Digital Commons Network^™

Clonality And Epidemiological Studies Of E. Coli Strain Collected From Abu Dhabi Emirate Using Ngs And Bioinformatic Tools, Ahmed Abdelrahman Mohamed

Theses

In the current landscape, where antibiotic resistance in bacteria is steadily rising, the role of bacterial genomics has assumed increasing significance. Therefore, it is necessary for microbiologists to acquire proficiency in the utilization of these methods and tools to harness their potential in gaining valuable insights into bacterial genomes. This can facilitate the development of innovative strategies for managing and treating bacterial infections. Here we present the power of the whole-genome sequencing technology in characterization of multidrug resistant Escherichia coli isolates. Fourteen Escherichia coli isolates were selected for this study. Following the standard microbiological techniques to confirm the sample identification, …

Mathematical Modeling Of An Epidemic In Scalefree Network With Imperfect Vaccination, Heba Hameed

Theses

In light of the recent COVID-19 pandemic, the mathematical epidemiological model has proven to be essential for understanding the disease dynamic and finding the best control tool to help contain the disease and minimize its impact. This thesis investigates the dynamics of an infectious disease spread with latent infection and vaccination. The aim is to study this model’s dynamic in a network that reflects the heterogeneity of the environment where the disease spreads. The vaccination is assumed to be not perfect, which means that vaccinated persons are likely to be infected and that the vaccinated person could lose their immunity, …

The Anticancer Activity Of A Novel 8-Hydroxyquinoline Derivatives Against 5-Fluorouracil Resistant Colorectal Cancer Cells, Mazoun Talal Al Azzani

Theses

Cancer is a global health crisis for which 20 million new cases were diagnosed in 2022 alone, with 9.3 million cancer-related deaths. Nearly 900,000 deaths were due to colorectal cancer (CRC), which is the third leading cause of cancer related mortality. In the United Arab Emirates, 550 new cases of CRC were reported in 2022. A major clinical challenge with CRC treatment is the development of resistance to 5-fluorouracil (5FU)-based chemotherapy regimens, which are the standard treatment for CRC. In the present study, the anticancer activity of two novel 8-hydroxyquinoline (8-HQ) derivatives AS45 and AS47 was examined against 5FU-sensitive (HCT116) …

Relationship Between Parents’ Feeding Styles, Nutrition Practices And Risk Of Obesity Among 3-5 Years Old Children In The United Arab Emirates, Reem Mohamed Alkarbi

Theses

Previous studies suggest that parental feeding practices shape preschool eating and physical activity habits, ultimately influencing children's weight status. Despite the high obesity rate in UAE youth, preschoolers’ nutrition habits and their links to parental feeding styles are explored. This study aims to describe parental feeding styles: Emotional (E), Instrumental (I), Prompting and Encouragement (PE), Control Over Eating (COE)), and their associations with nutrition practices, socio-demographic factors, and obesity in UAE preschoolers. Using an online questionnaire, a cross-sectional study surveyed Emirati families with 3-5-year-old children. Data was analyzed using SPSS v.29. 70 preschool Emirati children living in Abu Dhabi participated. …

Salivary Microbiome Signature In Pediatric Inflammatory Bowel Disease, Ghaidaa Mohammed Mesto

Theses

Inflammatory bowel disease (IBD) is a complex disorder characterized by chronic inflammation of the gastrointestinal tract (GIT). IBD mainly includes two distinct diseases, namely Crohn’s disease (CD) and ulcerative colitis (UC). To date, the precise etiology of these conditions is not fully elucidated, although a strong relationship between microbial dysbiosis in the GIT and IBD has been proposed. In general, limited data is available on the oral microbiome of IBD patients, despite its recognizable role in impacting gut health. There is a paucity of research on IBD in the pediatric population, although this disease is becoming more prevalent than in …

The Differences Between Metacognitive Reading Strategies Used By Native Arabic Speakers In The Uae When Reading Digital Versus Printed Materials, Razan Majed Shehadeh

Theses

This study explores the differences between the metacognitive reading strategies that native Arabic speakers college students use in the UAE when reading digital vs. printed texts. A convergent Mixed-Methods Design was employed to achieve the purpose of this study. The first data comprised a background questionnaire and two metacognitive reading surveys reflecting reading from digital materials that were conducted with college students (n=100), and the second data set comprised semi-structured interviews with a subset of students sampled from the original pool (n= 8). This study's participants were college students selected randomly from some of the UAE universities. Generally, the results …

Mitochondrial Control Of Tumorigenicity And Immunogenicity Of Colorectal Cancer, Maram Esam Ahmed

Theses

The Methylation-controlled J protein (MCJ), also known as DNAJC15, serves as an endogenous negative regulator of mitochondrial respiration. MCJ plays a crucial role in cellular bioenergetics by regulating cellular metabolism, and its expression is inversely proportional to the extent of mitochondrial ATP production. In the current study, we aimed to investigate the relationship between MCJ expression and the tumorigenicity and immunogenicity of colon adenocarcinoma. To this aim, we utilized MCJ knockout (KO) mice to assess the impact of tumor-extrinsic MCJ expression in host cells, particularly immune cells, on anti-tumor responses. Comparing the growth of MCJ-expressing cancer cells in wild-type vs. …

Diversity, Distribution, And Determinants Of Bacterial Communities In Arctic Soil, Amna Khaleefa Alhemeiri

Theses

Arctic soils host diverse bacterial communities crucial for ecosystem functioning and nutrient cycling. Understanding the factors shaping their diversity and distribution is essential to assess ecosystem responses to climate warming. This study aimed to assess and compare bacterial diversity and community structure between high- and sub-arctic ecosystems and explore the environmental and climatic factors determining their distribution. We collected 16S rRNA gene amplicon sequence data from 999 samples of high- and sub-arctic soils. All the data was pre-processed and quality-controlled using a similar bioinformatics methodology, followed by statistical analyses including alpha and beta diversity assessments, and volatility analysis using QIIME2. …

Produced Water Management From Production Sites In The State Of Kuwait, Feras Adel Alsalem

Dissertations

Extraction of crude oil also produces large volumes of water, termed produced water (PW). PW is by far the most significant by-product in the process of extracting hydrocarbons from the subsurface. Consequently, managing PW has become a great concern to oil and gas producers. The increasing amounts of PW and more stringent environmental and safety regulations in regard to PW make more efficient treatment methods necessary, where sustainable long-term solutions for PW management need to be provided. The focus of this study is on PW from onshore operations as the majority of the oil and gas extraction operations (upstream processes) …

Germination And Seedling Growth Of Native Uae Plant Species: The Combined Effects Of Elevated Co2 And Temperature, Nour Elhouda Debouza

Dissertations

Understanding how indigenous plant species respond to arid environmental stressors is critical for biodiversity preservation and the development of sustainable agricultural practices in the United Arab Emirates (UAE). This study investigated the morphological and physiological aspects of the germination and early growth stages, along with the adaptation strategies of three indigenous plant species—Senna italica, Prosopis cineraria, and Tephrosia nubica. The controlled chamber experiments aimed to subject the three selected indigenous species to elevated CO2 (400 ppm ambient to 800 ppm) and temperature (35°C ambient to 50°C) for simulating future atmospheric carbon dioxide (CO2) and temperature scenarios. …

A Case Study: Impacts Of A Building Retrofit On Employee Efficiency And Productivity, Rigo Zepeda

Construction Management

This case study explores the effects of retrofitting building systems on operational efficiency and employee productivity in the contemporary office environment. As concerns over sustainability and the well-being of employees are now at the forefront of modern workplace design, the retrofitting of outmoded building systems has been seen as an option to enhance energy efficiency and occupant satisfaction. This research paper focuses on the recently retrofitted Performance Contracting office building in Benicia, California. As heating and ventilation systems, and lighting are two big contributors to energy consumption in buildings and comfort, analyzing these systems provided insight into its building performance. …

Atp1a3 Disease Spectrum Includes Paroxysmal Weakness And Encephalopathy Not Triggered By Fever, Chetan Immanneni, Daniel Calame, Song Jiao, Lisa T Emrick, Miguel Holmgren, Sho T Yano

Faculty, Staff and Students Publications

BACKGROUND AND OBJECTIVES: Heterozygous pathogenic variants in ATP1A3, which encodes the catalytic alpha subunit of neuronal Na+/K+-ATPase, cause primarily neurologic disorders with widely variable features that can include episodic movement deficits. One distinctive presentation of ATP1A3-related disease is recurrent fever-triggered encephalopathy. This can occur with generalized weakness and/or ataxia and is described in the literature as relapsing encephalopathy with cerebellar ataxia. This syndrome displays genotype-phenotype correlation with variants at p.R756 causing temperature sensitivity of ATP1A3. We report clinical and in vitro functional evidence for a similar phenotype not triggered by fever but associated with protein loss-of-function.

METHODS: We …

Amino-Modified Upcycled Biochar Achieves Selective Chromium Removal In Complex Aqueous Matrices, Kenneth Flores, Diego F. Gonzalez, Helia Magali Morales, Arnulfo Mar, Sergi Garcia-Segura, Jorge L. Gardea-Torresdey, Jason Parsons

School of Earth, Environmental, & Marine Sciences Faculty Publications

Chromium pollution of groundwater sources is a growing global issue, which correlates with various anthropogenic activities. Remediation of both the Cr(VI) and Cr(III), via adsorption technologies, has been championed in recent years due to ease of use, minimal energy requirements, and the potential to serve as a highly sustainable remediation technology. In the present study, a biochar sorbent sourced from pineapple skins, allowed for the upcycling of agricultural waste into water purification technology. The biochar material was chemically modified, through a green amination method, to produce an efficient and selective adsorbent for the removal of both Cr(VI) and Cr(III) from …

Cadherin-11 Targeted Cell-Specific Liposomes Enabled Skin Fibrosis Treatment By Inducing Apoptosis, Himanshu N Bhatt, Rimpy Diwan, Igor L Estevao, Rui Dong, Jennifer Smith, Chuan Xiao, Sandeep K Agarwal, Md Nurunnabi

Faculty, Staff and Students Publications

Continuous and aberrant activation of myofibroblasts is the hallmark of pathological fibrosis (e.g., abnormal wound healing). The deposition of excessive extracellular matrix (ECM) components alters or increases the stiffness of tissue and primarily accounts for multiple organ dysfunctions. Among various proteins, Cadherin-11 (CDH11) has been reported to be overexpressed on myofibroblasts in fibrotic tissues. Anti-apoptotic proteins such as (B cell lymphoma-2) (BCL-2) are also upregulated on myofibroblasts. Therefore, we hypothesize that CDH11 could be a targeted domain for cell-specific drug delivery and targeted inhibition of BCL-2 to ameliorate the development of fibrosis in the skin. To prove our hypothesis, we …

Convolutional Neural Networks To Study Contrast-Enhanced Magnetic Resonance Imaging-Based Skeletal Calf Muscle Perfusion In Peripheral Artery Disease, Bijen Khagi, Tatiana Belousova, Christina M Short, Addison A Taylor, Jean Bismuth, Dipan J Shah, Gerd Brunner

Faculty, Staff and Students Publications

Peripheral artery disease (PAD) is associated with impaired blood flow in the lower extremities and histopathologic changes of the skeletal calf muscles, resulting in abnormal microvascular perfusion. We studied the use of convolution neural networks (CNNs) to differentiate patients with PAD from matched controls using perfusion pattern features from contrast-enhanced magnetic resonance imaging (CE-MRI) of the skeletal calf muscles. We acquired CE-MRI based skeletal calf muscle perfusion in 56 patients (36 patients with PAD and 20 matched controls). Microvascular perfusion imaging was performed after reactive hyperemia at the midcalf level, with a temporal resolution of 409 ms. We analyzed perfusion …

Efemp1 Haploinsufficiency Causes A Marfan-Like Hereditary Connective Tissue Disorder, Irman Forghani, Steven H Lang, Matthew J Rodier, Stephanie A Bivona, Alejo A Morales, Stephan Zuchner, Guney Bademci, Mustafa Tekin

Faculty, Staff and Students Publications

Phenotypic features of a hereditary connective tissue disorder, including craniofacial characteristics, hyperextensible skin, joint laxity, kyphoscoliosis, arachnodactyly, inguinal hernia, and diverticulosis associated with biallelic pathogenic variants in EFEMP1 have been previously described in four patients. Genome sequencing on a proband and her mother with comparable phenotypic features revealed that both patients were heterozygous for a stop-gain variant c.1084C>T (p.Arg362*). Complementary RNA-seq on fibroblasts revealed significantly reduced levels of mutant EFEMP1 transcript. Considering the absence of other molecular explanations, we extrapolated that EFEMP1 could be the cause of the patient's phenotypes. Furthermore, nonsense-mediated decay was demonstrated for the mutant allele …

Expanding The Phenotype Of Ppp1r21-Related Neurodevelopmental Disorder, Mohammed Almannai, Dana Marafi, Maha S Zaki, Reza Maroofian, Stephanie Efthymiou, Nebal Waill Saadi, Bilal Filimban, Hormos Salimi Dafsari, Fatima Rahman, Shazia Maqbool, Eissa Faqeih, Fuad Al Mutairi, Hind Alsharhan, Omar Abdelaty, Saadoun Bin-Hasan, Ruizhi Duan, Mahmoud M Noureldeen, Alaa Alqattan, Henry Houlden, Jill V Hunter, Jennifer E Posey, James R Lupski, Ayman W El-Hattab

Faculty, Staff and Students Publications

PPP1R21 encodes for a conserved protein that is involved in endosomal maturation. Biallelic pathogenic variants in PPP1R21 have been associated with a syndromic neurodevelopmental disorder from studying 13 affected individuals. In this report, we present 11 additional individuals from nine unrelated families and their clinical, radiological, and molecular findings. We identified eight different variants in PPP1R21, of which six were novel variants. Global developmental delay and hypotonia are neurological features that were observed in all individuals. There is also a similar pattern of dysmorphic features with coarse faces as a gestalt observed in several individuals. Common findings in 75% of …

Anoctamin 4 Defines Glucose-Inhibited Neurons In The Ventromedial Hypothalamus, Longlong Tu, Yanlin He, Yong Xu

Faculty, Staff and Students Publications

No abstract provided.

Neighborhood-Level Disadvantage And Delayed Adjuvant Therapy In Head And Neck Cancer, Evan M Graboyes, Joshua Lee Cagle, Salma Ramadan, Kavita Prasad, Flora Yan, John Pearce, Angela L Mazul, Jean-Sebastien Anoma, Elizabeth G Hill, Bhisham S Chera, Sidharth V Puram, Ryan Jackson, Vlad C Sandulache, Samantha Tam, Michael C Topf, Russel Kahmke, Nosayaba Osazuwa-Peters, Brian Nussenbaum, Anthony J Alberg, Katherine R Sterba, Chanita Hughes Halbert

Faculty, Staff and Students Publications

Importance: For patients with head and neck squamous cell carcinoma (HNSCC), initiation of postoperative radiation therapy (PORT) within 6 weeks of surgery is recommended by the National Comprehensive Cancer Network Guidelines and the Commission on Cancer. Although individual-level measures of socioeconomic status are associated with receipt of timely, guideline-adherent PORT, the role of neighborhood-level disadvantage has not been examined.

Objective: To characterize the association of neighborhood-level disadvantage with delays in receiving PORT.

Design, setting, and participants: This retrospective cohort study included 681 adult patients with HNSCC undergoing curative-intent surgery and PORT from 2018 to 2020 at 4 US academic medical …

Continuous Renal Replacement Therapy: Current State And Future Directions For Worldwide Practice, Katja M Gist, Dana Y Fuhrman, Akash Deep, Taiki Haga, Demet Demirkol, Michael J Bell, Ayse Akcan-Arikan

Faculty, Staff and Students Publications

No abstract provided.

Humanism Rounds: A Multifaceted "Back To Bedside" Initiative To Improve Meaning At Work For Internal Medicine Residents, Jennifer M Kaplan, Suchi Agrawal, Disha Kumar, Ann Xu, Kristen A Staggers, Anna G Symmes, Reina U Styskel, Brett Styskel, Anoop Agrawal, Stacey R Rose

Faculty, Staff and Students Publications

INTRODUCTION: Burnout is an increasingly prevalent problem among resident physicians. To address this problem, the Accreditation Council on Graduate Medical Education (ACGME) created the Back to Bedside initiative, supporting resident-driven projects focused on increasing direct interactions with patients. In 2017, Baylor College of Medicine (BCM) Internal Medicine Residency received a Back to Bedside grant to develop and implement “Humanism Rounds,” a multifaceted program which sought to promote personal connections between residents and patients and foster reflection about patients’ non-clinical stories, with the hopes of reducing burnout and increasing residents’ sense of meaning at work.

MATERIALS AND METHODS: Between 2018 and …

Serum Extracellular Vesicle Protein Profiling For Prediction Of Corneal Transplant Rejection, Hyun Ju Lee, Eun-Hye Bae, Jong Min Choi, Hyemee Kim, Hyeon Ji Kim, Heather Barreda, Sung Yun Jung, Joo Youn Oh, Ryang Hwa Lee

Faculty, Staff and Students Publications

Background: Corneal transplantation is the most common transplant procedure worldwide. Despite immune and angiogenic privilege of the cornea, 50% to 70% of corneal transplants fail in high-risk recipients, primarily because of immune rejection. Therefore, it is crucial to identify predictive biomarkers of rejection to improve transplant survival.

Methods: In search for predictive biomarkers, we performed proteomics analysis of serum extracellular vesicles (EVs) in a fully major histocompatibility complex-mismatched (C57BL/6-to-BALB/c) murine corneal transplantation model, wherein 50% of transplants undergo rejection by day 28 following transplantation.

Results: Our time course study revealed a decrease in the number of serum EVs on day …

Grafting The Alfa Tag For Structural Studies Of Aquaporin Z, Lauren Stover, Hanieh Bahramimoghaddam, Lie Wang, Samantha Schrecke, Gaya P Yadav, Ming Zhou, Arthur Laganowsky

Faculty, Staff and Students Publications

Aquaporin Z (AqpZ), a bacterial water channel, forms a tetrameric complex and, like many other membrane proteins, activity is regulated by lipids. Various methods have been developed to facilitate structure determination of membrane proteins, such as the use of antibodies. Here, we graft onto AqpZ the ALFA tag (AqpZ-ALFA), an alpha helical epitope, to make use of the high-affinity anti-ALFA nanobody (nB). Native mass spectrometry reveals the AqpZ-ALFA fusion forms a stable, 1:1 complex with nB. Single-particle cryogenic electron microscopy studies reveal the octameric (AqpZ-ALFA)

Endotoxin, A Novel Biomarker For The Rapid Risk Assessment Of Faecal Contamination Of Coastal And Transitional Waters, Christian R. Good, Alistair White, Joao Brandao, Simon Jackson

School of Biomedical Sciences

Current methods for testing water for faecal contamination rely on the culture of faecal indicator bacteria (FIB; Escherichia coli and Enterococci) that take 24–48 h, which leads to delays in taking proactive measures and poses a risk to public health. More rapid methods are therefore required. Here, we have tested a rapid, portable assay (Bacterisk) that detects the bacterial biomarker endotoxin in 30 min to quantify the bacterial biomass present, to evaluate 159 coastal water samples and to compare the results with the traditional culture of FIB. There was a significant correlation between the Bacterisk data given in endotoxin risk …

Development Of Highly Efficient Hybridfunctionalized Membranes For Sustainable Water Harvesting, Ahmed Z. Abuibaid

Dissertations

Water scarcity has emerged as a critical global challenge. This problem catches the world's interest through events such as the severe drought in Europe during the summer of 2022. While desalination plants offer a solution, their high energy consumption necessitates the exploration of alternative, sustainable water resources. Addressing the urgent need for alternative water resources in the face of increasing water scarcity. A viable option was presented by fog harvesting, which is a method to collect water from atmospheric fog. This method was initially developed to meet the demands of a variety of sectors such as agricultural purposes, and household …

Design, Synthesis And Characterization Of Zinc And Gold-Based Metal Organic Frameworks And Complexes For The Detection And Treatment Of Cancer, May Reda Mohamed

Dissertations

The early detection of cancer plays a pivotal role in improving patient outcomes, emphasizing the urgent need for highly sensitive and selective biosensing platforms. Metal-Organic Frameworks (MOFs) have emerged as promising candidates in this domain due to their tunable properties, large surface area, and high porosity. Herein, the utilization of zinc-based MOF as a sophisticated biosensing platform tailored for the precise detection of the HER2 cancer biomarker is presented. HER2, a critical protein marker in breast cancer diagnostics and treatment, demands highly selective and accurate detection methods for effective patient management. Simple hydrothermal synthesis methodology has been adopted to synthetize …

Development Of A Food Composition Database For The Estimation Of Dietary S-Methyl Cysteine Sulfoxide From Vegetables, Caroline R. Hill, Emma L. Connolly, Armaghan Shafaei, Lois Balmer, Liezhou Zhong, Taulant Muka, Antonietta Hayhoe, Shikha Saha, Richard J. Woodman, Joshua R. Lewis, Jonathan M. Hodgson, Lauren C. Blekkenhorst

Research outputs 2022 to 2026

A food composition database estimating S-methyl cysteine sulfoxide (SMCSO) was created following a systematic literature search. SMCSO data (705 entries) from 19 vegetables were summarised: brassicas (n = 10) and alliums (n = 9). The highest SMCSO in brassicas was reported in Brussels sprouts (median [range]: 318 [68−420] mg/100 g fresh weight (FW)) whilst the lowest was in radish (19 [4–45] mg/100 g FW). Brussels sprouts were almost twice as concentrated in SMCSO as cauliflower, followed by cabbage, kale, broccoli, kohlrabi, swede, Chinese cabbage, and turnips. The alliums highest in SMCSO were Chinese chives (271 [185−413] mg/100 g FW) followed …

Factors Associated With Poor Adherence To Medication In Patients With Diabetes And Hypertension In Peru: Findings From A Pooled Analysis Of Six Years Of Population-Based Surveys, Pablo M. Calderon-Ramirez, Edson Huamani-Merma, Mayu G. Mirano-Ortiz-De-Orue, Daniel Fernandez-Guzman, Carlos J. Toro-Huamanchumo

Research outputs 2022 to 2026

Objective: To evaluate the factors associated with poor medication adherence in patients with DM and HTN in Peru. Study design: A cross-sectional study. Methods: We analyzed data from the Peruvian Demographic and Family Health Survey from 2014 to 2019. Adjusted prevalence ratios (aPR) and their respective 95% confidence intervals (CI) were estimated to determine the factors associated with poor medication adherence. Results: We included 15,184 participants with a known diagnosis of DM and HTN. The frequency of poor medication adherence was 37.1%, with 36.7% among individuals with HTN and 29.2% among individuals with DM. Those belonging to age groups above …

Sorghum Grain Polyphenolic Extracts Demonstrate Neuroprotective Effects Related To Alzheimer’S Disease In Cellular Assays Sorghum Grain Polyphenolic Extracts Demonstrate Neuroprotective Effects Related To Alzheimer’S Disease In Cellular Assays, Nasim Rezaee, Eugene Hone, Hamid R. Sohrabi, Stuart Johnson, Leizhou Zhong, Prakhar Chatur, Stuart Gunzburg, Ralph N. Martins, W. M.A.D.Binosha Fernando

Research outputs 2022 to 2026

Sorghum grain contains high levels and a diverse profile of polyphenols (PPs), which are antioxidants known to reduce oxidative stress when consumed in the diet. Oxidative stress leading to amyloid-β (Aβ) aggregation, neurotoxicity, and mitochondrial dysfunction is implicated in the pathogenesis of Alzheimer’s disease (AD). Thus, PPs have gained attention as possible therapeutic agents for combating AD. This study aimed to (a) quantify the phenolic compounds (PP) and antioxidant capacities in extracts from six different varieties of sorghum grain and (b) investigate whether these PP extracts exhibit any protective effects on human neuroblastoma (BE(2)-M17) cells against Aβ- and tau-induced toxicity, …

Workshop Report - Interdisciplinary Metabolomic Epidemiology: The Pathway To Clinical Translation, Krista A. Zanetti, Lining Guo, Deeba Husain, Rachel S. Kelly, Jessica Lasky-Su, David Broadhurst, Craig E. Wheelock

Research outputs 2022 to 2026

Metabolomic epidemiology studies are complex and require a broad array of domain expertise. Although many metabolite-phenotype associations have been identified; to date, few findings have been translated to the clinic. Bridging this gap requires understanding of both the underlying biology of these associations and their potential clinical implications, necessitating an interdisciplinary team approach. To address this need in metabolomic epidemiology, a workshop was held at Metabolomics 2023 in Niagara Falls, Ontario, Canada that highlighted the domain expertise needed to effectively conduct these studies -- biochemistry, clinical science, epidemiology, and assay development for biomarker validation -- and emphasized the role of …