Digital Commons Network^™

Multi-Omics Analysis Of Nf1 Deficiency In Various Cell Types Implicates Roles Outside Of Ras For Cells And Their Microenvironment, Christian Xavier Fay

All ETDs from UAB

Neurofibromatosis type 1 is an autosomal dominant disease in which many patients develop the hallmark feature, neurofibromas, benign tumors that develop along the peripheral nerves. Currently there is no known cure for NF1, and more than 3000 germline pathogenic variants (PVs) in NF1 have been observed. The neurofibromin gene encodes the 320kDa NF1 protein which has multiple predicted functions. Its most under-stood molecular role is in binding GTP-Ras and stimulating Ras-GTPase to cleave GTP to GDP and inactivate Ras signaling. In fact, the only FDA-approved therapeutic is the MEK inhibitor selumetinib which acts downstream of Ras. NF1 also has Ras …

Improving Direct Oncolytic Effect Of Oncolytic Hsv To Overcome Therapeutic Resistance Of Brain Tumors, Sam Edward Gary

All ETDs from UAB

Central nervous system tumors, especially malignant brain tumors, account for the most years of potential life lost in adults and children with cancer. Malignant brain tumors are typically fatal cancers due to their highly aggressive nature, inability to obtain gross total resection, location in sensitive brain areas, and intra- and intertumoral heterogeneity, making therapeutic targeting difficult. High-grade glioma (HGG), malignant brain tumors of glial cell origin invariably recur due to intrinsic and adaptive resistance mechanisms against standard therapies. Therefore, novel treatments that overcome therapeutic resistance are desperately needed. One promising approach is oncolytic viruses (OVs), which achieve tumor regression by …

Computational Approaches To Identify Circular Rnas In Parkinson's Disease, Lisa Shrestha

All ETDs from UAB

Parkinson’s Disease (PD) is the second most common neurodegenerative disease, affecting approximately a million individuals in the United States. Despite its high prevalence, PD is generally diagnosed at a progressed stage after the manifestation of characteristic motor symptoms (bradykinesia, tremor, rigidity, etc.). Hence, it is imperative to understand the underlying molecular mechanisms involved in the progression of PD at an early stage. Several non-coding RNAs have emerged as important regulators in several key cellular processes, among which circular RNAs' role has not been studied well enough. Here, we explore the changes in the expression of circRNAs with respect to the …

The Role Of Micromobility In The Changing Urban Mobility Landscape, Mostafa Jafarzadehfadaki

All ETDs from UAB

The growing prevalence of micromobility has significantly impacted urban mo-‎bility, offering a sustainable and convenient alternative for short trips in urban settings. ‎As cities grapple with increasing congestion, pollution, and the demand for efficient ‎mobility solutions, micromobility options like e-scooters and e-bikes have emerged as ‎popular modes of transportation, particularly in densely populated areas. While earlier ‎research has contributed to understanding micromobility and its impact on urban set-‎tings, significant knowledge gaps still exist. Therefore, a comprehensive study is neces-‎sary to explore the multifaceted dimensions of e-scooter adoption, usage patterns of mi-‎cromobility, and their implications for urban transportation systems and traffic …

Investigating The Impact Of Pavement Condition On Recurring Traffic Congestion, Afrin Hossain Anni

All ETDs from UAB

Traffic congestion impacts the quality of traffic operations and transportation users’ satisfaction. In addition to adverse impacts on travel time and on-time arrivals, traffic congestion may also affect traffic safety, environmental quality, and economic development. Therefore, gaining a good understanding of congestion patterns and identify contributing factors and countermeasures to reduce them are of key importance toward effective traffic management and investment decision-making for transportation improvements. Travel demand, geometric characteristics of transportation facilities, special events, crashes, adverse weather, and other environmental conditions can play a role in the occurrence of traffic congestion. Pavement deterioration is also viewed as a factor …

Hope In Hyperbaric Medicine: A New Approach To Treat Neurological Injury, Lucas Andrew Lowe

All ETDs from UAB

Hyperbaric oxygen therapy (HBOT) has emerged as a promising adjunctive treatment approach for various neurological diseases. This literature review explores the role of HBOT in the treatment of spinal cord injuries. The review discusses the mechanisms of action by which HBOT exerts its effects on neural tissues, such as oxygen delivery, anti-inflammatory actions and neuroprotection. The analysis also highlights the findings from cellular biology, animal studies and clinical trials, offering insights into the potential benefits of HBOT in improving neurological injury outcomes and enhancing patients' quality of life. Furthermore, it addresses the safety considerations and guidelines for the application of …

Promoting Endogenous Cardiomyocyte Proliferation In Large Mammal Hearts Via Cell Transfer Therapy Or Apical Resection: Understanding The Underlying Mechanism, Yuhua Wei

All ETDs from UAB

Cardiovascular diseases are the leading causes of global death. Due to the limit regenerative capacities of adult mammalian cardiomyocytes (CMs), myocardium is repaired with non-contractile fibrotic scar after a myocardial infarction (MI). Various strategies, including apical resection (AR) and cardiac cell therapy, are being explored to promote heart regeneration after MI. This dissertation research aimed to identify proliferating pig CM population after AR and understand the underlying mechanism of human induced pluripotent stem cells (hiPSCs) derived CMs (hiPSC-CMs) implantation for regenerating the pig hearts after MI. Our previous study showed that AR prolonged the heart regeneration window to postnatal day-28 …

Surface-Engineered Nano/Micro-Hybrid Polymer Systems For Environmental Health And Safety, Renjith Rajan Pillai

All ETDs from UAB

Environmental pollution involves the introduction of harmful substances into the natural environment, leading to detrimental effects on ecosystems, wildlife, and human health. This dissertation aims to advance comprehension of environmental pollution and explore efficient, environmentally friendly, and cost-effective methods of remediation. Recently, there has been increasing concern about the environmental impact of Polycyclic Aromatic Hydrocarbons (PAHs), a subgroup of Volatile Organic Compounds (VOCs), and Heavy Metals (HMs) pollution, both known for their carcinogenic and mutagenic properties. These pollutants can significantly harm human health through inhalation, ingestion, or contact with contaminated soil, potentially resulting in conditions such as encephalopathy, kidney dysfunction, …

A Histone Methyltransferase Contributes To Treatment Resistance In Npm1c Aml, Neha Srinivas

All ETDs from UAB

Acute myeloid leukemia (AML) is a blood cancer marked by the rapid growth of abnormal myeloid cells, driven by various genetic mutations. AML accounts for approximately 1% of all cancers and presents complicated prognosis and treatment. Menin inhibitors have shown potential in targeting AML. However, resistance to these inhibitors presents a significant clinical obstacle, as patients treated with menin inhibitors are increasingly developing resistance to the treatment. Using CRISPR-Cas9 mediated screening, we identified an epigenetic regulator contributing to resistance against menin inhibitors in AML. Utilizing knockout (KO) models of the epigenetic regulator in-vitro, ex-vivo, and in-vivo, we observed a growth …

The Impact Of Substrate Stiffness On Glycocalyx Expression In Cultured Endothelial Cells, Frances Green

All ETDs from UAB

Cardiovascular diseases associated with aging pose a significant public health challenge, with vascular stiffening playing a central role in disease progression. This research explores the complex relationship between vascular stiffening and endothelial cell (EC) dysfunction, focusing specifically on the endothelial glycocalyx (eGCX), a critical protective layer of proteins and glycans that covers endothelial cells (ECs). Our approach involves culturing lung microvascular ECs on various ratios of polydimethylsiloxane (PDMS) substrates to simulate vascular stiffening conditions. The results of our study demonstrate an inverse correlation between substrate stiffness and eGCX expression, with softer substrates promoting eGCX integrity. Future research directions will incorporate …

Reduced Order Modeling (Rom) Using Machine Learning Techniques For Analyzing Fluid Flow Around A Ground Vehicle, Emmanuel Ong'aro Ramogi

All ETDs from UAB

Predicting wind and temperature fields around military vehicles during extended missions is crucial to avoid detectability by infrared (IR) devices. Also, the abrupt shifting of wind direction can have a significant impact on vehicle stability. This is a challenging task due to the vehicles' geometric complexity and the unpredictable nature of wind direction, which can shift abruptly. Computational Fluid Dynamics (CFD) is routinely used for calculating the flow fields around ground vehicles. However, this requires extensive computational time and memory, making it unsuitable for real-time analysis. To address these challenges, this research focuses on machine learning (ML) techniques for accurate …

Radiotherapy Dose Calculation Algorithm Sensitivity To High-Density Artifacts, Kylie Blue

All ETDs from UAB

Radiotherapy planning can be adversely affected by inaccurate dose calculations due to the presence of high-density objects. High-density objects, such as surgical clips, produce artifacts in CT images which can result in errors in dose calculation. Manual correction of voxels containing incorrect information is recommended to prevent calculation errors, but this process can be cumbersome and sometimes results in planners compromising with crude corrections to save time. In this study we aim to determine the significance of small high-density objects and the artifacts they cause in radiotherapy treatment plans. To evaluate the impact of density overrides on calculations, a phantom …

The Rider (2024-09-09), Natalie Lapsley

The Rider Archives

Vol.10 No.3

Biology Department Publications: 2021, Sam Lindgren

Biology Department Bibliographies

This document is a noncomprehensive list of publications made by graduate students, post-doctoral researchers, and faculty members in the Biology Department in 2021. It indexes those publications available through major databases, and serves as an archival record of the Department’s robust scholarly contributions.

A Case Demonstration Of The Open Health Natural Language Processing Toolkit From The National Covid-19 Cohort Collaborative And The Researching Covid To Enhance Recovery Programs For A Natural Language Processing System For Covid-19 Or Postacute Sequelae Of Sars Cov-2 Infection: Algorithm Development And Validation, Sijia Liu, David A Hanauer, Daniel R Harris, Ramakanth Kavuluru, Rui Zhang, Karthik Natarajan, Nishanth P Pavinkurve, Janos Hajagos, Sritha Rajupet, Veena Lingam, Mary Saltz, Corey Elowsky, Richard A Moffitt, Farrukh M Koraishy, Matvey B Palchuk, Jordan Donovan, Lora Lingrey, Garo Stone-Derhagopian, Robert T Miller, Andrew E Williams, Peter J Leese, Paul I Kovach, Emily R Pfaff, Mikhail Zemmel, Robert D Pates, Nick Guthe, Melissa A Haendel, Christopher G Chute, Hongfang Liu, National Covid Cohort Collaborative, Recover Initiative

Faculty, Staff and Student Publications

BACKGROUND: A wealth of clinically relevant information is only obtainable within unstructured clinical narratives, leading to great interest in clinical natural language processing (NLP). While a multitude of approaches to NLP exist, current algorithm development approaches have limitations that can slow the development process. These limitations are exacerbated when the task is emergent, as is the case currently for NLP extraction of signs and symptoms of COVID-19 and postacute sequelae of SARS-CoV-2 infection (PASC).

OBJECTIVE: This study aims to highlight the current limitations of existing NLP algorithm development approaches that are exacerbated by NLP tasks surrounding emergent clinical concepts and …

The George-Anne Daily, Georgia Southern University

George-Anne Media Group: Newsletters & Magazines

No abstract provided.

High-Frequency-Based Transmission Line Percentage Differential Protection With Traveling Wave Alignment, Igor F. Prado, Flavio Costa, Kleber M. Silva, Rodrigo P. Medeiros, Bruce A. Mork

Michigan Tech Publications

This paper presents a wavelet-based differential protection algorithm for transmission lines. It uses restraint and operating components obtained with high-frequency components of a few kHz from instantaneous energy values of the real-time boundary stationary wavelet transform instead of low-frequency components from phasor estimation. It does not require capacitive current suppression as well. Therefore, the proposed method overcomes the limitations of conventional percentage differential protection. Furthermore, the proposed technique uses traveling wave theory to perform the current sample alignment at a few kHz, thereby, not requiring the global positioning system (GPS). The performance of the proposed method is evaluated through extensive …

Designing Organizational Systems To Support Achievement Of Performance Goals In Student Mental Health, Maritza Prieto Rodriguez

Walden Dissertations and Doctoral Studies

Delivering first-rate services that addresses the needs of high school students is crucial to the structural sustainability for a counseling department within a high school setting. A well-planned improvement of the structural profile of a counseling department which supports students seeking mental health assistance will become an important part in capacity building. The focus of this study was to recognize the necessity for creating a specific and successful plan that will support both counselors and students within a high school counseling center. The Baldrige Excellence Framework was used to direct this case study of a behavioral health organization in the …

Creating The E-Buzz Around Collaborative And Collective Dei Efforts In Academic Libraries, Essraa Nawar, Kristin Laughtin-Dunker

Library Articles and Research

Like many academic libraries, the Leatherby Libraries at Chapman University (USA) is committed to supporting and promoting diversity, equity, and inclusion (DEI) for students, faculty, researchers, and staff and has increased its efforts in the last several years to reflect that commitment through its resources, services, and outreach activities. However, in the wider literature, the efforts of scholarly communication librarians in DEI initiatives outside of openaccess advocacy are less discussed. Nevertheless, precisely because scholarly communication librarians are concerned with advancing the dissemination of knowledge, they fit naturally into DEI efforts that seek to elevate new or historically marginalized voices and …

Aars Online: A Collaborative Database On The Structure, Function, And Evolution Of The Aminoacyl-Trna Synthetases, Jordan Douglas, Haissi Cui, John J. Perona, Oscar Vargas-Rodriguez, Henna Tyynismaa, Claudia Alvarez Carreño, Jiqiang Ling, Lluís Ribas De Pouplana, Xiang-Lei Yang, Michael Ibba, Hubert Becker, Frédéric Fischer, Marie Sissler, Charles W. Carter Jr., Peter Wills

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The aminoacyl-tRNA synthetases (aaRS) are a large group of enzymes that implement the genetic code in all known biological systems. They attach amino acids to their cognate tRNAs, moonlight in various translational and non-translational activities beyond aminoacylation, and are linked to many genetic disorders. The aaRS have a subtle ontology characterized by structural and functional idiosyncrasies that vary from organism to organism, and protein to protein. Across the tree of life, the 22 coded amino acids are handled by 16 evolutionary families of Class I aaRS and 21 families of Class II aaRS. We introduce AARS Online, an interactive Wikipedia-like …

Analyzing Student Prompts And Their Effect On Chatgpt’S Performance, Ghadeer Sawalha, Imran Taj, Abdulhadi Shoufan

All Works

Large language models present new opportunities for teaching and learning. The response accuracy of these models, however, is believed to depend on the prompt quality which can be a challenge for students. In this study, we aimed to explore how undergraduate students use ChatGPT for problem-solving, what prompting strategies they develop, the link between these strategies and the model’s response accuracy, the existence of individual prompting tendencies, and the impact of gender in this context. Our students used ChatGPT to solve five problems related to embedded systems and provided the solutions and the conversations with this model. We analyzed the …

Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness And Parameterized Bounds, Erik D. Demaine, Elize Grizzell, Jayson Lynch, Ahmed Shalaby, Timothy Gomez, Markus Hecher, Robert Schweller, Damien Woods

Computer Science Faculty Publications

Molecular programmers and nanostructure engineers use domain-level design to abstract away messy DNA/RNA sequence, chemical and geometric details. Such domain-level abstractions are enforced by sequence design principles and provide a key principle that allows scaling up of complex multistranded DNA/RNA programs and structures. Determining the most favoured secondary structure, or Minimum Free Energy (MFE), of a set of strands, is typically studied at the sequence level but has seen limited domain-level work. We analyse the computational complexity of MFE for multistranded systems in a simple setting were we allow only 1 or 2 domains per strand. On the one hand, …

Training Robust T1-Weighted Magnetic Resonance Imaging Liver Segmentation Models Using Ensembles Of Datasets With Different Contrast Protocols And Liver Disease Etiologies, Nihil Patel, Adrian Celaya, Mohamed Eltaher, Rachel Glenn, Kari Brewer Savannah, Jessica I Sanchez, Darrel Cleere, Ahmed Elsaiey, Matthew Cagley, Nakul Gupta, David Victor, Laura Beretta, Eugene J Koay, Tucker J Netherton, David T Fuentes

Faculty, Staff and Student Publications

Image segmentation of the liver is an important step in treatment planning for liver cancer. However, manual segmentation at a large scale is not practical, leading to increasing reliance on deep learning models to automatically segment the liver. This manuscript develops a generalizable deep learning model to segment the liver on T1-weighted MR images. In particular, three distinct deep learning architectures (nnUNet, PocketNet, Swin UNETR) were considered using data gathered from six geographically different institutions. A total of 819 T1-weighted MR images were gathered from both public and internal sources. Our experiments compared each architecture's testing performance when trained both …

Three-Dimensional Analysis Of Mitochondria In A Patient-Derived Xenograft Model Of Triple Negative Breast Cancer Reveals Mitochondrial Network Remodeling Following Chemotherapy Treatments, Audra Lane, Larry Vang, Mokryun L Baek, Andrea G Marshall, Mason Killion, Faben Zeleke, Bryanna Shao, Dominque Parker, Autumn Peterson, Julie Sterling Rhoades, Estevão Scudese, Lacey E Dobrolecki, Michael T Lewis, Antentor Hinton, Gloria V Echeverria

Faculty, Staff and Students Publications

Mitochondria are hubs of metabolism and signaling and play an important role in tumorigenesis, therapeutic resistance, and metastasis in many cancer types. Various laboratory models of cancer demonstrate the extraordinary dynamics of mitochondrial structure, but little is known about the role of mitochondrial structure in resistance to anticancer therapy. We previously demonstrated the importance of mitochondrial structure and oxidative phosphorylation in the survival of chemotherapy-refractory triple negative breast cancer (TNBC) cells. As TNBC is a highly aggressive breast cancer subtype with few targeted therapy options, conventional chemotherapies remain the backbone of early TNBC treatment. Unfortunately, approximately 45% of TNBC patients …

Integrated Environmental Vulnerability Assessment And Adaptation Strategies For Coastal Areas Under Sustainable Development, Lien-Kwei Chien, Yu-Chi Li, Chia-Feng Hsu

Journal of Marine Science and Technology–Taiwan

This research focuses on the holistic management and environmental vulnerability of coastal areas in Taiwan within the framework of sustainable development. With economic and social growth gravitating towards coastal regions, the strain on the natural environment is increasing. Therefore, discovering a balance between economic progress and environmental conservation is paramount. To decipher the vulnerability of Taiwan's coastal zones, this study first defines ‘Integrated Environmental Vulnerability of Coastal Areas.’Key vulnerability factors were identified across environmental, social, and economic dimensions. Seven core determinants were determined using the Fuzzy Delphi method: biodiversity, coastal erosion, water pollution, population density, population aging, land utilization, and …

Evalution Of The Ability To Infer Tilt Angle And Size Distributions Of Fish Using A Broadband Scientific Echosounder Based On Simulation, Jing Liu

Journal of Marine Science and Technology–Taiwan

The biological information, such as species, size, and tilt angle, is crucial for converting the echo data into biomass information in acoustic surveys. Typically, the information can be obtained through trawl net sampling or underwater camera observations. However, both methods have some limitations. To overcome these limitations, scientists have utilized inversion methods with multi-frequency and broadband echosounders to derive biological information about fish, plankton, and krill. However, evaluating the reliability and accuracy of these inversion methods has been challenging due to the difficulty in obtaining accurate biological information. In this study, a numerical simulation method was used to generate fish …

Experimental Support For A New Drift Block Design To Assess Seabird Mortality From Oil Pollution, Francis K. Wiese, Ian L. Jones

The Auk

No abstract provided.

Do Golden-Cheeked Warblers Select Nest Locations On The Basis Of Patch Vegetation?, Donald C. Dearborn, Laura L. Sanchez

The Auk

No abstract provided.

Timing Of Mineral Sequestration In Leg Bones Of White-Tailed Ptarmigan, James R. Larison, J. G. Crock, Christine M. Snow

The Auk

No abstract provided.

Avian Nesting Success In Forested Landscapes: Influence Of Landscape Composition, Stand And Nest-Patch Microhabitat, And Biotic Interactions, Amanda D. Rodewald, Richard H. Yahner

The Auk

No abstract provided.