Digital Commons Network^™

Mmp-7 Expression And Rs11225307 Polymorphism In Breast Cancer And Fibroadenoma: A Molecular Study In Basrah, Iraq, Heba Jassam, Wijdan Nazar Ibraheim, Mazin Hawwaz Abdulridha, Rafid Adil Abood, Karam B. Nanjem

AUIQ Complementary Biological System

Breast cancer (BC) progression relies heavily on extracellular matrix degradation, mediated in part by matrix metalloproteinase-7 (MMP-7). While overexpression of MMP-7 has been implicated in multiple cancers, data from Middle Eastern populations remain limited.

This study examined MMP-7 gene expression and polymorphism patterns, with emphasis on rs11225307, in breast cancer versus benign fibroadenoma (FA) tissues among women in Basrah, Iraq. Thirty-seven BC and twenty-three FA patients were enrolled. MMP-7 mRNA expression was quantified using qRT-PCR and normalized to β-actin, while polymorphisms were analyzed through Sanger sequencing of eight SNPs and allele-specific PCR for rs11225307. Statistical significance was set at …

Population Structure Analysis Of Four Basal Higher-Attines Using Bioinformatic Approaches, Gabriel Mcdanield

Biology Theses

Metapopulations within the family Formicidae are unique among other animals due to the large colonies they build, and the mating strategies required to fertilize a specialized reproductive caste that will often produce young for the life of the colony. One group of ants, the fungus-gardeners (tribe Attini). The population structure of North American non-leafcutting, fungus-gardening ants has been understudied, especially in the southwest of the United States. Additionally, not much is known about their dispersal biology, so the dynamics of dispersal of these species and how they affect population structure is likewise not well known. To shed light on the …

Warmer Temperatures Increase Egg Laying And Egg Hatching Frequency In The Invasive Freshwater Snail Physa Gyrina From Pennsylvania, Usa, Peter Fong, Morgan Nieman

Biology Faculty Publications

Climate change continues to impact populations of organisms and to affect physiological adaptations to their environments. Freshwater snails have been so impacted globally, not only by climate change, but by the concomitant exposure to environmental pollutants like human antidepressants released from wastewater treatment plants. To test the effect of climate change and antidepressants, we exposed the freshwater snail, Physa gyrina to three temperatures (12 °C, 20 °C, and 25 °C) and to a concentration of the antidepressant fluoxetine, known to modulate snail behavior, and measured time to egg laying and egg hatching. Snails exposed to 20 °C and 25 °C …

Dog Snapper (Lutjanus Jocu) Neurocranium, Camila Avila Escobar, David W. Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

First-Line Met Tyrosine Kinase Inhibitors Versus Immunotherapy ± Chemotherapy For Patients With Met Exon 14 Skipping Mutant Metastatic Nsclc, Federica Pecci, Hui Li, Alessandro Di Federico, Jia Wu, Hong Chen, Eleonora Gariazzo, Francesco Mantuano, Edoardo Garbo, Mihaela Aldea, Valentina Santo, Don Gibbons, Hai Tran, Francesco Paoloni, Guilherme Rossato De Almeida, Giulio Metro, Andrea De Giglio, Francesco Gelsomino, Xinan Wang, Marcello Tiseo, Julia Rotow, Andrea Ardizzoni, J Jack Lee, Mark M Awad, Alfredo Addeo, Lingzhi Hong, Marcelo V Negrao, Pasi A Jänne, John V Heymach, Jianjun Zhang, Biagio Ricciuti, Xiuning Le

Faculty, Staff and Student Publications

Purpose: First-line treatment options for MET exon 14 skipping-mutant metastatic non-small cell lung cancer vary because of differences in drug approvals and clinical experience. This study investigates factors influencing outcomes with first-line MET tyrosine kinase inhibitors (TKI) versus immune checkpoint inhibitors (ICI) ± chemotherapy.

Experimental design: Clinicopathologic data were collected from patients with metastatic MET exon 14 skipping-mutant non-small cell lung cancer treated with first-line MET TKI or ICI ± chemotherapy at five centers. Primary endpoints were real-world progression-free survival (rwPFS) and overall survival (OS) to first-line MET TKI versus ICI ± chemotherapy. Subgroup analyses by clinical and tumor characteristics …

Effect Of Freezing And Freeze-Thaw Cycles On Equine Serum Insulin Concentration: A Pilot Study, Molly Wallace, Shea Porr, Lydia O'Sullivan

Honors College Theses

Insulin dysregulation is a key component of Equine Metabolic Syndrome (EMS), and is often a predisposing factor to conditions such as laminitis and hepatic lipidosis. Diagnosis of EMS is most often reached through a combination of glucose and insulin measurements in equine serum. Achieving an accurate result of insulin concentration is vital for diagnosis, making proper sample handling essential. The aim of this project was to evaluate the effect of repetitive freeze-thaw cycles on equine serum insulin concentrations. Serum was collected from 10 university-owned horses and split into four treatment groups: Unfrozen, Once Frozen, Twice Frozen, and Thrice Frozen. Unfrozen …

Vitamin D Is Glucoprotective In Aging Males But Not Females, Olivia Z B Ginnard, Maria Morales, Ji Youn Youn, Yong Xu, Stephanie R Sisley

Faculty, Staff and Students Publications

Vitamin D supplementation is linked to many beneficial health outcomes in the geriatric population, such as decreased mortality, epigenetic aging, and fracture risk. Conversely, type 2 diabetes is strongly linked to vitamin D deficiency in older adults. However, there is a discrepancy between clinical trials in adults on the efficacy of vitamin D treatment in prediabetes and diabetes. In addition, human data indicates there may be sexual dimorphism in the effect of vitamin D deficiency on dysglycemia that is more pronounced in men. These incongruities may be due to our limited understanding of the underlying mechanisms of vitamin D in …

Chronosort: Revealing Hidden Dynamics In Alphafold3 Structure Predictions, Matthew J. Argyle, William P. Heaps, Corbyn Kubalek, Spencer Gardiner, Bradley C. Bundy, Dennis Della Corte

Faculty Publications

Protein function emerges from dynamic conformational changes, yet structure prediction methods provide only static snapshots. While AlphaFold3 (AF3) predicts protein structures, the potential for extracting dynamic information from its ensemble predictions has remained underexplored. Here, we demonstrate that AF3 structural ensembles contain substantial dynamic information that correlates remarkably well with molecular dynamics simulations (MD). We developed ChronoSort, a novel algorithm that organizes static structure predictions into temporally coherent trajectories by minimizing structural differences between neighboring frames. Through systematic analysis of four diverse protein targets, we show that root-mean-square fluctuations derived from AF3 ensembles can correlate strongly with those from MD …

Black Grouper (Mycteroperca Bonaci) Neurocranium, Layla Lacelle, David W. Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Comparing Machine Learning, Deep Learning, And Reinforcement Learning Performance In Culex Pipiens Predictive Modeling, Wei Yin, Sanad H. Ragab, Michael G. Tyshenko, Teresa Patricia Feria-Arroyo, Tamer Oraby

School of Mathematical & Statistical Sciences Faculty Publications

Several machine learning (ML) and deep learning (DL) methods have been used to predict the presence of species in classification problems. Another set of methods, called reinforcement learning (RL), has been used in training agents to perform various tasks, but not in predicting species distribution. Culex pipiens (Diptera: Culicidae), commonly known as the common house mosquito, is a globally distributed species prevalent in temperate and subtropical regions. They serve as a primary vector for West Nile Virus (WNV), a mosquito-borne pathogen that affects humans and other animals. The study objective is to compare the performance of logistic regression, random forest …

The Unfolded Protein Response-Novel Mechanisms, Challenges, And Key Considerations For Therapeutic Intervention, P M Quan Mai, Tam-Anh Truong, Sai Kumar Samala, Bhoomika Muruvekere Lakshmisha, Prapannajeet Biswal, Khadijeh Koushki, Prudhvi Chand Mallepaddi, Geraldine Vijay, Sunil Krishnan

Faculty, Staff and Student Publications

Background: The unfolded protein response (UPR) is an evolutionarily conserved, synchronized, and orchestrated process triggered by eukaryotic cells in response to endoplasmic reticulum (ER) stress. UPR restores the ER's capacity to handle large protein loads within it, and still fold and process these proteins accurately. Many recent studies have documented the non-canonical roles of the UPR, outside of protein quality control, in the context of lipid metabolism and the immune system in cancer. Cancer cells have been known to hijack the UPR to promote survival and evade immune surveillance. However, the underlying mechanisms remain poorly understood.

Objectives: Here, we critically …

Primary Intramedullary Spinal Melanocytomas: Case Report And Review Of Clinical Features, Diagnosis, And Management, Gil Kimchi, Samantha Varela, Juan Pablo Zuluaga-Garcia, Francisco Call-Orellana, Esteban Ramirez Ferrer, Romulo Augusto Andrade De Almeida, Maria A Gubbiotti, Isabella C Glitza, Andrew J Bishop, Jonathan D Grant, Robert Y North, Christopher A Alvarez-Breckenridge, Laurence D Rhines, Claudio E Tatsui

Faculty, Staff and Student Publications

Objective: Intramedullary melanocytomas are extremely rare spinal cord tumors with distinct histopathological and imaging characteristics. This report reviews the literature on this pathology and presents a representative case study, highlighting aspects of diagnosis and management.

Methods: A scoping review of PubMed, Web of Science, and Embase databases was conducted to identify reports on intramedullary melanocytomas, focusing on clinical presentation, imaging features, histopathology, treatment, and outcomes. Case reports and case series were included due to the rarity of these tumors.

Results: Twelve manuscripts met the inclusion criteria, including 15 patients. In the majority of patients, intramedullary melanocytomas present with progressive myelopathy …

Culture-Independent Meta-Pangenomics Enabled By Long-Read Metagenomics Reveals Associations With Pediatric Undernutrition, Jeremiah J Minich, Nicholas Allsing, M Omar Din, Michael J Tisza, Kenneth Maleta, Daniel Mcdonald, Nolan Hartwick, Allen Mamerto, Caitriona Brennan, Lauren Hansen, Justin Shaffer, Emily R Murray, Tiffany Duong, Rob Knight, Kevin Stephenson, Mark J Manary, Todd P Michael

Faculty, Staff and Students Publications

The human gut microbiome is linked to child malnutrition, yet traditional microbiome approaches lack resolution. We hypothesized that complete metagenome-assembled genomes (cMAGs), recovered through long-read (LR) DNA sequencing, would enable pangenome and microbial genome-wide association study (GWAS) analyses to identify microbial genetic associations with child linear growth. LR methods produced 44-64× more cMAGs per gigabase pair (Gbp) than short-read methods, with PacBio (PB) yielding the most accurate and cost-effective assemblies. In a Malawian longitudinal pediatric cohort, we generated 986 cMAGs (839 circular) from 47 samples and applied this database to an expanded set of 210 samples. Machine learning identified species …

Effect Of Chronic Heat Stress On Duodenal Epithelial Barrier Integrity In Low- And High-Water-Efficient Broiler Chickens, Lulu Liu, Elizabeth S. Greene, Brooklee Roach, Sara Orlowski, Sami Dridi

Poultry Science Faculty Publications and Presentations

Heat stress (HS) has long posed a significant challenge to the poultry industry due to its adverse effects, such as depressed feed intake, decreased growth performance, and increased water consumption. Water efficiency (WE, conversion of water intake into body weight gain), although often neglected, is a key economic and production trait that is significantly affected by HS. Recently, we selected two broiler lines for high WE (HWE) and low WE (LWE) and showed a differential hypothalamic expression of genes involved in water homeostasis regulation. As the gut also plays a significant role in water absorption, the present study aimed to …

Single Vs. Whole Muscle Group Assessments: Does The Specific Muscle Influence Its Association With Performance?, Carina M. Velasquez, Kealey J. Wohlgemuth, Mckenzie M. Hare, Kathryn E. Southall, Jacob A. Mota

Topics in Exercise Science and Kinesiology

Topics in Exercise Science and Kinesiology Volume 6: Issue 1, Article 11, 2025. Biometric Muscle size and echo intensity are thought to influence muscle function. Unfortunately, previous works often will examine a single muscle from a group of agonists as a metric of whole muscle performance. This approach may not always be the most appropriate to assess performance outcomes. The purpose of the study was to 1) quantify the association of muscle size and echo intensity with vertical jump performance (VJ), 2) Compare the associations between individual and whole muscle group size and echo intensity, 3) determine whether single or …

Berberine–Piperine Co-Treatment As A Potential Therapeutic Strategy For Triple Negative Breast Cancer: An In Vitro Study, Aysha Suliman Alshamsi

Thesis/ Dissertation Defenses

Massive applications were implemented to limit the risks of breast cancer, especially for the aggressive and treatment-resistant subtype triple-negative breast cancer that pose substantial obstacles for conventional approaches; therefore, natural substances have come to light as potential alternatives for anticancer therapy, especially in aggressive subtypes such as triple-negative breast cancer (TNBC). In this respect, berberine (barberry) and piperine (black pepper) are natural substances found in plants that have received extensive attention for their role as phytotherapeutic agents. Berberine has shown anti-inflammatory, antioxidant, and anticancer activities. Piperine is known to improve the bioavailability of other medications and has its own anticancer …

Bluefish (Pomatomus Saltatrix) Neurocranium, Courtney R. Schober, Alyssa Olmeda, David W. Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Adsorptive Removal Of Arsenite And Cobalt By Commercial Sorbents, Sevda Joudiazar, Sushma Yadav, Zhiming Zhang, Anshuman Satpathy, Eustace Fernando, Roxana Rahmati, Junchul Kim, Rupali Datta, Dibyendu Sarkar

Michigan Tech Publications

Despite the prevalence and toxicity of heavy metals in the environment, arsenic and cobalt are of particular concern due to their high mobility and bioaccumulation potential, particularly in contaminated groundwater. Herein, we studied the adsorption behavior of commercially available sorbents, including Fluorosorb-100 (FS-100), Fluorosorb-200 (FS-200), and Filtrasorb-400 (F-400), for the removal of arsenite (As(III)) and cobalt (Co(II)), aiming at the selection of filter media in terms of future groundwater remediation. Kinetic analysis revealed that As(III) adsorption followed a pseudo-second-order model, while Co(II) showed mixed first- and second-order behavior, reflecting sorbent-dependent mechanisms. Equilibrium isotherm modeling revealed strong correlations with both Langmuir …

In Vitro Antiviral Activity Of Cat’S Claw (Uncaria Tomentosa) Bark Extract Against Human Influenza A Virus, Juliann N. Makau, Keith K. Talaam, Mike Odiwuor, Janet M. Majanja, Sophia Musenjeri, Ratika Rahmasari, Samoel A. Khamadi, Ken Watanabe

Pharmaceutical Sciences and Research

Influenza A viruses mutate very fast and this leads to the development of resistance to antivirals, hence the need to find new therapeutics. Due to their extensive traditional use, natural products are crucial resources for the discovery of drugs. Cat’s claw (Uncaria tomentosa), is a tropical vine known for various health benefits and in this study we evaluated its anti-influenza activity. Pulverized material of the stem bark was extracted using 80% ethanol, hot water, and 1% sodium bicarbonate. The extracts were dried and dissolved in dimethylsulfoxide before testing for cytotoxicity and antiviral activity using crystal violet assay. The …

Nepenthes Megastoma (Nepenthaceae), A Micro-Endemic Pitcher Plant From Puerto Princesa Subterranean River National Park, Palawan, Philippines, John Charles A. Altomonte, John Paul R. Collantes, Vernaluz Mangussad, Rene Alfred Anton Bustamante, Alastair S. Robinson

Environmental Science Faculty Publications

Nepenthes megastoma is described and illustrated as a new species from the Puerto Princesa Subterranean River National Park, a UNESCO World Heritage Site in Palawan Philippines. This carnivorous tropical pitcher plant is currently known from just three locations in the Mount Saint Paul karst formation, where it grows on vertical limestone walls. Morphologically, N. megastoma is characterised by its highly branched stems, campanulate pitchers, peltate tendril exsertion, dimorphic upper pitchers, and unidirectionally upturned female flowers. It is assessed as Critically Endangered under the IUCN Red List criteria, based on its restriction to three subpopulations comprising few total individuals. Pitcher morphology …

Antibiofilm Potential Of Zanthoxylum Zanthoxyloides Bark-Extract Against Biofilm-Producing Streptococcus Mutans In Dental Caries, Efunwole Omonike Omolade, Olaitan J. Olubukola, Wahab Abideen A, Oyedara Opemipo Omotayo, Oluwajide O. Odunola

Tanzania Journal of Science

Streptococcus mutans is the major cause of dental caries, which is costly to treat. The burden is worse in low- and middle-income countries, due to poor access to oral health services and diets high in free sugars. Conventional antibiofilm agents in oral health often have side effects, prompting the search for safer and affordable alternatives. This study investigates the antibiofilm activity of Zanthoxylum zanthoxyloides bark extract against biofilm-forming S. mutans. Dental plaque and tooth samples were collected from hospitals after ethical approval. S. mutans was identified using standard microbiological methods on Mitis Salivarius agar supplemented with Bacitracin and potassium tellurite. …

Morphometric And Meristic Analysis Of Labeo Coubie In Esa-Odo Water Reservoir, Esa-Odo, Osun State Nigeria, Olugbemi V. Ekundare, Funmilayo B. Oyekanmi, Mahmud Sanni, Azeez Aransi, Dorcas O. Owolabi

Tanzania Journal of Science

One of the common species of family Cyprinidae found in Nigeria and West Africa is Labeo coubie. They are of commercial importance in West Africa. This study embarked on the assessment of the length- weight relationship, condition factor, morphometrics and meristic characteristics of L. coubie from Esa-Odo water reservoir, Esa-Odo, Osun State Nigeria. A total of 135 (65 males and 70 females) individual L. coubie collected from fishermen were subjected to morphometric and meristic analysis. Results showed 4.90, 5.46 and 5.24 as the b value for male, female and combined sexes respectively, describing positive allometric growth for all the fish …

Shade As An Agro-Technique To Improve Gas Exchange, Productivity, Bioactive Potential, And Antioxidant Activity Of Fruits Of Hylocereus Costaricensis, Milena Maria Tomaz De Oliveira, Noemi Tel-Zur, Francisca Gislene Albano-Machado, Daniela Melo Penha, Monique Mourão Pinho, Marlos Bezerra, Maria Raquel Alcântara De Miranda, Carlos Farley Herbster Moura, Ricardo Elesbão Alves, William Natale, Márcio Cleber De Medeiros Corrêa

Plants, Soils, and Climate Faculty Publications

Hylocereus species are promising for enhancing fruit productivity in arid regions, but high solar radiation often leads to yield loss. This study aimed to evaluate the short-term impact of different shading levels on the physiological performance, productivity, and post-harvest quality of Hylocereus costaricensis under semi-arid conditions. Plants were grown in the field under two shade levels, i.e., 35 and 50% and their performances were compared to plants under control, i.e., 0% of shade or full sunlight. The nighttime CO₂ assimilation and productivity increased significantly by 310.5 and 114.6% and 34.3 and 50.14% for plants under 35 and 50% of …

Life As An Intern For Njit Stem For Success, Christopher Tava

STEM Month

I joined the STEM for Success Team in May 2023 with two main goals. The first goal was to reach 100 hours worth of contributions, as part of a mandatory internship requirement to graduate from the Academy for Mathematics, Science, & Engineering (AMSE). I reached that goal by early October 2023, although I have been motivated to continue my work with NJIT beyond that hour target. The second goal was to accomplish something that I was proud of with the resources that the New Jersey Institute of Technology (NJIT) provided me. I had heard of former students of AMSE that …

Genomic And Metabolic Network Characterization Of Fusarium Species, Hend Hussain Mueenuddin

Thesis/ Dissertation Defenses

Fusarium covers the wide genus of fungi with over 400 species that are key in agricultural and medical practice. The purpose of the current study was to perform a comprehensive genomic profiling of the 19 Fusarium species that were captured in the National Centre of Biotechnology Information (NCBI) database. The study was made to make a comparison of the data, based on the descriptive statistics of every species, with graphical representation images enabling clear demonstration of the numbers. The study indicated that the chromosomal numbers were in the range of 0-15, the gene count was roughly 11000 -19000, while that …

Cv: Philip Blankenship (Behavioral Neuroscience), Philip Blankenship

Psychology Department Faculty Curricula Vitae

No abstract provided.

The Web Of Tpd Reform: A Reflective Tool For Analyzing And Improving Teaching Professional Development Programs For Teaching Assistants, Adam J. Chouinard, Diyala S. Shihadih, Star W. Lee, Stephanie J. Gutzler, Kaleb K. Heinrich, Mitra Asgari, Erin Shortlidge

Biology Faculty Publications and Presentations

Teaching assistants (TAs) play a pivotal role in the teaching mission of higher education, but too often they are asked to do this important job without adequate teaching professional development (TPD). By receiving training in inclusive and evidence-based teaching practices, TAs can in turn help disseminate effective teaching methods for the benefit of students throughout the nation; as future faculty, TPD also better prepares TAs for their careers, helps solve longstanding problems of inclusion and retention in STEM, and reforms disciplinary educational norms through cultural evolution. Thanks to prior research and advocacy efforts, there is a growing awareness that STEM …

Reprogramming Tumor Microenvironment Via Systemic Delivery Of Tlr3 Agonist And Manganese Nanoparticle, Young Seok Cho, Xingwu Zhou, Xiaoqi Sun, Ziye Wan, Julia Crowther, Mariko Takahashi, Swetha Kodamasimham, Qi Wu, May Thazin Phoo, Youngseo Na, Kai Han, Zaiye Li, Anna Schwendeman, Steven P Schwendeman, Yu Leo Lei, James J Moon

Faculty, Staff and Student Publications

Toll-like receptor (TLR) agonists, as potent immunostimulatory adjuvants, play a critical role in linking the innate and adaptive immune responses. However, their antitumor effects as cancer immunotherapeutic agents have been limited. Here, we report our finding that manganese ion (Mn2+) potentiates various TLR agonists, leading to robust activation of the TLR pathway and the stimulator of interferon genes (STING) pathway among innate immune cells. In particular, we have observed robust antitumor efficacy after intratumoral administration of a TLR3 agonist and Mn2+. To achieve systemic codelivery of TLR3 agonist and Mn2+, we have developed a low-molecular-weight poly(inosinic:cytidylic acid)-Mn2+ coordination lipid nanoparticle …

Epigenetic Landscape In Lysosomal Storage Disorders: Mechanisms And Modulation, Andrés Felipe Leal, Harry Pachajoa, Shunji Tomatsu

Department of Pediatrics Faculty Papers

Lysosomal storage disorders (LSDs) are rare substrate-accumulating diseases primarily characterized by mutations in genes encoding proteins involved in lysosomal function, most of which have enzymatic activity. Resulting lysosomal dysfunction leads to the overaccumulation of non- or partially degraded substrates. While it is true that enzyme deficiency is the primary cause of LSDs, the epigenetic alterations in DNA methylation, miRNA expression, and histone modifications appear to be critical mechanisms involved in the pathogenesis of LSDs. As epigenetic marks are, in most cases, reversible, their study becomes vital to developing strategies aimed at reversing epigenome alterations. Although classical therapeutic alternatives aim to …

Hydration Strategies In Ultra-Endurance Running: A Narrative Review Of Programmed Versus Thirst-Driven Approaches, Shawn C. Wierick, Rosie I. Perez, Xiujing Zhao, Brendon P. Mcdermott

Health, Human Performance and Recreation Faculty Publications and Presentations

Background/Objectives: Ultra-endurance running (UER) presents unique hydration challenges due to prolonged duration, variable terrain, environmental extremes, and gastrointestinal limitations. Athletes often use either programmed fluid intake (PFI), which prescribes fluid volumes based on estimated sweat rate, or thirst-driven fluid intake (TDFI), which relies on internal cues. This review examines the effectiveness and limitations of each strategy in the context of UER performance and safety. Methods: A narrative review was conducted using a targeted selection of peer-reviewed studies. Both laboratory- and field-based research were included to evaluate the physiological rationale, practical feasibility, and outcomes associated with PFI and TDFI. A total …