Life Sciences Commons^™

Identifying Relevant Covariates In Rna-Seq Analysis By Pseudo-Variable Augmentation, Yet Nguyen, Dan Nettleton

Mathematics & Statistics Faculty Publications

RNA-sequencing (RNA-seq) technology allows for the identification of differentially expressed genes, which are genes whose mean transcript abundance levels vary across conditions. In practice, RNA-seq datasets often include covariates that are of primary interest in addition to a set of covariates that are subject to selection. Some of these covariates may be relevant to gene expression levels, while others may be irrelevant. Ignoring relevant covariates or attempting to adjust for the effect of irrelevant covariates can compromise the identification of differentially expressed genes. To address this issue, we propose a variable selection method that uses pseudo-variables to control the expected …

Investigation Of Genx Exposure To Pathways Associated With Colorectal Cancer Risk, Emily J. Ferguson

Theses and Dissertations--Toxicology and Cancer Biology

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants widely detected in drinking water and food sources, resulting in chronic human exposure. Among these compounds, hexafluoropropylene oxide dimer acid (HFPO-DA), commonly known as GenX, has been introduced as a short-chain replacement for legacy PFAS such as perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA). Although GenX is believed to be a safer alternative, emerging research suggests it can still affect human health.

Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the second leading cause of cancer-related death in the United States, highlighting the need to better understand environmental …

Uncovering The Mechanism Of Reep2-Mediated Emt-Driven Membrane Trafficking In Lung Adenocarcinoma, Kevin Fulp

Theses and Dissertations--Toxicology and Cancer Biology

Membrane trafficking is frequently disrupted during cancer progression, and the underlying mechanisms remain largely unknown. Currently, no effective drugs target dysregulated membrane trafficking for cancer treatment. Recent evidence has demonstrated that epithelial-to-mesenchymal transition (EMT) in lung adenocarcinoma (LUAD) employs a membrane trafficking program to coordinate cancer cell invasion and immunosuppression. To further dissect the pro-tumorigenic membrane trafficking program, we initiated an in vivo CRISPRi screen to assess more than 2,000 membrane trafficking-related genes in a syngeneic mouse LUAD model. We identified REEP2, an endoplasmic reticulum (ER) shaping protein, as a novel regulator of EMT-driven membrane trafficking. High REEP2 expression is …

Reep2-Driven Pro-Metastatic Secretion Promotes Lung Cancer Progression, Oluwafunminiyi E. Obaleye

Theses and Dissertations--Toxicology and Cancer Biology

Membrane trafficking plays a critical role in cellular function and is frequently dysregulated in cancer to promote metastasis. In lung adenocarcinoma (LUAD), the epithelial-to-mesenchymal transition (EMT) activating transcription factor, ZEB1, drives a pro-metastatic membrane trafficking program; however, the underlying molecular mechanisms remain poorly understood. Using a CRISPR interference (CRISPRi) in vivo screen of 2,099 membrane trafficking regulators in a syngeneic mouse model of EMT-driven LUAD, we identified REEP2 — an endoplasmic reticulum (ER) shaping protein — as a critical regulator of tumor progression. REEP2 mRNA expression correlates with poor prognosis, EMT signatures, and an immunosuppressive tumor microenvironment in LUAD patients. …

31p Solution Nmr Investigation Of Abasic Dna, Clarissa R. Krimmel

Graduate Theses/Dissertations

Base excision repair (BER) mechanisms fix single base lesions in DNA, such as T:G mismatches. During the base excision repair mechanism, an abasic site (AP site) is formed as an intermediate. AP sites are unstable and highly mutagenic; they can stop DNA replication. This research investigates how the conformational properties of abasic sites in DNA affect the binding recognition of enzymes involved in DNA repair mechanisms, including BER. Three different abasic sequences are being analyzed for this research project. A second project looks at the effects of a naturally occurring purine derivative, hypoxanthine, on the DNA backbone. These hypoxanthine lesions …

Remediation Impacts Metal Concentrations And Metal Tolerant Bacteria In Soils Of The Missouri Tri-State Mining District, Ophelia R. Pettington

Graduate Theses/Dissertations

After over 100 years of Zn and Pb mining in the Tri-State mining district (TSMD), former mines continue to be sources of metals. Metal contaminated soils can be remediated using plant-microbe interactions. Plants manipulate their microbiome and recruit microbes to increase metal tolerance. Remediating bacteria are site-specific and identifying native microbes can accelerate remediation efforts. Studies relating microbes and metal concentrations in remediated areas in the TSMD are scarce. I collected root and bulk zone soils associated with Andropogon virginicus from remediated and non-remediated sites in Webb City, MO. I used 16S rRNA gene amplicon sequencing to evaluate the bacterial …

Transcriptomic And Epigenetic Analysis Of Dormant Grape Buds During Chilling Fulfillment, Imasha Thilakarathna

Electronic Theses and Dissertations

No abstract provided.

Investigation Of Perennial Clover Living Mulch And Reduced Tillage Effects On Weed Suppression, Crop Metrics, And Yield Of Organic Cabbage And Sweet Corn In The Northern Great Plains, Kristina Harms

Electronic Theses and Dissertations

Vegetable farmers often face weed management and soil health challenges, such as nitrate leaching, soil compaction, and top-soil loss. Sustainable agriculture is a forefront of innovation compared to conventional agriculture. Living mulches, non-cash crops grown alongside cash crops, have demonstrated weed suppression and impact on the promotion of sustainable agriculture. Yet studies have not evaluated established living mulch systems on cash crop quality and yield. This study conducted in 2023, 2024, and 2025 at SDSU Southeast Research Farm, Beresford, SD, USA evaluates the impact of established ‘Dynamite’ red clover (Trifolium pratense), ‘Domino’ white clover (T. repens), and ‘Aberlasting’ white × …

Assessing The Impact Of Local–State Revenue Shares And Property Tax Structure On Effective Farmland Tax Rates: Panel Evidence From Seven Midwestern States, 2009–2022, Imtiaz Amin Chy

Electronic Theses and Dissertations

Property taxes are the primary revenue instrument of local governments in the United States, yet the burdens they impose are distributed unevenly. Farmland, because it cannot be relocated, often absorbs a disproportionate share. This paper examines two related questions: what fiscal factors determine how heavily agricultural land is taxed, and do those tax rates capitalize into farmland asset values? Using an annual panel of Iowa, Illinois, Indiana, Kansas, Minnesota, Nebraska, and Wisconsin from 2009 to 2022, we first document how each state allocates property tax revenue across four major spending categories (education, public welfare, health, and utilities) finding that all …

Accelerating The Discovery Of The Genetic And Molecular Bases Of Neurodevelopmental Disorders In Vivo Using Breasi-Crispr, Claire Mae Kittock

Dissertations and Theses

Many neurodevelopmental disorders occur due to perturbations in prenatal brain development. More genetic variants associated with neurodevelopmental disorders are continuously being identified. However, there is a lack of understanding of the pathogenic mechanisms. Here, we describe a novel application of the technique Breasi-CRISPR in modeling specific patient variants in the embryonic mouse brain. Breasi-CRISPR is a highly efficient system combining in utero electroporation with CRISPR-CAS9 genome editing. We hypothesized that Breasi-CRISPR would be sufficient at inserting patient analogous variants into endogenous loci to be used as a new paradigm for modeling neurodevelopmental disorders. We aimed to test if Breasi-CRISPR could …

The Effect Of Different Nutrient Concentrations For Hydroponically Grown Pothos, Keaton Roether

A with Honors Projects

An experiment where Pothos plants are grown in three different solutions of water, NPK diluted into water, tap water, and distilled water. Data is recorded for multiple weeks and is then compiled into a comprehensible lab report of a minimum of 1000 words with graphs and data.

Ion-Imprinted Polymer-Based Sensors For Toxic Metal-Ion Detection In Water: Coordination Chemistry, Transduction Strategies, And Environmental Applications, Ghita Yammouri, Gymama Slaughter

Center for Bioelectronics Publications

Toxic metal contamination in aquatic environments remains a persistent threat to human health and ecosystems. Yet, the high cost, infrastructure demands, and centralized nature of conventional analytical methods constrain routine monitoring. Ion-imprinted polymers (IIPs), a subclass of molecularly imprinted polymers, have emerged as promising synthetic recognition materials for metal-ion sensing because they generate coordination-defined binding sites with high selectivity, chemical stability, low cost, and reusability. This review summarizes recent advances in Ion-imprinted polymer (IIP)-based sensing technologies for toxic metal-ion detection in water from 2016 to 2026. It examines the fundamental recognition chemistry of IIPs, major synthesis strategies used to generate …

Orexin Receptor Modulation In Amygdalar Stress Circuitry Differentiates Resilient And Vulnerable Phenotypes, Megan Marie John

Dissertations and Theses

Social stress is important for evaluating threats and resource opportunities, however, chronic exposure initiates the onset of psychological disorders, such as anxiety, depression, and post-traumatic stress disorder (PTSD). Stress responsiveness varies between individuals and sexes, resulting in disproportionate diagnoses and ineffective treatment outcomes. Enhancing therapeutic efficacy requires understanding of stress responsivity, phenotype development, and neurocircuitry modifications. Key contributors to stress responsiveness, such as threat of aggression and motivational initiation, influence the development of resilient or vulnerable phenotypes through behavioral and molecular adaptations to stress-related neurocircuitry. The basolateral amygdala (BLA) is a brain region associated with fear learning and integrates stress …

Crispr-Cas9: Transforming Biomedical Technology Through Gene Editing, Zaina Issa

A with Honors Projects

The research paper describe the gene editing technique CRISPR-Cas9 and the implications of its use in different fields, including medicine and agriculture.

Rail Sign By Doppler Ultrasound As A Predictor Of Outcome Of Placenta Accreta Spectrum, Ola Khaled Mosaad El Malahy, Mohammed Nezar El Shahat, Lotfy Sherif Sherif, Khaled Samir, Amany A Makroum, Alhussein Ahmed Mohamed

Mansoura Medical Journal

Background: Placenta accreta spectrum (PAS) involves abnormal placental invasion into uterine wall and is associated with life-threatening maternal complications. Doppler ultrasound is the primary diagnostic tool, though its ability to determine invasion depth and predict outcomes remains uncertain. Multidisciplinary management improves safety, and treatment often requires planned cesarean hysterectomy, or conservative management. The aim of this work was to correlate rail signs by Doppler US as a predictor of deep villous invasion and to detect whether rail signs can predict maternal and fetal outcomes.

Methods: This prospective observational study was conducted on 59 patients aged > 20 years old, with PAS …

Serum Vascular Endothelial Growth Factor Level And Its Correlation With Nail Fold Capillaroscopic Patterns In Patients With Systemic Sclerosis, Samah M. Barakat, Yousra Sadeq, Marwa Besar, Shereen S. Metwally

Mansoura Medical Journal

Objective: to assess the correlation between blood levels of vascular endothelial growth factor (VEGF) and microvascular changes identified by nail fold videocapillaroscopy (NVC) in individuals with systemic sclerosis. Methods: A videocapillaroscope was used to evaluate the microvascular alterations in nail folds in SSc patients. The ELIZA technique was used to measure serum vascular endothelial growth factor (VEGF). Results: Nailfold videocapillaroscopy reveals significant microvascular alterations in patients with systemic sclerosis when compared to controls. Patients' capillary breadth, length, and diameter have increased but their capillary numbers have dramatically decreased. 75% of patients have hemorrhages, although controls do not. Patients with systemic …

Epidemiology Of Closed Ruptured Tendoachilles, Hesham Mousad Alsakaan, Wael Mansour Wafa, Mohieb Sayed Ahmed, Ahmed El Sayed Magdy Elhawary

Mansoura Medical Journal

Background: To restore tendon function and avoid long-term impairment, early diagnosis and adequate treatment are crucial. The purpose of this study was to ascertain the incidence pattern of ATR and to pinpoint possible variables related to presentation and management approach.

Aim  identifying potential risk factors either patient or environmental related and to assess the incidence rate of ATR

Patients and Methods: This retrospective cross-sectional study was performed on 87 achilles tendon rupture patients. All the patients were subjected to full medical history taking. Clinical examination was performed including thompson test and Matles test and radiological investigations.

Results: The median age …

The Neuroprotective And Synergistic Effects Of Carbamoylated Erythropoietin And Insulin-Like Growth Factor-1 In Alzheimer's Disease, Morgan Jean Rothschadl

Dissertations and Theses

Alzheimer’s disease (AD) is a prominent neurodegenerative disease characterized by a decline in cognitive functioning. While current FDA-approved therapeutics exist, they fall short in creating significant and long-lasting improvements to cognition. A newer approach using neurotrophic factors has shown promising effects on improving cognition in clinical trials. Neurotrophic factors are secreted proteins that have multimodal effects in the brain, including supporting cell survival and functioning. Two neurotrophic factors of interest are carbamoylated erythropoietin (CEPO) and insulin-like growth factor-1 (IGF-1), and the goal of this study was to understand the synergistic and neuroprotective effects of CEPO and IGF-1 in AD. We …

Avian Use Of Early Successional Riparian Forest Along The Missouri River: What Do We Lose By Managing For Plovers And Terns?, Stephanie Nefas

Dissertations and Theses

Riparian ecosystems provide habitat for birds throughout their annual cycle, yet flow regulation along major rivers like the Missouri River has reduced early successional riparian forests. Following historic flooding in 2011, set-aside areas within the Missouri National Recreational River (MNRR) were established to allow natural riparian vegetation succession on newly created sandbars. I evaluated the value of these early successional forests for birds over three breeding seasons (2018–2020) and four migration periods (2020–2021). During migration, standardized point counts documented 7,462 individual birds representing 114 species across 828 surveys. Avian diversity was positively correlated with vertical habitat complexity, with the canopy …

Laparoscopic Versus Open Redo Anti-Reflux Surgery, Mohamed Barkok, Mohammed Said, Ahmed Shehta, Abdel-Raouf El-Geidie

Mansoura Medical Journal

Background

Gastroesophageal reflux disease (GERD) is common. Laparoscopic fundoplication became the gold standard for GERD surgery after medical treatment failed. If a previous anti-reflux surgery fails, redo surgery requires a thorough review to determine the cause and a skilled surgical team. Choosing the optimal approach during the redo surgeries, whether open or laparoscopic hasn’t been previously illustrated.

Aim

To compare the outcomes of laparoscopic versus open redo anti-reflux surgeries.

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Patients and methods

This study included 28 patients who underwent redo anti-reflux surgery. The patients were divided according to the approach into laparoscopic (n = 11) and open (n = …

Clinical Outcomes Of Bloodstop Ix Application In Crico-Tracheal Resection And Anastomosis For Laryngotracheal Stenosis, Mohamed Yasser Elnaggar, Hisham Atef Ebada, Hossam Elsisi, Ali Tawfik

Mansoura Medical Journal

Objectives: To assess the surgical outcomes among laryngotracheal stenosis patients who underwent tracheal/crico-tracheal resection anastomosis for with application of BloodSTOP iX on the anastomotic line as well as the operative field.

Methods: Fourteen patients participated in this prospective study. The stenotic airway segment was resected circumferentially using primary end-to-end anastomosis. The authors of this article used the same standardized surgical techniques described in the literature and used by them previously. All patients had suprahyoid release, and trachea-hyoid de-tensioning stitches were inserted to reduce the anastomotic tension. To promote healing, BloodSTOP iX was administered across the anastomosis line and surgical outcomes …

Prevalence And Spectrum Of Genitourinary Anomalies In Children With Anorectal Malformations, Adnan El-Ghazaly, Tamer A. Wafa, Ahmed M. Negm, Adham W. El-Saied

Mansoura Medical Journal

Background: Anorectal malformations (ARMs) encompass a broad range of congenital defects and are frequently associated with genitourinary (GU) anomalies, which may contribute to long-term morbidity if undetected. This study aimed to determine the prevalence and spectrum of GU anomalies in children with ARMs, describe the urological and genital findings, and assess associations with sex and ARM type.

Patients and Methods: A prospective survey enrolled children diagnosed with ARMs at a tertiary pediatric surgery center. All patients underwent standardized clinical assessment, including focused genital examination and structured imaging. Abdominal ultrasonography (US) served as baseline screening for urinary tract anomalies. Voiding cystourethrogram …

Clinico-Epidemiological Profile Of Iron Deficiency Anemia Among Egyptian Primary School Aged Children: A Hospital Based Study, Rabab Fathy Abdelhamid, Noha Essam, Mona Mohamed Taalab

Mansoura Medical Journal

Background: Iron deficiency anemia (IDA) is the most prevalent cause of anemia among Egyptian children and is associated with a range of hematologic and non-hematologic complications, some of which may be irreversible. This study aims to evaluate the clinical profile and identify factors associated with severe IDA in primary school–aged children.

Methods: This cross-sectional study included 420 primary school–aged children diagnosed with IDA who attended the outpatient clinic of Salamoun El-Qumash Family Medicine Centre. Data were collected through face-to-face interviews using a structured questionnaire. All participants underwent a thorough clinical examination and laboratory evaluation, including a complete blood count and …

Added Value Of T2 Space Stir In Magnetic Resonance Imaging Evaluation Of Post-Traumatic Brachial Plexus Injury, Nehal Tharwat, Ahmed Mohamed Abdelkhalek, Mohamed Ashraf Abd El-Moniem, Hesham Abdel Fattah Elsobky, Ahmed Alaa El-Din Elagamy

Mansoura Medical Journal

Background: Traumatic brachial plexus injuries (TBPIs) cause severe upper limb disability. Owing to the complex anatomic architecture of the brachial plexus (BP), TBPIs are difficult to diagnose. Magnetic resonance neurography of the BP using three-dimensional isotropic imaging provides excellent background fat suppression and adequate soft-tissue contrast, thereby allowing better delineation of the BP along its pathway. This study aimed to compare image quality between T2-Short tau inversion recovery (T2-STIR) and 3D-transverse relaxation time-sampling perfection with application of optimized contrasts using different flip-angle evolution short tau inversion recovery (3D-T2 SPACE STIR) sequences in cases of TBPIs.

Methods: This study included 44 …

Hypoalbuminemia As A Predictive Factor For Acute Kidney Injury In Pediatric Patients Running Title: Hypoalbuminemia In Aki Pediatrics, Kareem El-Saeed El-Maasrany, Ayman Hammad, Hosam Zaghloul, Ahmed Elhusseiny

Mansoura Medical Journal

Aim: Hypoalbuminemia is a well-known risk factor for illness and death, but its role as a particular predictor of acute kidney injury (AKI) is still not fully understood. This study intended to evaluate the role of hypoalbuminemia as a predictive factor for AKI outcome among pediatric patients, regarding hospital stay, kidney replacement therapy and mortality rate.

Subjects and Methods: This prospective observational cohort was conducted on 70 children with AKI divided into two groups: group I (35 AKI children combined with hypoalbuminemia) and group II (35 AKI children without hypoalbuminemia). All participants were subjected to full history taking, clinical examination …

Evaluation Of Β2-Microglobulin In Patients With Psoriasis Vulgaris Case Controlled Study, Ishraq Mazhar Shaaban, Fatma Faisal El Dakrory, Alshaimaa Hamdi Abd Elmaksoud, Youssef El-Bayoumi Youssef Soliman

Mansoura Medical Journal

Background: Psoriasis is a persistent, immune-mediated dermatological condition influenced by complex genetic architectures and systemic inflammation. This investigation evaluated the diagnostic utility of serum β2-microglobulin β2 as a quantitative indicator for gauging clinical severity in psoriatic patients.

Aim of the work: The primary objective of this investigation was to evaluate the diagnostic utility of serum β2-microglobulin (β2M) as a quantitative biomarker for assessing disease severity in patients with psoriasis vulgaris. Specifically, the study sought to determine the correlation between circulating β2M levels and established clinical parameters, including the Psoriasis Area and Severity Index (PASI), body mass index (BMI), and …

Diagnostic Accuracy Of Combined B-Mode Ultrasound, Color Doppler And Strain Elastography In Assessment Of Cervical And Axillary Lymph Nodes, Marwa Mostafa, Nihal M. Batouty, Amani Ezzat Mousa

Mansoura Medical Journal

Background: Lymphadenopathy is a common condition caused by many benign and malignant disorders; therefore, determining their nature is important in clinical setting. The objective of research is to assess diagnostic accuracy of B-mode ultrasound, color Doppler, and strain elastography in lymph nodes evaluation with pathological correlation and to determine cut-off value of strain ratio that differentiates benign from malignant nodes.

Methods: All patients underwent ultrasound examination, Doppler study and strain elastography in supine position using a high-frequency probe (6.2-12 MHz). Out of 80 enrolled patients, only 53 were subjected to biopsy from the lymph nodes, then their pathological results …

Diagnostic Performance Of Digital Breast Tomosynthesis In The Characterisation Of Breast Lesions: Correlation With Sono-Mammography And Histopathology., Amira Hamed Megahed, Mona Mahmoud Zaky, Maha Mohamed Bilal

Mansoura Medical Journal

Background: Breast lesions range from benign to malignant, with early detection critical for management. Digital mammography is the standard screening tool but may be limited in dense breasts. Ultrasound (US) aids lesion characterisation, while digital breast tomosynthesis (DBT) reduces tissue overlap, enhancing lesion detection.

Objective: To evaluate the diagnostic performance of digital breast tomosynthesis in the characterisation of breast lesions compared with sono-mammography, using histopathology as the reference standard.

Methods: This prospective study included 33 symptomatic female patients with a mean age (45.4 ± 8.2 years) who presented with symptoms such as palpable breast lumps, Mastalgia and nipple discharge between …

Roles Of Transcription Factors In Mediating Abiotic Stress Responses In Cereals, Shikha Bharti, Joshwa A. Gandy, Ishita Bajaj Hengge, Javier Ramos, Bradley O. Christoffersen, Michael W. Persans, Manohar Chakrabarti

School of Integrative Biological & Chemical Sciences Faculty Publications

Cereals are staple crops for the majority of the global population, making their sustained productivity essential for food security. However, abiotic stresses significantly threaten their growth and overall yield by disrupting essential physiological, cellular, and biochemical processes. Enhancing stress resilience in cereals is therefore a critical objective for agricultural improvement under changing climatic conditions. A fundamental step toward this goal involves understanding the roles of transcription factors (TFs), which are primary regulators of changes in gene expression in response to stresses. TFs regulate complex signaling networks that enable plants to adjust their biochemical and physiological functions under abiotic stress conditions. …

A Preliminary Investigation Of Research Collaboration Through Scientific Paper Co-Authorship In The Gulf Of Mexico, Juliet Vallejo, Evelyn Roozee, Dongkyu Kim, Andrew M. Song, Christopher A. Gabler, Jasper R. De Vries, Antonia Sohns, Gordon M. Hickey, Owen Temby

School of Earth, Environmental, & Marine Sciences Faculty Publications

It is well known that publications with collaborators from external institutions increase citations. This effect scales with spatial distance. There are also many barriers to long-distance collaborations, including linguistic differences, funding constraints, and the incremental costs of remote collaboration. This paper uses the Gulf of Mexico as a case study to examine long-distance research collaboration because it consists of three countries with diverse development levels and two prominent diplomatic languages, within a singular regional ecosystem of tremendous natural and economic value. This paper uses bibliometric network analysis to examine scientific research article co-authorship in the Gulf of Mexico from 2000 …