Digital Commons Network^™

Sox On Tumors, A Comfort Or A Constraint?, Junqing Jiang, Yufei Wang, Mengyu Sun, Xiangyuan Luo, Zerui Zhang, Yijun Wang, Siwen Li, Dian Hu, Jiaqian Zhang, Zhangfan Wu, Xiaoping Chen, Bixiang Zhang, Xiao Xu, Shuai Wang, Shengjun Xu, Wenjie Huang, Limin Xia

Faculty, Staff and Student Publications

The sex-determining region Y (SRY)-related high-mobility group (HMG) box (SOX) family, composed of 20 transcription factors, is a conserved family with a highly homologous HMG domain. Due to their crucial role in determining cell fate, the dysregulation of SOX family members is closely associated with tumorigenesis, including tumor invasion, metastasis, proliferation, apoptosis, epithelial-mesenchymal transition, stemness and drug resistance. Despite considerable research to investigate the mechanisms and functions of the SOX family, confusion remains regarding aspects such as the role of the SOX family in tumor immune microenvironment (TIME) and contradictory impacts the SOX family exerts on tumors. This review summarizes …

Prebiotic Proanthocyanidins Inhibit Bile Reflux–Induced Esophageal Adenocarcinoma Through Reshaping The Gut Microbiome And Esophageal Metabolome, Katherine M. Weh, Connor L. Howard, Yun Zhang, Bridget A. Tripp, Jennifer Clarke, Amy B. Howell, Joel H. Rubenstein, Julian A. Abrams, Maria Westerhoff, Laura A. Kresty

Department of Statistics: Faculty Publications

The gut and local esophageal microbiome progressively shift from healthy commensal bacteria to inflammation-linked pathogenic bacteria in patients with gastroesophageal reflux disease, Barrett’s esophagus, and esophageal adenocarcinoma (EAC). However, mechanisms by which microbial communities and metabolites contribute to reflux-driven EAC remain incompletely understood and challenging to target. Herein, we utilized a rat reflux-induced EAC model to investigate targeting the gut microbiome–esophageal metabolome axis with cranberry proanthocyanidins (C-PAC) to inhibit EAC progression. Sprague-Dawley rats, with or without reflux induction, received water or C-PAC ad libitum (700 μg/rat/day) for 25 or 40 weeks. C-PAC exerted prebiotic activity abrogating reflux-induced dysbiosis and mitigating …

Unimer Suppression Enables Supersaturated Homopolymer Swollen Micelles With Long-Term Stability After Glassy Entrapment, Eric R. Williams, Christian X. Ruff, Morgan Stefik

Faculty Publications

Micelle sizes are critical for a range of applications where the simple ability to adjust and lock in specific stable sizes has remained largely elusive. While micelle swelling agents are well-known, their dynamic re-equilibration in solution implies limited stability. Here, a non-equilibrium processing sequence is studied where supersaturated homopolymer swelling is combined with glassy-core (“persistent”) micelles. This path-dependent process was found to sensitively depend on unimer concentration as revealed by DLS, SAXS, and TEM analysis. Here, lower-selectivity solvent combinations led to the formation of unimer-homopolymer aggregates and eventual precipitation, reminiscent of anomalous micellization. In contrast, higher-selectivity solvents enabled supersaturated homopolymer …

Determining The Surface PKA Of Perfluorooctanoic Acid, Lila J. Musegades, Owen P. Curtin, Jenée D. Cyran

Chemistry and Biochemistry Faculty Publications and Presentations

Perfluorooctanoic acid (PFOA) is an environmentally prevalent and persistent organic pollutant with toxic and bioaccumulative properties. Despite the known importance of perfluorinated pollutants in the global environment, molecular-level details of the physicochemical behavior of PFOA on aqueous interfaces remain poorly understood. Here, we utilized two surface-specific techniques, vibrational sum frequency generation spectroscopy (SFG) and surface tensiometry, to investigate the pH-induced structural changes of PFOA and octanoic acid (OA) and determined the apparent pK_a at the air–water surface. The SFG spectra and surface activity model were investigated over a wide range of pHs. With the surface tension measurements, the …

Unimer Suppression Enables Supersaturated Homopolymer Swollen Micelles With Long-Term Stability After Glassy Entrapment, Eric R. Williams, Christian X. Ruff, Morgan Stefik

Faculty Publications

Micelle sizes are critical for a range of applications where the simple ability to adjust and lock in specific stable sizes has remained largely elusive. While micelle swelling agents are well-known, their dynamic re-equilibration in solution implies limited stability. Here, a non-equilibrium processing sequence is studied where supersaturated homopolymer swelling is combined with glassy-core (“persistent”) micelles. This path-dependent process was found to sensitively depend on unimer concentration as revealed by DLS, SAXS, and TEM analysis. Here, lower-selectivity solvent combinations led to the formation of unimer-homopolymer aggregates and eventual precipitation, reminiscent of anomalous micellization. In contrast, higher-selectivity solvents enabled supersaturated homopolymer …

There Is Life On Mars, Colin M. Johnston, Olivier B. Cohen

CAFE Symposium 2024

An extensive research project that involved the research of multiple major experiments and discoveries about possible life on the planet Mars. Facts, Data, conspiracies and theories have all been taken into account and provided in this project.

Artificial Intelligence-Based Evaluation Of The Factors Affecting The Sales Of An Iron And Steel Company, Mehmet Pekkaya, Zafer Uysal, Aytaç Altan, Seçkin Karasu

Turkish Journal of Electrical Engineering and Computer Sciences

It is important to predict the sales of an iron and steel company and to identify the variables that influence these sales for future planning. The aim in this study was to identify and model the key factors that influence the sales volume of an iron and steel company using artificial neural networks (ANNs). We attempted to obtain an integrated result from the performance/sales levels of 5 models, to use the ANN approach with hybrid algorithms, and also to present an exemplary application in the base metals industry, where there is a limited number of studies. This study contributes to …

Machine Learning Approaches In Comparative Studies For Alzheimer’S Diagnosis Using 2d Mri Slices, Zhen Zhao, Joon Huang Chuah, Chee-Onn Chow, Kaijian Xia, Yee Kai Tee, Yan Chai Hum, Khin Wee Lai

Turkish Journal of Electrical Engineering and Computer Sciences

Alzheimer’s disease (AD) is an illness that involves a gradual and irreversible degeneration of the brain. It is crucial to establish a precise diagnosis of AD early on in order to enable prompt therapies and prevent further deterioration. Researchers are currently focusing increasing attention on investigating the potential of machine learning techniques to simplify the automated diagnosis of AD using neuroimaging. The present study involved a comparison of models for the detection of AD through the utilization of 2D image slices obtained from magnetic resonance imaging brain scans. Five models, namely ResNet, ConvNeXt, CaiT, Swin Transformer, and CVT, were implemented …

The Hsp90-Myc-Cdk9 Network Drives Therapeutic Resistance In Mantle Cell Lymphoma, Fangfang Yan, Vivian Jiang, Alexa Jordan, Yuxuan Che, Yang Liu, Qingsong Cai, Yu Xue, Yijing Li, Joseph Mcintosh, Zhihong Chen, Jovanny Vargas, Lei Nie, Yixin Yao, Heng-Huan Lee, Wei Wang, Johnnelson R Bigcal, Maria Badillo, Jitendra Meena, Christopher Flowers, Jia Zhou, Zhongming Zhao, Lukas M Simon, Michael Wang

Faculty, Staff and Student Publications

Brexucabtagene autoleucel CAR-T therapy is highly efficacious in overcoming resistance to Bruton's tyrosine kinase inhibitors (BTKi) in mantle cell lymphoma. However, many patients relapse post CAR-T therapy with dismal outcomes. To dissect the underlying mechanisms of sequential resistance to BTKi and CAR-T therapy, we performed single-cell RNA sequencing analysis for 66 samples from 25 patients treated with BTKi and/or CAR-T therapy and conducted in-depth bioinformatics™ analysis. Our analysis revealed that MYC activity progressively increased with sequential resistance. HSP90AB1 (Heat shock protein 90 alpha family class B member 1), a MYC target, was identified as early driver of CAR-T resistance. CDK9 …

Transcription Factor Bach1 In Cancer: Roles, Mechanisms, And Prospects For Targeted Therapy, Dian Hu, Zerui Zhang, Xiangyuan Luo, Siwen Li, Junqing Jiang, Jiaqian Zhang, Zhangfan Wu, Yijun Wang, Mengyu Sun, Xiaoping Chen, Bixiang Zhang, Xiao Xu, Shuai Wang, Shengjun Xu, Yufei Wang, Wenjie Huang, Limin Xia

Faculty, Staff and Student Publications

Transcription factor BTB domain and CNC homology 1 (BACH1) belongs to the Cap 'n' Collar and basic region Leucine Zipper (CNC-bZIP) family. BACH1 is widely expressed in mammalian tissues, where it regulates epigenetic modifications, heme homeostasis, and oxidative stress. Additionally, it is involved in immune system development. More importantly, BACH1 is highly expressed in and plays a key role in numerous malignant tumors, affecting cellular metabolism, tumor invasion and metastasis, proliferation, different cell death pathways, drug resistance, and the tumor microenvironment. However, few articles systematically summarized the roles of BACH1 in cancer. This review aims to highlight the research status …

Final 2024 Residential Metals Abatement Program (Rmap) Whitehall Borrow Submittal #2, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Real-World Trends, Rural-Urban Differences, And Socioeconomic Disparities In Utilization Of Narrow Versus Broad Next-Generation Sequencing Panels, Yiqing Zhao, Anastasios Dimou, Zachary C Fogarty, Jun Jiang, Hongfang Liu, William B Wong, Chen Wang

Faculty, Staff and Student Publications

UNLABELLED: Advances in genetic technology have led to the increasing use of genomic panels in precision oncology practice, with panels ranging from a couple to hundreds of genes. However, the clinical utilization and utility of oncology genomic panels, especially among vulnerable populations, is unclear. We examined the association of panel size with socioeconomic status and clinical trial matching. We retrospectively identified 9,886 eligible adult subjects in the Mayo Clinic Health System who underwent genomic testing between January 1, 2016 and June 30, 2020. Patient data were retrieved from structured and unstructured data sources of institutional collections, including cancer registries, clinical …

Multi-Agent System For Portfolio Profit Optimization For Future Stock Trading, Usha Devi, Mohan R

Karbala International Journal of Modern Science

Stock trading highly contributes to the economic growth of the country. The stock trading objective is to earn profits with buy/sell/hold decisions on the set of stocks in the portfolio. The portfolio optimization problem is finding the decision sequence that leads to higher profit and lower risk. Portfolio optimization is challenging due to complex price history patterns and an uncertain environment. Incorrect decisions in stock trading lead to massive losses. The proposed Multi-Agent System for Portfolio Profit Optimization (MASPPO) aims to optimize trading profit and reduce risk with accurate predictions. The proposed model integrates the Fuzzy c-means with the Deep …

Use Of Dft Calculations As A Tool For Designing New Solvatochromic Probes For Biological Applications, Cynthia M. Dupureur

Educator Preparation & Leadership Faculty Works

The intramolecular charge transfer behavior of push–pull dyes is the origin of their sensitivity to environment. Such compounds are of interest as probes for bioimaging and as biosensors to monitor cellular dynamics and molecular interactions. Those that are solvatochromic are of particular interest in studies of lipid dynamics and heterogeneity. The development of new solvatochromic probes has been driven largely by the need to tune desirable properties such as solubility, emission wavelength, or the targeting of a particular cellular structure. DFT calculations are often used to characterize these dyes. However, if a correlation between computed (dipole moment) and experimentally measured …

Identification Of New Egfr Inhibitors By Structure-Based Virtual Screening And Biological Evaluation, Shuyi Wang, Xiaotian Xu, Chuxin Pan, Qian Guo, Qinlan Li, Shanhe Wan, Zhonghuang Li, Jiajie Zhang, Xiaoyun Wu

Faculty, Staff and Student Publications

Epidermal growth factor receptor (EGFR) inhibitors have been used in clinical for the treatment of non-small-cell lung cancer for years. However, the emergence of drug resistance continues to be a major problem. To identify potential inhibitors, molecular docking-based virtual screening was conducted on ChemDiv and Enamine commercial databases using the Glide program. After multi-step VS and visual inspection, a total of 23 compounds with novel and varied structures were selected, and the predicted ADMET properties were within the satisfactory range. Further molecular dynamics simulations revealed that the reprehensive compound ZINC49691377 formed a stable complex with the allosteric pocket of EGFR …

Emoji Use In Social Media Posts: Relationships With Personality Traits And Word Usage, Shelia Kennison, Kameryn Fritz, Maria Andrea Hurtado Morales, Eric Chan-Tin

Computer Science: Faculty Publications and Other Works

Prior research has demonstrated relationships between personality traits of social media users and the language used in their posts. Few studies have examined whether there are relationships between personality traits of users and how they use emojis in their social media posts. Emojis are digital pictographs used to express ideas and emotions. There are thousands of emojis, which depict faces with expressions, objects, animals, and activities. We conducted a study with two samples (n = 76 and n = 245) in which we examined how emoji use on X (formerly Twitter) related to users’ personality traits and language use …

Protein And Polysaccharide-Based Optical Materials For Biomedical Applications., Gianna Riviello, Brendan Connor, Jake Mcbrearty, Gianna Rodriguez, Xiao Hu

College of Science & Mathematics Departmental Research

Recent advances in biomedical research, particularly in optical applications, have sparked a transformative movement towards replacing synthetic polymers with more biocompatible and sustainable alternatives. Most often made from plastics or glass, these materials ignite immune responses from the body, and their production is based on environmentally harsh oil-based processes. Biopolymers, including both polysaccharides and proteins, have emerged as a potential candidate for optical biomaterials due to their inherent biocompatibility, biodegradability, and sustainability, derived from their existence in nature and being recognized by the immune system. Current extraction and fabrication methods for these biomaterials, including thermal drawing, extrusion and printing, mold …

Blood Cell Image Segmentation And Classification: A Systematic Review, Muhammad Shahzad, Farman Ali, Syed Hamad Shirazi, Assad Rasheed, Awais Ahmad, Babar Shah, Daehan Kwak

All Works

Background Blood diseases such as leukemia, anemia, lymphoma, and thalassemia are hematological disorders that relate to abnormalities in the morphology and concentration of blood elements, specifically white blood cells (WBC) and red blood cells (RBC). Accurate and efficient diagnosis of these conditions significantly depends on the expertise of hematologists and pathologists. To assist the pathologist in the diagnostic process, there has been growing interest in utilizing computer-aided diagnostic (CAD) techniques, particularly those using medical image processing and machine learning algorithms. Previous surveys in this domain have been narrowly focused, often only addressing specific areas like segmentation or classification but lacking …

Analysis Of The Impact Of Water Treatment By Liming Sedimentation And Dredging On The Content Of Heavy Metals In Fish Intended For Consumption, Asfie Maidie, Ismail Fahmy Almadi, Muchlis Efendi, Rekha Yusdha Nilawardhani, Komsanah Sukarti, Henny Pagoray

Journal of Sustainable Mining

The present study sought to determine the presence of metals and arsenic, a metalloid, among the fish of a coal mine reservoir, where the water was treated regularly through liming sedimentation combined with dredging, and the fish living in an adjoining river. The potential hazard of metals in fish as human food was analyzed. Except for selenium (an important metal to the human body), which was higher among the river fish than in the reservoir fish (P < 0.01), there were no particular patterns of other studied metals found in either habitat (P > 0.05), and apparently not related to the fish family that consumed by local people. Measurements of bioaccumulation factor (BAF) yielded scattered values from …

Long Term Sustainable Use Of Demersal Gillnet And Demersal Longline In Western Australia’S Temperate Shark Fisheries - Fisheries Research Report 340, Matias Braccini, Jack Parker, Daniela Waltrick, Maddison Watt, Nick Blay, Clinton Syers

Fisheries Research Reports

The Temperate Demersal Gillnet and Demersal Longline Fisheries (TDGDLF) are one of the main commercial shark fisheries in Australia. Most fishers in the TDGDLF use demersal gillnets to target sharks with scalefish taken in smaller amounts. Demersal longlines are also permitted but are not widely used. Demersal gillnets are size selective, but they do not necessarily discriminate among species, catching target and non-target species.

The Western Australian Fishing Industry Council (WAFIC) received funding as part of the Australian Government’s Our Marine Parks Grants Program to undertake research on the TDGDLF. This project was administered under the direction of a steering …

Spontaneous Transfer Of Small Peripheral Peptides Between Supported Lipid Bilayer And Giant Unilamellar Vesicles, Emanuela Efodili, Ashlynn Knight, Maryem Mirza, Cedric Briones, Il Hyung Lee

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Vesicular trafficking facilitates material transport between membrane-bound organelles. Membrane protein cargos are trafficked for relocation, recycling, and degradation during various physiological processes. In vitro fusion studies utilized synthetic lipid membranes to study the molecular mechanisms of vesicular trafficking and to develop synthetic materials mimicking the biological membrane trafficking. Various fusogenic conditions which can induce vesicular fusion have been used to establish synthetic systems that can mimic biological systems. Despite these efforts, the mechanisms underlying vesicular trafficking of membrane proteins remain limited and robust in vitro methods that can construct synthetic trafficking systems for membrane proteins between large membranes (>1 …

Expanding Karst Groundwater Tracing Techniques: Incorporating Population Genetic And Isotopic Data To Enhance Flow-Path Characterization, Benjamin Tobin, Benjamin V. Miller, Matthew Niemiller, Andrea Erhardt

Earth and Environmental Sciences Faculty Publications

Karst aquifers are unique among groundwater systems because of variable permeability and flow-path organization changes resulting from dissolution processes. Over time, changes in flow-path connectivity complicate interpretations of conduit network evolution in karst hydrogeology. Natural and artificial tracer techniques have long provided critical information for protecting karst aquifers and understanding the potential impacts on ecosystems and human populations. Conventional tracer methods are useful in karst hydrogeologic studies for delineating flow paths and defining recharge, storage, and discharge properties. However, these methods only provide snapshots of the current conditions and do not provide sufficient information to understand the changes in interconnection …

Geotechnical Characterisation Of Coal Spoil Piles Using High-Resolution Optical And Multispectral Data: A Machine Learning Approach, Sureka Thiruchittampalam, Bikram Pratap Banerjee, Nancy F. Glenn, Simit Raval

Geosciences Faculty Publications and Presentations

Geotechnical characterisation of spoil piles has traditionally relied on the expertise of field specialists, which can be both hazardous and time-consuming. Although unmanned aerial vehicles (UAV) show promise as a remote sensing tool in various applications; accurately segmenting and classifying very high-resolution remote sensing images of heterogeneous terrains, such as mining spoil piles with irregular morphologies, presents significant challenges. The proposed method adopts a robust approach that combines morphology-based segmentation, as well as spectral, textural, structural, and statistical feature extraction techniques to overcome the difficulties associated with spoil pile characterisation. Additionally, it incorporates minimum redundancy maximum relevance (mRMR) based feature …

When Evolutionary Computation Meets Privacy, Bowen Zhao, Wei-Neng Chen, Xiaoguo Li, Ximeng Liu, Qingqi Pei, Jun Zhang

Research Collection School Of Computing and Information Systems

Recently, evolutionary computation (EC) has experienced significant advancements due to the integration of machine learning, distributed computing, and big data technologies. These developments have led to new research avenues in EC, such as distributed EC and surrogate-assisted EC. While these advancements have greatly enhanced the performance and applicability of EC, they have also raised concerns regarding privacy leakages, specifically the disclosure of optimal results and surrogate models. Consequently, the combination of evolutionary computation and privacy protection becomes an increasing necessity. However, a comprehensive exploration of privacy concerns in evolutionary computation is currently lacking, particularly in terms of identifying the object, …

Frameworks For Measuring Population Health: A Scoping Review, Sze Ling Chan, Clement Zhong Hao Ho, Nang Ei Ei Khaing, Ezra Ho, Candelyn Pong, Jia Sheng Guan, Calida Chua, Zongbin Li, Trudi Lim Wenqi, Sean Shao Wei Lam, Lian Leng Low, Choon How How

Research Collection School Of Computing and Information Systems

Introduction Many regions in the world are using the population health approach and require a means to measure the health of their population of interest. Population health frameworks provide a theoretical grounding for conceptualization of population health and therefore a logical basis for selection of indicators. The aim of this scoping review was to provide an overview and summary of the characteristics of existing population health frameworks that have been used to conceptualize the measurement of population health. Methods We used the Population, Concept and Context (PCC) framework to define eligibility criteria of frameworks. We were interested in frameworks applicable …

Detecting Outdated Code Element References In Software Repository Documentation, Wen Siang Tan, Markus Wagner, Christoph Treude

Research Collection School Of Computing and Information Systems

Outdated documentation is a pervasive problem in software development, preventing effective use of software, and misleading users and developers alike. We posit that one possible reason why documentation becomes out of sync so easily is that developers are unaware of when their source code modifications render the documentation obsolete. Ensuring that the documentation is always in sync with the source code takes considerable effort, especially for large codebases. To address this situation, we propose an approach that can automatically detect code element references that survive in the documentation after all source code instances have been deleted. In this work, we …

An Itpa Enzyme With Improved Substrate Selectivity, Nicholas E. Burgis, Kandise Vanwormer, Devin Robbins, Jonathan Smith

Chemistry and Biochemistry Faculty Publications

Recent clinical data have identified infant patients with lethal ITPA deficiencies. ITPA is known to modulate ITP concentrations in cells and has a critical function in neural development which is not understood. Polymorphism of the ITPA gene affects outcomes for both ribavirin and thiopurine based therapies and nearly one third of the human population is thought to harbor ITPA polymorphism. In a previous site-directed mutagenesis alanine screen of the ITPA substrate selectivity pocket, we identified the ITPA mutant, E22A, as a gain-of function mutant with enhanced ITP hydrolysis activity. Here we report a rational enzyme engineering experiment to investigate the …

Struvite-Phosphorus Effects On Greenhouse Gas Emissions And Plant And Soil Response In A Furrow-Irrigated Rice Production System In Eastern Arkansas, Diego Della Lunga, Kristofor R. Brye, Trenton L. Roberts, Jonathan Brye, Michelle Evans-White, Christopher G. Henry, Daniel J. Lessner, Chandler Arel

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Phosphorus (P) fertilizers with low water solubility, like struvite (MgNH₄PO₄·6H₂O), have been identified to possibly reduce nutrient losses in furrow-irrigated cropping systems. However, there is a lack of research on the impacts of P and nitrogen (N) fertilization on greenhouse gas [GHG; i.e., methane (CH₄), nitrous oxide (N₂O), and carbon dioxide (CO₂)] production in furrow-irrigated rice (Oryza sativa). The objective of this study was to evaluate the effects of electrochemically precipitated struvite (ECST), chemically precipitated struvite (CPST), triple superphosphate (TSP), diammonium phosphate (DAP), environmentally smart nitrogen …

Vaccine Immunogenicity Versus Gastrointestinal Microbiome Status: Implications For Poultry Production, Chrysta N. Beck, Jiangchao Zhao, Gisela F. Erf

Poultry Science Faculty Publications and Presentations

At the turn of the 21st century, the importance of maintaining a balanced microbiome was brought to the forefront of the microbiology, immunology, and physiology research fields. Exploring the complex interactions between vaccine administration, mucosal microbiome, oral tolerance, and enteric inflammation in health and disease is challenging since environmental factors (such as diet and sanitation) have major influences on gut microbiota composition. High enteric pathogen load has been shown to contribute to dampened cell-mediated and humoral immune responses to vaccines in human case studies, either through elevated enteric inflammation or increased tolerance to environmental microbes. Although antibiotic and probiotic interventions …

Trees In Urban Environments: How Soil Quality Impacts Tree Performance, Saidan Qi

Dissertations, Theses, and Capstone Projects

Cities around the world are increasingly investing in reforestation and afforestation efforts to mitigate impacts from climate change and population growth. However, urban soil conditions can be unfavorable for tree growth. Street trees are widely known to suffer from poor soil quality, but there has been no comprehensive review of this topic so far. Clean soils can be transported from nonurban areas to support cities’ green projects, but this approach is not sustainable. Artificial (constructed) soils can be created from various materials and have been proposed as an alternative medium for urban tree growth, but no research has been done …