Digital Commons Network^™

Stemdriver: A Knowledgebase Of Gene Functions For Hematopoietic Stem Cell Fate Determination, Yangyang Luo, Jingjing Guo, Jianguo Wen, Weiling Zhao, Kexin Huang, Yang Liu, Grant Wang, Ruihan Luo, Ting Niu, Yuzhou Feng, Haixia Xu, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

StemDriver is a comprehensive knowledgebase dedicated to the functional annotation of genes participating in the determination of hematopoietic stem cell fate, available at http://biomedbdc.wchscu.cn/StemDriver/. By utilizing single-cell RNA sequencing data, StemDriver has successfully assembled a comprehensive lineage map of hematopoiesis, capturing the entire continuum from the initial formation of hematopoietic stem cells to the fully developed mature cells. Extensive exploration and characterization were conducted on gene expression features corresponding to each lineage commitment. At the current version, StemDriver integrates data from 42 studies, encompassing a diverse range of 14 tissue types spanning from the embryonic phase to adulthood. In order …

Fusionneoantigen: : A Resource Of Fusion Gene-Specific Neoantigens, Himansu Kumar, Ruihan Luo, Jianguo Wen, Chengyuan Yang, Xiaobo Zhou, Pora Kim

Faculty, Staff and Student Publications

Among the diverse sources of neoantigens (i.e. single-nucleotide variants (SNVs), insertions or deletions (Indels) and fusion genes), fusion gene-derived neoantigens are generally more immunogenic, have multiple targets per mutation and are more widely distributed across various cancer types. Therefore, fusion gene-derived neoantigens are a potential source of highly immunogenic neoantigens and hold great promise for cancer immunotherapy. However, the lack of fusion protein sequence resources and knowledge prevents this application. We introduce 'FusionNeoAntigen', a dedicated resource for fusion-specific neoantigens, accessible at https://compbio.uth.edu/FusionNeoAntigen. In this resource, we provide fusion gene breakpoint crossing neoantigens focused on ∼43K fusion proteins of ∼16K in-frame …

The Fallacy Of Composition, Its Wide-Ranging Applications In Economics/Business And Why Systems Science Is Appropriate For Economic And Business Research, Jeffrey Yi-Lin Forrest, Joachim Wagner, Jennifer Nightingale, Huan Guo, Jennifer Roy

Pennsylvania Economic Review

This paper explores how widely the erroneous logic of reasoning of the fallacy of composition has been employed in many areas of knowledge, especially in economic and business studies. It then shows why systems science and methodology are truly appropriate for investigating organizations, evolutions and interactions of business entities by focusing on emergent macro-level properties that are not explainable by the characteristics of micro-level individuals. To demonstrate the potentially magnificent consequence of this proposal, a theorem of general systems is displayed to confirm how unintended and uncoordinated micro-level individual desires can naturally lead to macro-level phenomena, such as racial segregation …

Young Professionals: Fireside Chat With Jacques Lewiner And J. Keith Nelson At The Ieee Conference On Electrical Insulation And Dielectric Phenomena, Mattewos Tefferi, Allen Andersen, Sneha Hedge, Moein Borghei

Journal Articles

At the IEEE Conference on Electrical Insulation and Dielectric Phenomena (CEIDP), the Dielectrics and Electrical Insulation Society’s Young Professionals (DEIS-YP) Committee has initiated a YP luncheon event. This event aims to feature keynote speakers who share insights into their career trajectories with young professionals. In the current CEIDP edition, we had the privilege of hosting two distinguished speakers: Jacques Lewiner, the 2023 Whitehead Memorial Lecturer, and J. Keith Nelson, the 2022 recipient of the Dakin Award who also presented his award lecture at the CEIDP 2023. The fire- side chat was moderated by Allen Andersen, who began with initial questions …

Questioning Reality: The Progressive Development Of Modern Physics, Joshua Lancman

STEM for Success Showcase

Humanity has a tendency to divide time. The past is distinct from the present which is entirely separate from the future. In supposedly 20-20 vision history is neatly divided into different sections, distinct eras with sharp lines between them. What is present and in the future is always modern. What is past is something else with another name.

Yet time is not divided so neatly. We know this living through it: years and decades blend into one another in a non-uniform progression. To divide human history into separate eras is a necessary simplification, as it helps to ascribe order onto …

Upi Guide Ii, Yoshihiko Ariizumi

Learning, Teaching, & Researching Optimization

This book guides you to apply the principles of the UPI (Chigen-iku) method into your performance improvement projects.

Exploring Advanced Analysis Technique For Shallow Water Flowmodels With Diverse Applications, Rasha F. El-Agamy, Hijaz Ahmad, Gamal M. Ismail, Ibrahim Alraddadi, Mohammad Aljanabi, Umar Farooq

Iraqi Journal for Computer Science and Mathematics

The present article focuses on the analytical approach using fractional orders and its applicationin the dynamics of physical processes. Fractional order models align better with experimental data compared tonon-fractional ones. This study primarily focuses on employing the new approximate analytical method to solveshallow water models with fractional orders. Numerical examples within the Caputo fractional derivative showcasethe method’s application. Results for both integer and fractional orders are graphically depicted, demonstrating thefractional solutions’ closeness to actual data. Analysis of 3D and 2D fractional order graphs reveals convergencetoward integer order graphs as fractional derivatives approach non-fractional ones. This method shows promise fordirect application …

Barley As A Human Companion Species - Exploring The Relationship Between Barley And North Atlantic Peoples: 4000 Bc – Ad 1200, Chloe Combs

Theses and Dissertations

Barley (Hordeum vulgare) is an ancient cereal crop originating in the Fertile Crescent approximately 12,000 years ago and is presently one of the most important cereal crops globally. Barley has a long and complex history. This thesis aims to explore one dimension of this history through the lens of human companion species using archaeobotanical data collected from the islands of the North Atlantic from the Neolithic (4,000 BC) to the Norse period (AD 1200).

Crucifixion Can Happen To Anyone: Embodying Christ Through The Queer Artist, Xander Guyer

Theses and Dissertations

In the late 20th century, queer artists incorporated the Crucifixion into their artworks, embodying a crucified Christ in the process. This thesis seats these contemporary works within traditional Christian art history, a position long denied to these transgressively queer artists.

Go Big Or Go Flat: Life Satisfaction After Mastectomy With Or Without Reconstruction, Susan T. Smith

Theses and Dissertations

Prior research on psychosocial functioning after mastectomy has focused on comparing women with different types of reconstruction to women who “remained flat.” We found that women who remained “flat by choice” had the highest overall psychosocial functioning, followed by the reconstructed group and lastly, by “flat without choice" women.

Through Their Eyes: Illuminating The Nature Of Animal Use In Conservation Research Through An Analysis Of Peer-Reviewed Literature In The Journal Conservation Biology, Sarah Hollmann

Theses and Dissertations

Non-human animals habitually have been treated as a resource in the service of humans and human-driven values. The field of conservation is not immune to this fact. But, because conservation is seemingly dedicated to the saving and protection of species and nature, until recently the field historically has been given a pass for the use and treatment of animals that are done “in the name of conservation”. This treatment is evident in common conservation practices such as capture, captivity, invasive sampling, aversive treatment, experimental manipulation, and intentional killing. A principal question we are asking is how individual animals are impacted …

Routed Through Rubber: Ulises Carrión And Marginal Media (1972–1980), Mary-Elisabeth Moore

Theses and Dissertations

Directed by Aart van Barneveld with support from his partner Ulises Carrión, the Stempelplaats gallery (1976–1981) in Amsterdam developed out of larger trends in independent publishing and mail art, as artists on the margins of conceptual art explored the potential of rubber stamps toward various ends. The thesis examines the role the rubber stamp played in Ulises Carrión's early poetic book works and his later mail art activities: how it allowed him to draw out the sequential aspects of a book's structure and forged strong links through his network.

The Rise Of Domestic Travel Imagery During Isolation: Looking At The Seclusion Of Japan And England, Tiffany I. Kang

Theses and Dissertations

This thesis outlines the periods and conditions of isolation, of Japan and England, and how they have contributed to the rise of domestic travel imagery. The limited travel caused by isolation provided a time for interior thinking which resulted in distinct artistic genres central to the identity of both countries.

Francesco Clemente: In One's Self Lies The Whole World, Lorraine Robinson

Theses and Dissertations

Francesco Clemente’s body of work, especially between 1992 and 2014, theoretically draws from the Hindu concept of the avatāra, wherein the figures he portrays interminably exist in a state of flux and unraveling. Many of the figures discussed are inspired by Indian spirituality, mythology, and popular culture. Nonetheless, rather than comprehending them as literal interpretations, they exist through a prism of references.

The research conducted throughout this thesis combines analyses gathered from academic essays and books by notable Indian scholars, such as Jyotindra Jain and Partha Mitter. These two distinct voices coalesce to elucidate deep insight into Clemente’s aesthetic, personal, …

A Year As A Monk Parakeet, Eric Thompson

Theses and Dissertations

Monk parakeets are a species of parrot native to subtropical and temperate regions of Argentina, Brazil, Uruguay, Paraguay, and Bolivia that have been introduced to many parts of the world. Monk Parakeets have lived in Brooklyn, New York since the 1970s and many myths and legends surround how these birds came to live here. This thesis is a description of the behavior of monk parakeets in Brooklyn, New York’s Greenwood Cemetery based on observations I conducted twice a week from January through October of 2023. Because of the unusual nature of this population of parakeets as well as their unique …

Budget Capping Health Care: Its Impact On Health, Susan Chen

Theses and Dissertations

The goal of a budget cap on healthcare is to constrain total healthcare expenditure without compromising quality. This paper examines the impacts of budget capping on health and behavioral health outcomes, exploiting the completed Maryland All-Payer Model and the ongoing, extensional Maryland Total Cost of Care model, both of which capped healthcare budgets in Maryland. I use data from 2011-2021 surveys of the Behavioral Risk Factor Surveillance system and generalized difference-in-difference regression models to find that budget capping improves health and behavioral health outcomes with a greater favorable effect during the Maryland Total Cost of Care model.

Scattered Fragments: Art, Architecture, And Archives In Revolutionary Urban Cairo, Mounira M. Makar

Theses and Dissertations

This thesis analyzes how revolutions impact urban Cairo and its communities, specifically within artistic, architectural and archival practice while acknowledging the central role of public spaces in giving way to such revolutionary practices. Fundamentally, this paper highlights the foundational nature of such practices in developing urban communities.

Lutz Bacher: 1975-2019, Jeremy Gloster

Theses and Dissertations

"Lutz Bacher: 1975-2019" is a monographic study of the artist Lutz Bacher (1943-2019), detailing the artist's trajectory from participant in the Bay Area photography scene of the mid-1970s to an established figure in the art world. Alongside this exposition, the thesis contends theoretically with Bacher's work, turning toward the theorist Peter Osborne's recent writings to examine Bacher's multifarious engagements with the photographic image and her own stagings of contemporaneity.

Stourhead In Arcadia Ego: The English Countryside And The Expanding British Empire In Eighteenth-Century, Rachel C. Sherr

Theses and Dissertations

Stourhead Gardens, an emblematic eighteenth-century landscape, reflects Britain's socio-cultural and imperial changes. Owned by the Hoare family, it melds classical influences and Enlightenment ideals. Existing research deciphers its iconography, but this thesis broadens the perspective, placing Stourhead in its era's socio-cultural context. It's a narrative rich in cultural and historical significance, shedding light on identity, art, and culture, past and present.

Learning From One’S Own Errors Vs From Observing Other People's Errors: Ego Engagement Vs Ego Threat, Viktoriya Andreevskaya

Theses and Dissertations

Do people learn better from their own errors or from observing other people’s errors? A sense of ego-threat may impede learning from negative corrective feedback directed to self. A series of two experiments manipulated the degree of ego-threat between subjects. In the neutral ego-threat condition, results showed better learning from self-generated errors.

Individual Concepts And Personal Identity Judgement, Molly M. Ye

Theses and Dissertations

Previous research into personal identity judgments has yielded conflicting outcomes. This paper introduces an alternative argument, proposing that the concept PERSON and HUMAN BEING provide different ways of thinking about the identity of people. Two experiments in this study provide evidence for this claim.

Advancing Cell Segmentation Methods Through An Innovative Technique And Systematic Evaluation, Yuxing Wang

Theses

In the biomedical field, downstream cell-level analysis is a crucial step for comprehensively characterizing cells' location, function, morphology, and phenotype, relying on the accurate identification of individual cells. Consequently, there is increasing interest in the high quality of identified cell boundaries for biologists or researchers. Currently, cell segmentation methods are categorized into two types: Image-based and RNA-based cell segmentation. However, these methods face significant challenges. For example, most image-based methods tend to identify cell nuclear boundaries rather than entire cell boundaries when only nuclear staining images are available, and their performance is affected by noise in images and training labels. …

Exploring Functional Connectivity In Chronic Spinal Cord Injury Patients With Neuropathic Pain Versus Without Neuropathic Pain, Shreya Mandloi, Mashaal Syed, Isaiah Ailes, Omid Shoraka, Benjamin Leiby, J. Miao, Sara Thalheimer, Joshua Pelta-Heller, Feroze Mohamed, Ashwini Sharan, James Harrop, Laura Krisa, M. Alizadeh

Farber Institute for Neuroscience Faculty Papers

The great majority of spinal cord injury (SCI) patients have debilitating chronic pain. Despite decades of research, these pain pathways of neuropathic pain (NP) are unknown. SCI patients have been shown to have abnormal brain pain pathways. We hypothesize that SCI NP patients’ pain matrix is altered compared to SCI patients without NP. This study examines the functional connectivity (FC) in SCI patients with moderate-severe chronic NP compared to SCI patients with mild-no NP. These groups were compared to control subjects. The Neuropathic Pain Questionnaire and neurological evaluation based on the International Standard Neurological Classification of SCI were utilized to …

Synthesizing Physiology With Aquaculture For Olympia Oyster Restoration In Elkhorn Slough, Ca, Jacob Harris

Master's Theses

Conservation aquaculture is an emerging restoration strategy for depleted and low-density foundation species. It was recently applied for Olympia oysters in California. The only native oyster species is at risk of local extinction in much of its range. Conservation aquaculture can support oyster abundance, but long-term restoration success will be constrained by habitat conditions that suppress early growth and reproductive fitness. Following years of reproduction failure in Elkhorn Slough, CA, we examined these two critical life stages: juvenile and brooding. Our aim was to improve restoration by evaluating aquaculture methods and studying their physiology. We tested site parameters, oyster size, …

Macrocephaly And Digital Anomalies Expand The Phenotypic Spectrum Of Pgap2 Variants In Hyperphosphatasia With Impaired Intellectual Development Syndrome 3 (Hpmrs3), Seda Susgun, Afif Ben-Mahmoud, Franz Rüschendorf, Bonsu Ku, Syeda Iqra Hussain, Solveig Schulz, Oliver Puk, Saskia Biskup, Jonathan D.J. Labonne, Dilan Wellalage Don, Vijay Gupta, Tae Ik Choi, Saadullah Khan, Naveed Wasif, Yves Lacassie, Lawrence C. Layman, Sibel Aylin Ugur Iseri, Cheol Hee Kim, Hyung Goo Kim

School of Medicine Faculty Publications

Glycosylphosphatidylinositols (GPIs) anchor over 150 proteins as GPI-anchored proteins (GPI-APs) with crucial roles in diverse biological processes. The highly conserved biosynthesis of GPI-APs involves precise steps with at least 21 genes, categorized as PIG and PGAP genes. Pathogenic variants in these genes are linked to human diseases, highlighting the importance of each biosynthesis step. PGAP2 stands out among these genes due to its association with an expanded clinical spectrum of neurodevelopmental disorder (NDD) phenotypes with biallelic pathogenic variants. We present four patients from two families, one consanguineous and the other nonconsanguineous, each displaying distinct clinical presentations, including intellectual disability, hyperphosphatasia, …

Critical-Size Defects Reconstruction With Four Different Bone Grafts Associated With E-Ptfe Membrane: A Histomorphometric Experimental In Vivo Study, Gustavo Fernandes, Filipe Castro, Rafael Martins Pereira, Wendel Teixeira, Sergio Gehrke, Julio Cesar Joly, Juan Blanco Carrion, Juliana Campos Hasse Fernandes

MOSDOH Faculty Publications

Objectives: The goal of this study was to assess the newly formed bone and the remnant biomaterial by comparing four different bone grafts used to treat critical-size defects, associated or not with the non-resorbable membrane.

Materials and methods: Two calvaria critical-size bone defects were created in 50 male Wistar rats. They were divided into blood (G1), autogenous (G2), bioglass (G3), hydroxyapatite (G4), and xenograft (G5) groups, associated or not with e-PTFE. The experimental periods were 15 and 45 days. Sections were prepared for histomorphometric assessment. All data were analyzed by the mixed-effects model with multiple comparisons (significance level, p < .05).

Results: …

Upi Guide I, Yoshihiko Ariizumi

Spiritual Proficiency

This book guides you to understand the basic theoretical foundation of this method (UPI or Chigen-iku).

Irrigation Of Sand-Based Creeping Bentgrass Putting Greens With Nanobubble-Oxygenated Water, Eric J. Deboer, Michael J. Richardson, John Mccalla

Horticulture Faculty Publications and Presentations

ultural and environmental factors can place creeping bentgrass (Agrostis stolonifera) under extreme stress during the summer months. This stress, coupled with the growth adaptation of creeping bentgrass, can result in shallow, poorly rooted stands of turf. To enhance root zone oxygen and rooting of creeping bentgrass, golf courses use methods such as core and solid-tine aerification, and sand topdressing. An additional method of delivering oxygen to the soil could be irrigation with nanobubble-oxygenated water. The properties of nanobubbles (NBs) allow for high gas dissolution rates in water. Irrigating with NB-oxygenated water sources may promote increased rooting of creeping …

A Review Of Optimization Techniques: Applications And Comparative Analysis, Ahmed Hasan Alridha, Fouad H. Abd Alsharify, Zahir Al-Khafaji

Iraqi Journal for Computer Science and Mathematics

Optimization algorithms exist to find solutions to various problems and then find out the optimal solutions. These algorithms are designed to reach desired goals with high accuracy and low error, as well as improve performance in various fields, including machine learning, operations research, physics, chemistry, and engineering. As technology continues to advance, optimization algorithms are increasingly needed to address complex real-world challenges and drive innovation across all disciplines. Quantitative leaps have been achieved in improving the efficiency of optimization algorithms through the diversity of sources of information feeding these algorithms according to the type of optimization problem, based on scientific …

Patient Satisfaction With The Quality Of Care Received Is Associated With Adherence To Antidepressant Medications, Macarius M. Donneyong, Mary Bynum, Ameena Kemavor, Norah L. Crossnohere, Anne Schuster, John Bridges

All Faculty and Staff Scholarship

Background

There is a paucity of evidence on the association between satisfaction with quality of care and adherence to antidepressants.

Objectives

To examine the association between patient satisfaction with healthcare and adherence to antidepressants.

Methods

A cohort study design was used to identify antidepressant users from the 2010-2016Medical Expenditure Panel Survey data, a national longitudinal complex survey study design on the cost and healthcare utilization of the noninstitutionalized population in the United States. The Consumer Assessment of Healthcare Providers and Systems were used to measure participants’ satisfaction with access and quality of care, patient-provider communication and shared decision-making (SDM). Patients …