Digital Commons Network^™

Fusionpdb:: A Knowledgebase Of Human Fusion Proteins, Himansu Kumar, Lin-Ya Tang, Chengyuan Yang, Pora Kim

Faculty, Staff and Student Publications

Tumorigenic functions due to the formation of fusion genes have been targeted for cancer therapeutics (i.e. kinase inhibitors). However, many fusion proteins involved in various cellular processes have not been studied for targeted therapeutics. This is because the lack of complete fusion protein sequences and their whole 3D structures has made it challenging to develop new therapeutic strategies. To fill these critical gaps, we developed a computational pipeline and a resource of human fusion proteins named FusionPDB, available at https://compbio.uth.edu/FusionPDB. FusionPDB is organized into four levels: 43K fusion protein sequences (14.7K in-frame fusion genes, Level 1), over 2300 + 1267 …

Drmref: Comprehensive Reference Map Of Drug Resistance Mechanisms In Human Cancer, Xiaona Liu, Jiahao Yi, Tina Li, Jianguo Wen, Kexin Huang, Jiajia Liu, Grant Wang, Pora Kim, Qianqian Song, Xiaobo Zhou

Faculty, Staff and Student Publications

Drug resistance poses a significant challenge in cancer treatment. Despite the initial effectiveness of therapies such as chemotherapy, targeted therapy and immunotherapy, many patients eventually develop resistance. To gain deep insights into the underlying mechanisms, single-cell profiling has been performed to interrogate drug resistance at cell level. Herein, we have built the DRMref database (https://ccsm.uth.edu/DRMref/) to provide comprehensive characterization of drug resistance using single-cell data from drug treatment settings. The current version of DRMref includes 42 single-cell datasets from 30 studies, covering 382 samples, 13 major cancer types, 26 cancer subtypes, 35 treatment regimens and 42 drugs. All datasets in …

Ageannomo: A Knowledgebase Of Multi-Omics Annotation For Animal Aging, Kexin Huang, Xi Liu, Zhaocan Zhang, Tiangang Wang, Haixia Xu, Qingxuan Li, Yuhao Jia, Liyu Huang, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

Aging entails gradual functional decline influenced by interconnected factors. Multiple hallmarks proposed as common and conserved underlying denominators of aging on the molecular, cellular and systemic levels across multiple species. Thus, understanding the function of aging hallmarks and their relationships across species can facilitate the translation of anti-aging drug development from model organisms to humans. Here, we built AgeAnnoMO (https://relab.xidian.edu.cn/AgeAnnoMO/#/), a knowledgebase of multi-omics annotation for animal aging. AgeAnnoMO encompasses an extensive collection of 136 datasets from eight modalities, encompassing 8596 samples from 50 representative species, making it a comprehensive resource for aging and longevity research. AgeAnnoMO characterizes …

Cov2var, A Function Annotation Database Of Sars-Cov-2 Genetic Variation, Yuzhou Feng, Jiahao Yi, Lin Yang, Yanfei Wang, Jianguo Wen, Weiling Zhao, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has resulted in the loss of millions of lives and severe global economic consequences. Every time SARS-CoV-2 replicates, the viruses acquire new mutations in their genomes. Mutations in SARS-CoV-2 genomes led to increased transmissibility, severe disease outcomes, evasion of the immune response, changes in clinical manifestations and reducing the efficacy of vaccines or treatments. To date, the multiple resources provide lists of detected mutations without key functional annotations. There is a lack of research examining the relationship between mutations and various factors such as disease severity, pathogenicity, patient age, patient gender, cross-species …

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 …

Emerging Perspectives Of Synaptic Biomarkers In Als And Ftd, Karthik Krishnamurthy, Raj Kumar Pradhan

Farber Institute for Neuroscience Staff Papers and Presentations

Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) are debilitating neurodegenerative diseases with shared pathological features like transactive response DNA-binding protein of 43 kDa (TDP-43) inclusions and genetic mutations. Both diseases involve synaptic dysfunction, contributing to their clinical features. Synaptic biomarkers, representing proteins associated with synaptic function or structure, offer insights into disease mechanisms, progression, and treatment responses. These biomarkers can detect disease early, track its progression, and evaluate therapeutic efficacy. ALS is characterized by elevated neurofilament light chain (NfL) levels in cerebrospinal fluid (CSF) and blood, correlating with disease progression. TDP-43 is another key ALS biomarker, its mislocalization linked …

Open-Label Extension Of A Randomized Trial Investigating Safety And Efficacy Of Rhpth(1-84) In Hypoparathyroidism, Aliya A. Khan, Lisa G. Abbott, Intekhab Ahmed, Olulade Ayodele, Claudia Gagnon, Richard D. Finkelman, Emese Mezosi, Lars Rejnmark, Istvan Takacs, Shaoming Yin, Steven W. Ing

Division of Endocrinology, Diabetes and Metabolic Diseases Faculty Papers

Hypoparathyroidism (HypoPT) is a rare disease, often inadequately controlled by conventional treatment. PARALLAX was a mandatory post-marketing trial assessing pharmacokinetics and pharmacodynamics of different dosing regimens of recombinant human parathyroid hormone 1-84 (rhPTH[1-84]) for treating HypoPT. The present study (NCT03364738) was a phase 4, 1-yr open-label extension of PARALLAX. Patients received only 2 doses of rhPTH(1-84) in PARALLAX and were considered treatment-naive at the start of the current study. rhPTH(1-84) was initiated at 50 μg once daily, with doses adjusted based on albumin-corrected serum calcium levels. Albumin-corrected serum calcium (primary outcome measure), health-related quality of life (HRQoL), adverse events, and …

The Human Phenotype Ontology In 2024: Phenotypes Around The World., Michael Gargano, Nicolas Matentzoglu, Ben D Coleman, Eunice B Addo-Lartey, Anna V Anagnostopoulos, Joel Anderton, Paul Avillach, Anita M Bagley, Eduard Bakštein, James P Balhoff, Gareth Baynam, Susan M Bello, Michael Berk, Holli Bertram, Somer Bishop, Hannah Blau, David F Bodenstein, Pablo Botas, Kaan Boztug, Jolana Čady, Tiffany J Callahan, Rhiannon Cameron, Seth J Carbon, Francisco Castellanos, J Harry Caufield, Lauren E Chan, Christopher G Chute, Jaime Cruz-Rojo, Noémi Dahan-Oliel, Jon R Davids, Maud De Dieuleveult, Vinicius De Souza, Bert B A De Vries, Esther De Vries, J Raymond Depaulo, Beata Derfalvi, Ferdinand Dhombres, Claudia Diaz-Byrd, Alexander J M Dingemans, Bruno Donadille, Michael Duyzend, Reem Elfeky, Shahim Essaid, Carolina Fabrizzi, Giovanna Fico, Helen V Firth, Yun Freudenberg-Hua, Janice M Fullerton, Davera L Gabriel, Kimberly Gilmour, Jessica Giordano, Fernando S Goes, Rachel Gore Moses, Ian Green, Matthias Griese, Tudor Groza, Weihong Gu, Julia Guthrie, Benjamin Gyori, Ada Hamosh, Marc Hanauer, Kateřina Hanušová, Yongqun Oliver He, Harshad Hegde, Ingo Helbig, Kateřina Holasová, Charles Tapley Hoyt, Shangzhi Huang, Eric Hurwitz, Julius O B Jacobsen, Xiaofeng Jiang, Lisa Joseph, Kamyar Keramatian, Bryan King, Katrin Knoflach, David A Koolen, Megan L Kraus, Carlo Kroll, Maaike Kusters, Markus S Ladewig, David Lagorce, Meng-Chuan Lai, Pablo Lapunzina, Bryan Laraway, David Lewis-Smith, Xiarong Li, Caterina Lucano, Marzieh Majd, Mary L Marazita, Victor Martinez-Glez, Toby H Mchenry, Melvin G Mcinnis, Julie A Mcmurry, Michaela Mihulová, Caitlin E Millett, Philip B Mitchell, Veronika Moslerová, Kenji Narutomi, Shahrzad Nematollahi, Julian Nevado, Andrew A Nierenberg, Nikola Novák Čajbiková, John I Nurnberger, Soichi Ogishima, Daniel Olson, Abigail Ortiz, Harry Pachajoa, Guiomar Perez De Nanclares, Amy Peters, Tim Putman, Christina K Rapp, Ana Rath, Justin Reese, Lauren Rekerle, Angharad M Roberts, Suzy Roy, Stephan J Sanders, Catharina Schuetz, Eva C Schulte, Thomas G Schulze, Martin Schwarz, Katie Scott, Dominik Seelow, Berthold Seitz, Yiping Shen, Morgan N Similuk, Eric S Simon, Balwinder Singh, Damian Smedley, Cynthia Smith, Jake T Smolinsky, Sarah Sperry, Elizabeth Stafford, Ray Stefancsik, Robin Steinhaus, Rebecca Strawbridge, Jagadish Chandrabose Sundaramurthi, Polina Talapova, Jair A Tenorio Castano, Pavel Tesner, Rhys H Thomas, Audrey Thurm, Marek Turnovec, Marielle E Van Gijn, Nicole A Vasilevsky, Markéta Vlčková, Anita Walden, Kai Wang, Ron Wapner, James S Ware, Addo A Wiafe, Samuel A Wiafe, Lisa D Wiggins, Andrew E Williams, Chen Wu, Margot J Wyrwoll, Hui Xiong, Nefize Yalin, Yasunori Yamamoto, Lakshmi N Yatham, Anastasia K Yocum, Allan H Young, Zafer Yüksel, Peter P Zandi, Andreas Zankl, Ignacio Zarante, Miroslav Zvolský, Sabrina Toro, Leigh Carmody, Nomi L Harris, Monica C Munoz-Torres, Daniel Danis, Christopher J Mungall, Sebastian Köhler, Melissa A Haendel, Peter N Robinson

Faculty Research 2024

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition …

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).

The Black Arts And Black Power Movements In The Artwork Of John T. Riddle, Jr., Isabella Vitti

Theses and Dissertations

This thesis examines the under-studied work of the Black sculptor John T. Riddle, Jr. and how he was influenced by the politics of Los Angeles in the 1960s and 1970s. Police brutality, the Vietnam War, the Black Power Movement, and the Watts uprising had a major impact on Riddle’s work.

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.

A Grid And A Shadow, Henry Glavin

Theses and Dissertations

Henry Glavin's acrylic paintings on panel of architectural interiors and facades use repetition, contrived light, unreliable shadows, photographic posture, and compressed detail to create uncanny spaces that generate an air of silence.

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.

Evaluating Differences In Expression Of Neuroticism In Individual Homed Cats And Feral Cat Colonies Across Varying Degrees Of Human Settlement, Sophie Ambrosino

Theses and Dissertations

Neuroticism is a dimension of personality that was first defined for human psychology as a collective measure of excessive tendencies towards stress, anxiety, fear, unwarranted aggression and/or instability. In a two-part study, this project aimed to identify neuroticism as an observable personality dimension in domesticated cats, and to investigate if the expression of neuroticism varies on an individual and population level in correlation with an increase in environmental stressors and scarcity based upon degree of urbanization of the site. One component of the study surveyed cat owners about personality traits and daily lifestyle of their cats to test the viability …

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.

May The Soil Be Everywhere: Portraying A Family's Love And Revolution Through Oral History, Performance, And Film From A Granddaughter's Perspective, Yehui Zhao

Theses and Dissertations

May the Soil Be Everywhere is a feature-length documentary film that tells an intimate four-generational family story about farming, survival, and regeneration. Set against a backdrop of war, famine, and rapid urbanization, May the Soil Be Everywhere delves into oral history, trauma, family heritage and generational love. It represents a community’s collective effort to preserve its identity.

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.

"This Other Way": Photography At Black Mountain College, Kyle Canter

Theses and Dissertations

Relying on the photographic collections of the Western Regional Archives in Asheville, NC, as well as oral histories, personal correspondence, course notes, official college records, and other archival material, this thesis examines the history and pedagogy of photography at Black Mountain College.

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.

"How Is Photography?": Robert Heinecken's Photographic Concept At The University Of California, Los Angeles, 1960–1991, Noa Wesley

Theses and Dissertations

This thesis examines the photography program Robert Heinecken established at UCLA, highlighting his interest in teaching photography as an idea rather than a technologically inflected medium. This pedagogical model provides a lens through which I trace the work of three of his students: Maria Nordman, John Divola, and Uta Barth.

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.

Lower Your Borrowing Costs: The Dividend Effect, Federal Home Loan Bank Of Chicago

Documents

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