearly 800 different genes encode for these cell membrane receptors which are responsible for mediating a variety of hormones, neurotransmitters, and sensory stimuli through the activation of intracellular G proteins. To date, roughly 34% of pharmaceuticals on the market target GPCR’s, but despite this fact, there are still many difficulties associated with targeting this family of receptors. The vast number of GPCR’s, disease states resulting from a dysregulation of multiple GPCR signaling pathways, and difficulties crystalizing and purifying the …

Phylogenetic And Genomic Characterization Of The Host-Pathogen Arms Race Between Bacterial Pathogens And Gossypium Hirsutum, Anne Zimmerman Phillips

Arts & Sciences Graduate Student Theses and Dissertations

Hosts and pathogens are eternally intertwined in an evolutionary arms race. When a pathogen causes a disease outbreak, scientists must identify resistance strategies that can durably tilt the arms race in favor of the host. This requires a deep understanding of both the genetic and environmental contexts in which the outbreak occurs. In this thesis I investigate the bacterial pathogens Xanthomonas citri pv. malvacearum (Xcm) and Pseudomonas syringae that caused disease outbreaks on Gossypium hirsutum from 2011-2017. I use pathogen genomics and host transcriptomics to develop hypotheses for how these pathogens emerged and how they cause disease. Phylogenetics and virulence …

Investigating Biological Mechanisms Of Radiation Resistance In Advanced Stage Cervical Cancer, Fiona Ruiz

Arts & Sciences Graduate Student Theses and Dissertations

The current standard of care treatment for locally advanced cervical cancer is curative intent pelvic radiation with concurrently administered platinum chemotherapy (CRT). This treatment strategy is effective for many patients, but 33-50% of patients treated with CRT develop disease recurrence. Metastatic and recurrent cervical cancer is an incurable condition, and many of the currently available treatments are associated with significant morbidity and mortality. Identifying these patients upfront is a challenge that clinicians face when developing treatment strategies. Previous studies used to catalog the genomic and transcriptomic landscape of cervical cancer lacked high quality corresponding clinical follow up data for patients, …

An Evolving Epigenome That Determines Tissue And Cell Specificity, Renee Louise Sears

Arts & Sciences Graduate Student Theses and Dissertations

Understanding the mechanisms driving phenotypic variation is a major goal of biology that unifies classical genetics with the emerging fields of genomics and epigenomics. Human and mouse share over 90% of genes and global tissue-specific patterns of expression are maintained between the species. Thus, it is hypothesized that gene expression is influenced through distinctive regulation among species in order to account for the unmistakable phenotypic divergence. DNA methylation, histone modifications, open chromatin patterns, transcription factor binding, and other epigenetic factors are all associated with shaping, maintaining, and repressing regulatory regions which in turn coordinate gene expression. It is vital to …

Physiologic And Pathologic Profiling Of Clonal Variations, Wing Hing Wong

Arts & Sciences Graduate Student Theses and Dissertations

This thesis sought to provide a better understanding of clonality in various malignant and non-malignant settings using a variety of genomic analytical tools. Clonality is pre-defined as the presence of a mixed population of cells in which each sub-population has distinct somatic mutation profile. It is a common feature in cancers where subpopulations of cells arise as a result of independent, yet continual acquisition of somatic mutations. The clonal architecture of cancers can be used as a diagnostic and prognostic biomarker as well as to monitor disease progression or resolution. Besides cancer, clonal variability and expansion is also implicated in …

Towards Interpretable Machine Learning With Applications To Clinical Decision Support, Zhicheng Cui

McKelvey School of Engineering Graduate Student Theses & Dissertations

Machine learning models have achieved impressive predictive performance in various applications such as image classification and object recognition. However, understanding how machine learning models make decisions is essential when deploying those models in critical areas such as clinical prediction and market analysis, where prediction accuracy is not the only concern. For example, in the clinical prediction of ICU transfers, in addition to accurate predictions, doctors need to know the contributing factors that triggered the alert, which factors can be quickly altered to prevent the ICU transfer. While interpretable machine learning has been extensively studied for years, challenges remain as among …

Development Of High-Speed Photoacoustic Imaging Technology And Its Applications In Biomedical Research, Yun He

McKelvey School of Engineering Graduate Student Theses & Dissertations

Photoacoustic (PA) tomography (PAT) is a novel imaging modality that combines the fine lateral resolution from optical imaging and the deep penetration from ultrasonic imaging, and provides rich optical-absorption–based images. PAT has been widely used in extracting structural and functional information from both ex vivo tissue samples to in vivo animals and humans with different length scales by imaging various endogenous and exogenous contrasts at the ultraviolet to infrared spectrum. For example, hemoglobin in red blood cells is of particular interest in PAT since it is one of the dominant absorbers in tissue at the visible wavelength.The main focus of …

Corrosion-Resistant Non-Carbon Electrocatalyst Supports For Proton Exchange Membrane Fuel Cells, Cheng He

McKelvey School of Engineering Graduate Student Theses & Dissertations

Proton exchange membrane fuel cells (PEMFCs) are a promising portable power source due to their low operating temperature, minimal pollutant generation and fast startup. However, several challenges remain concerning lifetime, reliability, and cost. A critical issue is PEMFC component durability. Platinum supported on high surface area carbon has been one of the most widely used electrocatalysts in PEMFCs. However, carbon corrosion over the course of normal PEMFC operation occurs due to the relatively low standard electrode potential for the carbon dioxide/carbon redox couple (0.207V vs. standard hydrogen electrode). Considering this challenge, it is imperative to identify alternative support materials to …

Contemporary Problems In Aerosol Aggregation And Gelation, Pai Liu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Aggregation of nanoparticles in aerosols is a fundamental phenomenon with important implications to diverse fields ranging from material synthesis to pollutant control. The past few decades have witnessed extensive research on investigating the structure and growth mechanism of aerosol aggregates with sizes spanning across several orders of magnitude. This dissertation focuses on some contemporary problems that remain unaddressed in this topical area. Aerosol aggregates in sub-micron regimes, which are formed via the irreversible collision and aggregation of solid nanoparticle monomers, are fractal-like in their morphology. A mathematical description of this seemingly random structure dates to the seminal works by Forest …

Kernel Methods For Graph-Structured Data Analysis, Zhen Zhang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Structured data modeled as graphs arise in many application domains, such as computer vision, bioinformatics, and sociology. In this dissertation, we focus on three important topics in graph-structured data analysis: graph comparison, graph embeddings, and graph matching, for all of which we propose effective algorithms by making use of kernel functions and the corresponding reproducing kernel Hilbert spaces.For the first topic, we develop effective graph kernels, named as "RetGK," for quantitatively measuring the similarities between graphs. Graph kernels, which are positive definite functions on graphs, are powerful similarity measures, in the sense that they make various kernel-based learning algorithms, for …

Pertumbuhan, Hasil Dan Karakter Fisiologis Padi Yang Diberi Pupuk Hayati Pada Pertanaman Kelapa Sawit Belum Menghasilkan I, Annisa Nuraisah, Cucu Suherman, Mira Ariyanti, Anne Nuraini, Mochamad Arief Soleh

Jurnal Kultivasi

ruang terbuka diantara tanaman kelapa sawit belum menghasilkan dapat dimanfaatkan untuk budidaya tanaman pangan, khususnya padi sebagai tanaman sela dalam rangka mendukung program ketahanan nasional. Penelitian dilakukan dengan tujuan untuk memperoleh dosis pupuk hayati yang berpengaruh paling baik terhadap pertumbuhan, hasil, dan karakter fisiologis tanaman padi yang ditanam pada pertanaman kelapa sawit TBM 1 serta melihat dampak penanaman padi sebagai tanaman sela terhadap pertumbuhan kelapa sawit. Percobaan dilakukan di Kebun Percobaan Ciparanje, Fakultas Pertanian, Universitas Padjadjaran, pada bulan Desember 2017 sampai bulan April 2018. Percobaan disusun menggunakan Rancangan Acak Kelompok (RAK) yang terdiri dari enam perlakuan dosis pupuk hayati, yaitu …

Fabrication Of Paraffin Wax Particles With Diameter 100 Um, Sida Xue, Patricia Weisensee

Mechanical Engineering and Materials Science Independent Study

This independent study project is a preparatory work for the research- paraffin wax particle impacting dynamics and phase change behavior on quiescent paraffin wax liquid surface. The purpose for this independent study project is to produce paraffin wax particles with diameter 100 um both in their original color and dyed color.

St. Benedict Parish For The Deaf Church Bulletin, December 15, 2019

Saint Benedict Parish for the Deaf Church Bulletin

A newsletter published for Deaf Catholics in San Francisco, CA

Saint Benedict Parish for the Deaf Church Bulletin Finding Aid

St. Francis Borgia Deaf Center Church Bulletin, December 15, 2019

Saint Francis Borgia Deaf Center Church Bulletin

A newsletter published for Deaf Catholics in Chicago, IL

Saint Francis Brogia Deaf Center Church Bulletin Finding Aid

Bradley Stifles Men’S Basketball, Downs Eagles 81-51, Georgia Southern University

Athletics: News & Publications

• Bradley Stifles Men’s Basketball, Downs Eagles 81-51

Territorialidad De Los Grupos Familiares De Pueblos Indígenas En Aislamiento (Pia) En La Región Del Yasuní, Amazonía Ecuatoriana, Roberto Esteban Narváez Collaguazo

Tipití: Journal of the Society for the Anthropology of Lowland South America

El artículo presenta información etnográfica y una interpretación etnológica sobre los Tagaeiri y Taromenane como parte de los grupos familiares en aislamiento que habitan en el Yasuní, su forma de vida tradicional y su territorio, en un contexto de actores externos que inciden en la generación de violencia y de amenaza a su supervivencia. Sobre los pueblos en aislamiento en Ecuador existe información referenciada en datos indirectos que han dado indicios de presencia a partir de registros de rastros e imágenes satelitales y algunos datos directos, como avistamientos, encuentros en la selva, fotografías aéreas y, el principal, encuentros que generaron …

Thinking Through Tubes: Flowing H/Air And Synaesthesia, Stephen P. Hugh-Jones

Tipití: Journal of the Society for the Anthropology of Lowland South America

The tube, as both object and concept, has cropped up from time to time in the ethnography of lowland South America, most notably in Rivière and Lévi-Strauss’s discussions of blowpipes, hair tubes and pottery and in Hill and Wright's writings on Yuruparí flutes and trumpets. Using data from Northwest Amazonia, this paper first seeks to provide a more rigorous definition of the tube as a concept, exploring its various manifestations and relating these to the body as an image of totalization and detotalization. With reference to myths about creation and Yuruparí, the paper then argues that flows from tubes provide …

Good Reasons Or Bad Conscience? Or Why Some Indian Peoples Of Amazonia Are Ambivalent About Eating Meat, Stephen P. Hugh-Jones

Tipití: Journal of the Society for the Anthropology of Lowland South America

Originally written for a conference on meat attended by farmers, anthropologists, people involved in cultural affairs, and other members of the public, and seeking to avoid emphasis on cultural difference, this paper explores common ground between Euro-American and Amerindian ambivalence about meat consumption. Meat-eating raises two shared concerns: an intuitive recognition of the resemblances between humans and animals and an uncomfortable awareness that human life often depends on the death and destruction of other living beings. I suggest that, behind some obvious cultural differences, Amazonian shamanic and ritual procedures aimed at the de-subjectification of meat share points in common with …

The "Uncontacted" As Third Infamy, George Mentore

Tipití: Journal of the Society for the Anthropology of Lowland South America

This paper principally addresses the "problem" of anthropological thinking, that is, on how and why it remains with us and not with the peoples who do not subscribe to our contested regimes of truth. From my research on the topic, it appears we have not achieved any substantial moral progress on the question of exposure to indigenous otherness since the first European "contact." This failure is primarily due to our hardheaded rationalist refusal to accept our inability to access the felt reality of the Other directly. Or, better still, of the failure of our language to obtain the shared reality …

Christianity + Schooling On Nature Versus Culture In Amazonia, Aparecida M. N. Vilaça

Tipití: Journal of the Society for the Anthropology of Lowland South America

Based on the analysis of Evangelical Biblical translations, as well as on the school writing of Wari' (Southwestern Amazonia) students, produced in indigenous secondary school classrooms and at the intercultural university, this article aims to show how, in both church and school, a nature separate from humans is invented with which they should relate in a utilitarian and also contemplative way. Simultaneously nature’s opposite is invented–a culture that excludes animals and subjects them.

Rexistência Nas Fronteiras Do Capitalismo/Colonialismo: A Ecologia Política Do Isolamento E Da Soberania, Felipe Milanez

Tipití: Journal of the Society for the Anthropology of Lowland South America

Ofereço a perspectiva da ecologia política para rever e atualizar a política de “isolamento” e “não-contato” com base nos conceitos de soberania e necropolítica, sugerindo uma nova proposta de prática política para situações de conflitos em territórios ocupados por povos indígenas que resistem à conquista pela guerra e distanciamento. Da perspectiva do estudo dos conflitos ambientais, a ecologia política questiona a noção de isolamento ao inseri-la como parte do sistema mundo capitalista/colonial. Diante do quadro crescente de fascistização social e violência do Estado, cuja pressão sobre os territórios tornou-se ainda mais intenso, é a morte e a vida destes coletivos …

Tubes And Androgyny: Comment On "Thinking Through Tubes", Françoise Barbira Freedman

Tipití: Journal of the Society for the Anthropology of Lowland South America

In this comment on Stephen Hugh-Jones’s "Thinking Through Tubes" Françoise Barbira Freedman offers a feminist meditation on the semiotics of androgyny in Northwest Amazonian shamanism, ritual life and mythology. By focusing on processes of detotalization and retotalization that move beings from an androgynous state to a single-sex identity and back again, Barbira Freedman reveals a dynamic "one sex, two genders model of androgyny" that could not be further from a concept of androgyny as blurred gender. These movements in and out of a one sex state are largely the preserve of men so that androgynous features of the cosmos are …