Digital Commons Network^™

The Role Of Homocysteine Redox Chemistry In Biomolecular Mechanisms, Megha Gupta

Dissertations and Theses

Homocysteine at elevated levels is a well-known independent risk factor for cardiovascular disease. However, it is still unclear, after large scale clinical trials, involving tens of thousands of patients, whether homocysteine is a disease mediator or marker. The disconnect between the basic science showing the association of homocysteine with cardiovascular disease and the outcomes of clinical trials based on vitamin therapy for homocysteine lowering, highlights the need for insights into the molecular mechanisms linking homocysteine to cardiovascular disease and other pathologies. For example, elevated homocysteine levels have also been associated with risk for stroke, venous thromboembolism, Alzheimer's disease, neural tube …

Epigenetic Insights Into Substance Use Disorder And Associated Psychiatric Conditions, Ambrose Loc Ngo, Christopher M. Ahmad, Niki Gharavi Alkhansari, Linda Nguyen, Huiping Zhang

Student Publications

Background: Substance use disorder (SUD) is closely associated with epigenetic modifications that significantly impact mental health outcomes. Alcohol and drug misuse induce widespread changes in the epigenome and transcriptome of the central nervous system, disrupting critical processes such as reward signaling and emotional regulation. These alterations in epigenetic regulation and gene expression often persist even after substance cessation, potentially contributing to the onset or worsening of psychiatric conditions, including schizophrenia, depression, stress, and anxiety.

Summary: This review delves into key epigenetic mechanisms underlying SUD and its comorbid psychiatric disorders, with a focus on DNA methylation, histone modifications, and noncoding RNA …

Spatialge Is A User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis., Oscar E. Ospina, Roberto Manjarres-Betancur, Guillermo Gonzalez-Calderon, Alex C. Soupir, Inna Smalley, Kenneth Y. Tsai, Joseph Markowitz, Mariam L. Khaled, Ethan Vallebuona, Anders E. Berglund, Steven A. Eschrich, Xiaoqing Yu, Brooke L. Fridley

Manuscripts, Articles, Book Chapters and Other Papers

Spatial transcriptomics (ST) is a powerful tool for understanding tissue biology and disease mechanisms. However, the advanced data analysis and programming skills required can hinder researchers from realizing the full potential of ST. To address this, we developed spatialGE, a web application that simplifies the analysis of ST data. The application spatialGE provided a user-friendly interface that guides users without programming expertise through various analysis pipelines, including quality control, normalization, domain detection, phenotyping, and multiple spatial analyses. It also enabled comparative analysis among samples and supported various ST technologies. The utility of spatialGE was demonstrated through its application in studying …

First-In-Human Clinical Trial Of A Small-Molecule Ebna1 Inhibitor, Vk-2019, In Patients With Epstein-Barr-Positive Nasopharyngeal Cancer, With Pharmacokinetic And Pharmacodynamic Studies, A Dimitrios Colevas, Zahra Talebi, Elizabeth Winters, Caroline Even, Victor Ho-Fun Lee, Maura L Gillison, Saad A Khan, Rong Lu, Benjamin A Pinsky, Samantha S Soldan, Olga Vladmirova, Paul M Lieberman, Troy E Messick

Faculty, Staff and Student Publications

Purpose: A first-in-human phase I study was conducted in patients with nasopharyngeal carcinoma to assess the safety and tolerability of VK-2019, a small-molecule selective inhibitor of Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1).

Patients and methods: Pharmacokinetic and pharmacodynamic studies were performed, including the measurement of EBV DNA plasma levels. Twenty-three patients received VK-2019 orally once daily at doses ranging from 60 to 1,800 mg using an accelerated titration design, with cohort expansion at 1,800 mg. EBV genome copy number and spatial transcriptomic analyses were conducted on biopsies collected from three patients at baseline and after treatment.

Results: VK-2019 was …

Ancestral Differences In Anticancer Treatment Efficacy And Their Underlying Genomic And Molecular Alterations, Mei Luo, Jingwen Yang, Alejandro A Schäffer, Chengxuan Chen, Yuan Liu, Yamei Chen, Chunru Lin, Lixia Diao, Yong Zang, Yanyan Lou, Huda Salman, Gordon B Mills, Eytan Ruppin, Leng Han

Faculty, Staff and Student Publications

Systematic multi-omics analysis revealed ancestry-dependent molecular alterations, but their impact on the efficacy of anti-cancer treatment is yet largely unknown. Here, we analyzed clinical trials from ClinicalTrials.gov and found that only 8,779/102,721 (8.5%) oncology clinical trials posted information on enrollment by race/ethnicity. The underrepresentation of non-White populations suggests that it remains challenging to determine differences in the efficacy of anti-tumor treatments among different racial groups. Through a comprehensive analysis of clinically actionable genes, imputed drug responses, and immune features, we identified potential differences in treatment response to targeted, chemo and immunotherapies between different ancestral populations. Further analysis of multiple independent …

Pleural Effusion: Shedding Light On Pleural Disease Beyond Infection And Malignancy, William C Harding, Abdul R Halawa, Mazen M Aiche, Bilal Zafar, Hyeon-Ju R Ali, Lara Bashoura, Saadia A Faiz

Faculty, Staff and Student Publications

Background and Objectives: Non-malignant pleural effusions (NMPEs) are the most frequently encountered pleural disease. They arise from various non-malignant, non-infectious clinical conditions, including cardiac, renal, and hepatic organ dysfunction. Despite their wide prevalence, there is a lack of literature for NMPE. This publication aims to provide an updated overview of the causes, diagnostic strategies, and management options for NMPE.

Materials and Methods: This review synthesizes findings from studies published on NMPE, focusing on the presentation, diagnosis (such as imaging and pleural fluid analysis), and management strategies. Studies were selected based on relevance and were analyzed to provide a comprehensive summary …

Accumulation Of Cd38 In Hybrid Epithelial/Mesenchymal Cells Promotes Immune Remodeling And Metastasis In Breast Cancer, Tanvi H Visal, Recep Bayraktar, Petra Den Hollander, Michael A Attathikhun, Tieling Zhou, Jing Wang, Li Shen, Corina-Elena Minciuna, Meng Chen, Elizve Barrientos-Toro, Harsh Batra, Maria Gabriela Raso, Fei Yang, Edwin R Parra, Aysegul A Sahin, George A Calin, Sendurai A Mani

Faculty, Staff and Student Publications

Triple-negative breast cancer (TNBC) is a highly metastatic subtype of breast cancer. The epithelial-to-mesenchymal transition is a nonbinary process in the metastatic cascade that generates tumor cells with both epithelial and mesenchymal traits known as hybrid EM cells. Recent studies have elucidated the enhanced metastatic potential of cancers featuring the hybrid EM phenotype, highlighting the need to uncover molecular drivers and targetable vulnerabilities of the hybrid EM state. Here, we discovered that hybrid EM breast tumors are enriched in CD38, an immunosuppressive molecule associated with worse clinical outcomes in liquid malignancies. Altering CD38 expression in tumor cell impacted migratory, invasive, …

Somatic Acupressure For The Management Of The Fatigue-Sleep Disturbance-Depression Symptom Cluster In Breast Cancer Survivors: A Study Protocol For A Phase Iii Randomised Controlled Trial, Mengyuan Li, Tao Wang, Xian Liang Liu, Ren Li Deng, Wai Hang Kwok, Li Qun Yao, Jing Yu Benjamin Tan

Research outputs 2022 to 2026

Introduction The fatigue-sleep disturbance-depression symptom cluster (FSDSC) is commonly experienced by breast cancer (BC) survivors, leading to a deteriorated quality of life (QoL). Somatic acupressure (SA) has been recommended as a promising non-pharmacological intervention for cancer-related fatigue (the core symptom of the FSDSC) in the guidelines, showing its encouraging role in relieving cancer-related sleep disorders, fatigue and depression. This phase III randomised controlled trial (RCT) is designed to evaluate the effects, safety and cost-effectiveness of SA for managing the FSDSC in BC survivors. Methods This phase III RCT will be a partial-blinded, sham-controlled, three-arm, parallel clinical trial, involving a 7-week …

Connectome-Based Predictive Modeling Of Ptsd Development Among Recent Trauma Survivors, Ziv Ben-Zion, Alexander J Simon, Matthew Rosenblatt, Nachshon Korem, Or Duek, Israel Liberzon, Arieh Y Shalev, Talma Hendler, Ifat Levy, Ilan Harpaz-Rotem, Dustin Scheinost

Staff and Researcher Publications

Importance: The weak link between subjective symptom-based diagnostics for posttraumatic psychopathology and objective neurobiological indices hinders the development of effective personalized treatments.

Objective: To identify early neural networks associated with posttraumatic stress disorder (PTSD) development among recent trauma survivors.

Design, setting, and participants: This prognostic study used data from the Neurobehavioral Moderators of Posttraumatic Disease Trajectories (NMPTDT) large-scale longitudinal neuroimaging dataset of recent trauma survivors. The NMPTDT study was conducted from January 20, 2015, to March 11, 2020, and included adult civilians who were admitted to a general hospital emergency department in Israel and screened for early PTSD symptoms indicative …

Racial Equity In Urine Drug Screening Policies In Labor And Delivery, Vahid Azimi, Cassandra Trammel, Lauren Nacke, Alexandra Rubin, Lori Stevenson, Brittaney Vaughn, Stephen M Roper, Mark A Zaydman, Ronald Jackups, Noor Riaz, Kim P Schamel, Jeannie C Kelly

2020-Current year OA Pubs

IMPORTANCE: Black pregnant patients are significantly more likely than their White counterparts to undergo peripartum urine drug screening (UDS) and subsequent reporting to child protective services (CPS).

OBJECTIVE: To evaluate the association of removing isolated cannabis use and limited prenatal care as order indications, combined with clinician-facing clinical decision support, with racial parity in peripartum UDS and CPS reporting.

DESIGN, SETTING, AND PARTICIPANTS: This quality improvement study assessed 9396 pregnant patients at a single tertiary care center in a Midwestern US urban metropolitan region who delivered before (June 1, 2021, to September 31, 2022) and after (October 1, 2022, to …

Environmental Hygiene Strategies To Combat Antimicrobial Resistance In Healthcare Settings, Mary Morgan Lee, Caroline A O'Neil, Lucy Vogt, Jennie H Kwon

2020-Current year OA Pubs

In this manuscript, we highlight current literature on environmental hygiene techniques to combat reservoirs of antibiotic resistant organisms in the healthcare environment. We discuss several topics for each strategy, including mechanism of action, assessment of effectiveness based on studies, cost, and real-world translatability. The techniques and topics summarized here are not inclusive of all available environmental hygiene techniques but highlight some of the more popular and investigated strategies. We focus on the following: Ultraviolet radiation, hydrogen peroxide vapor, copper-coated surfaces, phages, interventions involving sinks, and educational initiatives.

From Deliberate Indifference To Civil Negligence: Protecting Male Prisoners From Sexual Violence In United States Prisons, Olivia Martini

Immigration and Human Rights Law Review

Sexual violence in United States prisons is a pervasive issue that disproportionately impacts male inmates, revealing systemic failures in the current legal framework designed to protect incarcerated individuals. The deliberate indifference standard, established by the United States Supreme Court, imposes an excessively high burden of proof on survivors, requiring evidence of prison officials’ subjective awareness of specific, substantial risks.

This article critiques the shortcomings of the deliberate indifference standard and proposes a civil negligence framework as a promising alternative. Grounded in an objective duty of care, a civil negligence approach emphasizes proactive measures that institutions must take to avoid liability. …

Evaporating Natural Parent Childcare Liberties Under New Parentage Laws, Jeffrey A. Parness

Arkansas Law Review

This Article explores the evaporating Due Process interests of natural childcare parents who are not unfit and who do not knowingly consent to diminished childcare liberties when the state recognizes new nonadoptive and nonbiological parents. Childcare liberty losses need not involve neglect or comparable bad acts rendering a parent unfit. They need not involve consent, actual or implied, by an adversely affected parent. On the new forms of nonadoptive and nonbiological childcare parents, the most recent UPAs and their state counterparts are illustrative. They recognize parentage in an individual who resides with and holds out a child as the individual’s …

Arkansas Law Review - Volume 77 Issue 4, Journal Editors

Arkansas Law Review

No abstract provided.

Current Analytical Methods And Their Limitations In Quantifying Antidiabetic Drug Nateglinide And Repaglinide In Pharmaceutical Formulations And Biological Fluids, Sk Manirul Haque

Yanbu Journal of Engineering and Science

Pharmaceutical growth dominated a transformation in human health. These drugs need to attend to their target only, so they must be free from impurities and appropriately controlled. Due to that, diverse instrumental techniques were advanced at steady intervals to accomplish their intention to quantify the limits per the regulatory. NTG and RPG pharmaceuticals might generate impurities during the development phases, packing, and shipping, which could be risky to administer. Hence, detecting and quantifying them using various analytical techniques at multiple stages is necessary. This review highlights the function of different analytical methods, including UV–Vis, HPLC, HPTLC, UPLC, HPLC/MS and UPLC/MS, …

Design And Synthesis Of Ag Nps/Cellulose Nanofiber-Starch Nano-Bio Composites For Packaging Applications, Preetha Balakrishnan, Sreerag Gopi

Yanbu Journal of Engineering and Science

Addressing problems due to conventional plastics requires a comprehensive approach involving waste reduction, improved waste management practices, and the development of sustainable alternatives to conventional plastics. In this study, a system was designed that can decorate cellulose nanofiber with silver nanoparticles (AgNP) and then used as a reinforcing agent in thermoplastic starch matrix. The composites were characterized by Fourier Transform Infrared Spectroscopy (FTIR), Field emission scanning electron microscopy (FESEM), Transmission electron microscopy (TEM) and transport properties. The morphology and chemical modification of cellulose nanomaterials with silver nanoparticles were confirmed by FESEM, TEM and FTIR and the results indicated proper adhesion …

Hygrothermal Performance Of Roofs With High Initial Construction Moisture Subjected To Hot Climate, Hamed H. Saber

Yanbu Journal of Engineering and Science

Moisture accumulation in the building components/assemblies that form building envelopes can lead to material deterioration and moisture related issues such as mould growth. As a part of the building envelope, this study focusses on assessing the moisture performance and energy performance (i.e., hygrothermal performance) of roofing systems. As roofs can be built with high initial construction moisture, numerical simulations were conducted with and without high initial construction moisture in order to investigate: (a) the hygrothermal performance of cool and black roofs having material layer with high initial construction moisture content, (b) the time needed so that the moisture content reaches …

Production And Evaluation Of Activated Carbon From Saudi Arabian Acacia Tortilis Tree Bark By Microwave And Low Temperature Activation Process, Muhammad Saleem

Yanbu Journal of Engineering and Science

In the present work, activated carbon was prepared from Acacia Tortilis tree bark, utilizing phosphoric acid chemical activation, and microwave irradiation (AC-MWI). Activated carbon was also prepared by conventional phosphoric acid chemical activation and low temperature carbonization (AC-CA). Characterization of the activated carbons were performed by proximate analysis adopting ASTM standard procedures. BET-specific surface area, total ash content, bulk density, moisture content, pH, pore volume and iod- ine number were determined. Comparison of characteristics for both carbons, with the characteristics of AC available in the literature and commercially available in the market was performed. Comparison showed that activated carbon produced …

Accurate Mathematical Modeling Of Electronic Load Harmonics Using Machine Learning Software, Ahmad Al-Subhi

Yanbu Journal of Engineering and Science

This paper presents accurate mathematical models for several power system harmonics problems using an efficient machine learning tool, Eureqa. Three previously published research papers that included actual field measurements have been chosen to compare and assess the harmonics mathematical models presented in this paper. Following that, mathematical models of the output parameters as functions of the input parameters have been developed based on these data. For all these different research works and experiments, a total of 17 mathematical models have been built using basic curve fitting tools. Most of these proposed models couldn't fit the experimental data appropriately. Considerable error …

Optimized And Validated Box–Behnken Design Combined Response Surface Methodology To Quantify Acetic Acid Content In Potassium Clavulanate Using High–Performance Liquid Chromatography, Sk Manirul Haque

Yanbu Journal of Engineering and Science

A simple and robust high-performance liquid chromatography method with UV detection was developed to quantify acetic acid in potassium clavulanate. The chromatographic separation was performed on the Hypersil BDS C18 column (250×4.6 mm, 5 μm) with optimized response surface methodology combined Box–Behnken experimental design. The mobile phase comprises of a buffer prepared by ammonium dihydrogen orthophosphate (20 mM) containing 0.01% triethylamine, maintained pH between 2.8–3.2 using phosphoric acid and % acetonitrile as per Box–Behnken factorial design. The detection was performed at 235 nm with a mobile phase flow rate of 1 ml/min. The method was validated as per the ICH …

Transfer Learning Approach For Classification Of Widely Used Spices, Arunachalam Sundaram, Abdullahi Masud, Ali Almarhoon, Bhaskarjit Sarmah

Yanbu Journal of Engineering and Science

People around the world relish variety of food that are flavourful. Spices add flavours to the food without adding any fat or calories. People have used spices for many centuries and are an integral part of our food. In addition to aroma, spices also have anti-bacterial, anti-inflammatory properties and other health-promoting properties. Recognizing spices from images is a challenging problem for a machine as they come in varying sizes and shapes, different colours, high visual similarity, and texture. The classification of spices presents useful applications in the field of Artificial Intelligence-driven food industry, e-commerce, and health care. In the billion-dollar …

Investigation Of The Molecular Structures, Electronic Properties And Vibrational Spectrum Of Trifluoroacetophenone Using Density Functional Theory, Yunusa Umar

Yanbu Journal of Engineering and Science

Trifluroacetophenone is considered a highly efficient, inexpensive, and green organocatalyst that is used in organic synthesis. Geometry optimization, electronic properties, and frequency calculations of 2,2,2-trifluoroacetophenone are performed using the B3LYP density functional theory method and the 6-311++G(d, p) basis set. The geometrical parameters, frontier molecular orbitals, molecular electrostatic potential surface, and simulated infrared spectrum are reported. The structural parameters are compared with available X-ray diffraction experimental values, and the calculated electronic properties are compared with those of its structural analogue, acetophenone.

Estimating The Energy Recovery Potential From Municipal Solid Waste In Ha’Il Region (Kingdom Of Saudi Arabia), Noureddine Elboughdiri, Muhammad Imran Khan, Takwa Missaoui

Yanbu Journal of Engineering and Science

In the Kingdom of Saudi Arabia (KSA), the need of an agile solid waste management (SWM) system is vital to control safely the rapid growth of its municipal solid waste (MSW) with minimal environment toll. Further, the domestic energy production in KSA is thriving and putting a tremendous pressure on its reserves of fossil oil. Waste-to-energy (WTE) plants provides an excellent opportunity, even if MSW mitigation and energy production are usually considered separately. Energy recovery (ER) from waste is not a new field of study; however, its implementation remains a challenge in KSA. Although there is abundance of useful waste …

Solid-Phase Extraction And Gc/Ms Confirmation Of Heroin Abuse In Urine, Mahmoud A. Alabdalla

Yanbu Journal of Engineering and Science

A method for the analysis of urine for the heroin abuse is described. The analytical procedure uses solid-phase extraction (SPE), gas chromatography/mass spectrometry (GC/MS). It allows extraction, derivatization and analysis of 6-MAM and Morphine from urine. After solid-phase extraction was complete, the eluate was selectively derivatized with N-Methyltrimethylsilyltrifluoroacetamide (MSTFA). Analysis was performed using a GC/MS system operating in full scan mode. The mass spectrum of the derivatized metabolites was searched manually against reference libraries for positive identification and the retention time checked against that of the standard. This procedure has increased both the amount and the reliability of information given …

Efficient Removal Of Copper And Cadmium From Contaminated Soil Utilizing Electrokinetic Process, Muhammad Saleem

Yanbu Journal of Engineering and Science

Present manuscript demonstrates the efficient removal of copper and cadmium from contaminated soil utilizing electrokinetic process. The results of systematic bench-scale study on improved extraction of copper and cadmium shows the suitability of process to decontaminate low permeable soil. The influence of operating parameters such as electrode material, soil pH, current density, soil temperature, inter-electrode spacing and initial soil moisture content on the decontamination performance is investigated. Study revealed that, removal of copper and cadmium reached to 89.4% and 62.7% respectively while using titanium electrodes. Removal efficiency improved with the increase in current density, soil temperature and initial soil moisture …

Development Of An Optimal Path Planning Using Elite Opposition Based Bat Algorithm For A Mobile Robot, Zaharudeen Haruna, Muhammad B. Mu'azu Mu'azu, Prosper Oyibo, Salawuden A. Tijani

Yanbu Journal of Engineering and Science

This research work presents the development of an optimal path planning using elite opposition based bat algorithm (EOBA) for mobile robot, such that the robot avoids obstacle(s) without making contact with them. The bat algorithm (BA) is a nature. inspired meta-heuristic algorithm that works on the basis of the echolocation behavior of bat. It, however, has a poor exploration capability leading to it easily getting stuck in local optima. The EOBA is developed by modifying the BA with the elite opposition-based learning (EOBL) so as to diversify the solution search space and the inertial weight in order to balance its …

Microwave Against Thermal Treatment For Manufacturing Of Activated Carbon From Agricultural Wastes And Its Use To Adsorb Methylene Blue-Equilibrium Ad Kinetic Studies, Hossam Altaher, Fahd M. Al-Oufi, Yehia H. Magdy, Manar Hassan

Yanbu Journal of Engineering and Science

Dates pits, a widely available agricultural waste, was used to produce two samples of activated carbon. The first sample was prepared by thermal treatment at 500 °C for two hours, and the other one was prepared through microwave irradiation for 12 minutes. Zinc chloride was used as the chemical activator for the two samples. The efficiency of the two samples towards methylene blue adsorption was investigated. The effects of some parameters, such as initial pH of the solution, initial concentration of methylene blue, contact time and adsorbent dose, on the adsorption capacity were also investigated. Equilibrium and kinetic models were …

Study Of The Thermal Properties And Molecular Mass Of Polyhydroxybutyrate Produced By Rhodococcus Equi, Nadia Altaee, Ayad Fahdil, Kumar Sudesh, Emad Yousif

Yanbu Journal of Engineering and Science

In the present study, the ability of Rhodococcus equi for polyhydroxyalkanoates (PHA) production was closely observed in the presence of crude palm kernel oil as a carbon source. Gas chromatography analysis proved that the biopolymer was a homopolymer that comprised of 38% polyhydroxybutyrate (PHB). The melting temperature (at 173°C) and glass transition temperature (at 2.79 °C) of PHA was determined using differential scanning calorimetry analysis, and the decomposition temperature (at 276°C) was determined by thermogravimetric analysis. The gel permeation chromatography revealed the average molecular weight (M) to be at 6.42 KD, the number average weight (M) at 373 KD, and …

Theoretical Approach To Study Self-Organizing Properties Of A Nematic Liquid Crystal With Carbon Nanosolid Models, Mehdi Salih Shihab

Yanbu Journal of Engineering and Science

A theoretical study on stable geometries of a nematic liquid crystal (LC) molecule (4- methoxybenzylidene-4'-n-butylaniline (MBBA)) assembled on the carbon nanosolid (CNS) surface models (graphite sheet and carbon nanotube (CNT): zigzag, armchair) has been carried out by using semi-empirical molecular quantum calculations within the parameterized model number 3method as implemented in the Hyperchem package. The interaction of π,π-stacking between the MBBA molecules present on the CNS wall led to the formation of local short-range orientational order due to the LC-CNS binding energy. The binding energy of the LC molecule on the CNS surface was the typical van der Waals interaction. …

Synthesis And Characterization Of New Azo-Schiff Bases And Their Biological Activity, Hamid Hussein Eissa

Yanbu Journal of Engineering and Science

This work focused on the synthesis of new azo Schiff bases which were prepared by condensation of 3-formyl-4-hydroxy phenylazo benzene with both 1,3-diamino xylylene, 2,6-diamino Pyridine, 1,5-diamino-2-methyl pentane respectively. The Schiff bases were checked by different spectral technique (LC-MS, GC-MS, 1H-NMR, IR). The new azo Schiff Bases were studied for antibacterial activities against (Bacillus subtilis and Staphylococcus aureus) are Gram positive and (Salmonella typhi and Escherichia coli) is Gram negative. The azo compound ligand were exhibited a vari-able activity of inhibition on the growth of the bacteria.