Digital Commons Network^™

Crow's Nest, March 10, 2025, Crow's Nest Staff

Crow's Nest

The March 10, 2025, issue of Crow's Nest.

Apobec3a Drives Ovarian Cancer Metastasis By Altering Epithelial-Mesenchymal Transition, Jessica M. Devenport, Thi Tran, Brooke R. Harris, Dylan Fingerman, Rachel A. Deweerd, Lojain H. Elkhidir, Danielle Lavigne, Katherine Fuh, Lulu Sun, Jeffrey J. Bednarski, Ronny Drapkin, Mary M. Mullen, Abby M. Green

2020-Current year OA Pubs

High-grade serous ovarian cancer (HGSOC) is the most prevalent and aggressive histological subtype of ovarian cancer and often presents with metastatic disease. The drivers of metastasis in HGSOC remain enigmatic. APOBEC3A (A3A), an enzyme that generates mutations across various cancers, has been proposed as a mediator of tumor heterogeneity and disease progression. However, the role of A3A in HGSOC has not been explored. We observed an association between high levels of APOBEC3-mediated mutagenesis and poor overall survival in primary HGSOC. We experimentally addressed this correlation by modeling A3A expression in HGSOC, and this resulted in increased metastatic behavior of HGSOC …

Nad+ Prevents Chronic Kidney Disease By Activating Renal Tubular Metabolism, Bryce A. Jones, Sanjay Jain, Et Al.

2020-Current year OA Pubs

Chronic kidney disease (CKD) is associated with renal metabolic disturbances, including impaired fatty acid oxidation (FAO). Nicotinamide adenine dinucleotide (NAD+) is a small molecule that participates in hundreds of metabolism-related reactions. NAD+ levels are decreased in CKD, and NAD+ supplementation is protective. However, both the mechanism of how NAD+ supplementation protects from CKD, as well as the cell types involved, are poorly understood. Using a mouse model of Alport syndrome, we show that nicotinamide riboside (NR), an NAD+ precursor, stimulated renal PPARα signaling and restored FAO in the proximal tubules, thereby protecting from CKD in both sexes. Bulk RNA-sequencing showed …

Augmented Expression Of Superoxide Dismutase 2 Mitigates Progression And Rupture Of Experimental Abdominal Aortic Aneurysm, Huimin Yan, Ying Hu, Yang Lyu, Antonina Akk, Angela C Hirbe, Samuel A Wickline, Hua Pan, Elisha D O Roberson, Christine T N Pham

2020-Current year OA Pubs

No abstract provided.

Creating Sustainable School And Home Gardens: Organic Pest Management, Ruby Mohr, Kathy Cabe Trundle, Rita Hagevik

All Current Publications

This fact sheet on organic pest management outlines sustainable gardening practices that promote ecological balance and biodiversity. It defines organic pest management as a proactive method, using natural insecticides like sulfur and neem oil, along with unique pest control strategies such as beer traps and cinnamon repellents. Additionally, it highlights plants like mint and marigolds that repel harmful pests while attracting beneficial insects. By implementing these approaches, gardeners can protect crops sustainably, enhance soil health, and reduce reliance on synthetic pesticides, thus supporting a healthier food system.

Efficiency Of Enzyme Induced Carbonate Precipitation (Eicp) By Crude Extract Urease For Geotechnical And Geoenvironmental Applications, Kaniz Roksana

Theses and Dissertations

Geotechnical engineering is currently facing challenges, including accommodating rapid urbanization, adapting to climate change impacts, and prioritizing sustainability, all while ensuring the safety and stability of critical infrastructure. Biocementation is a recently developed new branch in geotechnical engineering that offers innovative and eco-friendly solutions by leveraging natural processes to enhance soil properties. This dissertation examines the potential of soybean extract urease as a cost-effective substitute for analytical-grade enzymes in Enzyme Induced Carbonate Precipitation (EICP) applications for biocementation. This research examines its effectiveness in various aspects, such as coastal erosion control, desiccation crack remediation, and the removal of heavy metals. Essential …

Pdxscholar Multi-Year Annual Report (2022-2024), Julia Stone, Sherry Buchanan, Bertrand Robinson, Stacey Schlatter, Carolee Harrison

Library Faculty and Staff Publications and Presentations

We are excited to share our 2022-2024 PDXScholar Multi-Year Annual Report. This multi-year report covers the period between January 1, 2022 and December 31, 2024. PDXScholar, Portland State University's institutional repository, provides access to the scholarly and creative output of PSU faculty, students, and staff. In this report, we aim to highlight PDXScholar’s growth and impact through readership data, new content and collections, and feedback from our users.

A Role For The Actin Cytoskeleton And Plastin-3 In Osteoblast Mineralization And Mechanosensation, Samantha Meagan Chin

Arts & Sciences Graduate Student Theses and Dissertations

The great diversity in actin network architectures and dynamics is exploited by cells to drive fundamental biological processes including cell migration, intracellular trafficking, and cell division. One such system that relies on the actin cytoskeleton to fulfill its physiological function are osteoblasts, which are mesenchymal lineage bone cells that promote bone formation through depositing a collagen scaffold and subsequently promoting mineralization of this matrix. A number of factors are known to drive osteogenic differentiation of pre-osteoblast cells including extracellular matrix cues such as substrate stiffness, which are primarily detected via mechanosensitive machinery linked to the actin cytoskeleton. Disruptions to β-actin, …

The Echo: March 10, 2025, Taylor University

2024-2025 (Volume 112)

No abstract provided.

The Lived Experiences Of Disabled Students In Inclusive Classrooms, Tanner Mizel

Dissertations

This dissertation explores the lived experiences of disabled students in inclusive classrooms, with a focus on those participating in extensive support needs (ESN) programs. Intentionally inclusive of students who communicate through diverse methods, including augmentative and alternative communication devices, picture exchange communication systems, American Sign Language, and other nonspoken forms, this phenomenological case study centers the perspectives of students in one middle school’s ESN program through mobile interviews and reflective document analysis. Student perspectives are triangulated through surveys reflecting the perspectives of parents, guardians, and school staff. Grounded in disability studies in education, this study challenges deficit-based approaches to inclusive …

The Rider (2025-03-10), Rebeca Salinas

The Rider Archives

Vol. 10, No. 22

Assessment Of Fish Biodiversity Of The Cimandiri Watershed, West Java, Indonesia, Rudhy Gustiano, Haryono Haryono, Gema Wahyudewantoro, Krismono Krismono, Rusdianto Rusdianto, Firman M. Nur

Makara Journal of Science

Information on the fish biodiversity of the Cimandiri Watershed is incomplete, and human activities and anthropogen-ic impacts pose a significant threat to this biodiversity. The purpose of this study was to assess the biodiversity of fish in the Cimandiri Watershed. The results indicated that fish biodiversity in the area included 104 species belonging to 49 families. There were 26 species in the upstream area, 47 species in the middle area, and 61 species in the downstream area. Forty-three species were native to Indonesia, and 7 of the native fish were endemic to the area. There were 11 introduced species belonging …

Chitosan Extraction From Anabas Testudineus Scales For Enhancing The Properties Of Edible Corn Starch-Based Films: Characterization And Performance Evaluation, Yuli Ristianingsih, Ivan Aldino Hernadin, Daniel Timotius

Makara Journal of Science

The papuyu fish (Anabas testudineus) is a freshwater species found in South and Southeast Asia. It is known for its ability to survive in extreme conditions, such as low oxygen levels and poor water quality, making it a potential candi-date for climate-resilient aquaculture. In this study, chitosan was extracted from the scales of papuyu fish through de-mineralization using 1 N HCl solution, deproteination using 5% NaOH solution, and deacetylation using 70% NaOH solution, resulting in an overall yield of 5.11%. The extracted chitosan was added to edible film made from corn starch, and the properties of the prepared films were …

Diversity And Distribution Of Macrofungi In The Mid-Hills Of Bagmati Province, Central Nepal, Hari Sharan Adhikari, Suman Shrestha, Manoj Gurung, Sushma Pandit, Sujan Balami

Makara Journal of Science

The current study was carried out at seven research sites in the mid-hills (900-2500m asl) across six districts in Bagmati province, central Nepal to analyze the variety and distribution of macrofungal communities. The survey was carried out in the wet seasons from August 2017 to September 2022, including frequent field visits to the selected forests. Vari-ous diversity indices were applied to ascertain the composition of the macrofungal communities in the study area. A total of 133 wild macrofungal species belonging to 80 genera, 50 families, and 19 orders were observed. The macro-fungal population in the Bagmati province was dominated by …

Development Of A Multi-Epitope Peptide Vaccine Against Monkeypox Virus: Immunoinformatics Analysis For South East Asian Hla Alleles, Nelson Chandra, Mochammad Aqilah Herdiansyah, Viol Dhea Kharisma, Arif Nur Muhammad Ansori, Arli Aditya Parikesit

Makara Journal of Science

The monkeypox virus (MPXV), a DNA virus causing zoonotic disease, poses major global public health challenges, with mortality rates between 3%–6%. Although smallpox vaccines provide partial cross-protection, there is a critical need for a dedicated, effective monkeypox (mpox) vaccine. This study aimed to design a multi-epitope peptide-based vaccine specifically adapted to the HLA allele profiles common in Southeast Asian populations, where MPXV cases are rising. Using immunoinformatics, we screened for and detected B and T cell epitopes from the MPXV cell surface antigen and IFN-alpha/beta receptor proteins. The vaccine design was validated through a rigorous evaluation of its antigenicity, immunogenicity, …

Cloning And Expression Of Scamp3 In Escherichia Coli Bl21(De3) With In Silico Sequence-Based Cancer Epitopes Prediction, Selly Setiati Rajagukguk, Sabar Pambudi, Astari Dwiranti, Doddy Irawan Setyo Utomo, Anom Bowolaksono

Makara Journal of Science

Secretory carrier membrane protein 3 (SCAMP3) is a crucial membrane protein involved in intracellular vesicle traffick-ing and exocytosis. The SCAMP3 expression has been observed in diverse cancer types, such as melanoma, glioma, hepatocellular and breast cancer. Increased SCAMP3 expression has been reported in certain cancer cells relative to that in normal cells, suggesting the potential role of SCAMP3 in cancer development or progression. In this study, we successfully cloned and expressed SCAMP3 in Escherichia coli strain BL21(DE3). SCAMP3 was amplified and insert-ed directionally into the prokaryotic expression vector pET21d(+). The transformation of recombinant plasmid into E. coli BL21(DE3) cells were …

Screening For Penicillin G Acylase (Pga)-Producing Bacteria And Gene Cloning Using Degenerate Oligonucleotide Primed-Pcr, Masdalifah Masdalifah, Sri Rezeki Wulandari, Gabriela Christy Sabbathini, Maria Ulfah, Dini Achnafani, Ahmad Wibisana, Feronika Heppy Sriherfyna, Is Helianti, Niknik Nurhayati

Makara Journal of Science

The growing concern over antibiotic resistance has driven global efforts to explore innovative solutions, including the use of Penicillin G acylase (PGA) to produce semisynthetic β-lactam antibiotics. This study screened four potential in-tracellular PGA-producing bacteria: Alcaligenes faecalis InaCC B444 (AfPGA), Kluyvera cryocrescens InaCC B850 (KcPGA), Providencia rettgeri InaCC B25 (Pr25PGA), and P. rettgeri InaCC B466 (Pr466PGA). Penicillin G Acylase encoding genes (pgas) were isolated from them using a Degenerate Oligonucleotide Primed-PCR (DOP-PCR) approach and sequenced. Microbiological assays confirmed all tested crude extracts to exhibit inhibitory effects. Penicillin G was used for evaluating hydrolytic activity and 6-Amino Penicillanic Acid (6-APA) coupled …

Molecular Interaction Of Purple Rice Ferulic Acid And Skin Aging-Related Enzymes, Ernanin Dyah Wijayanti, Fatchiyah Fatchiyah, Anna Safitri, Dian Siswanto

Makara Journal of Science

Purple rice is rich in ferulic acid, a phenolic acid abundant in rice. Ferulic acid (FA) has long been recognized for its anti-oxidant properties, which are linked to its skin anti-aging activity owing to its ability to scavenge free radicals and pro-tect cells from damage. Skin anti-aging activity could be assessed by inhibiting skin aging enzymes. However, there was limited information on the mechanism of FA inhibition of these enzymes. This study focused on the molecular interac-tion between purple rice FA and collagenase or tyrosinase, both with and without their substrates. The interaction be-tween FA (CID 445858), collagenase (2Y6I), tyrosinase …

Effect Of Temperature On Physicochemical Properties Of Plasticized Hydroxypropyl Methylcellulose K100–Carbopol 934 Films Containing Propylene Glycol As Plasticizer, Braja Bihari Panda, Rudra Narayan Sahoo, Amit Kumar Nayak

Makara Journal of Science

This paper studies the effect of different temperatures on different important physicochemical characteristics of plasti-cized hydroxypropyl methylcellulose (HPMC) K100-Carbopol 934 films containing propylene glycol (as a plasticizer), such as the rheology, thickness, folding endurance, tensile strength, elongation, and in vitro swelling with diffusion ki-netics. Rheology of HPMC K100-Carbopol 934 blend dispersions containing propylene glycol (before film casting) demonstrates that the flow is shear thinning and pseudoplastic. In the study of in vitro swelling, the relaxation-controlled transport is the predominant process of solvent diffusion into these plasticized HPMC K100–Carbopol 934 blend films under study. The results suggest that the solvent transport …

Roles Of The Survivin Bir Domain In Cellular Apoptosis And Proliferation: An In Silico Study, Silviatun Nihayah, Septelia Inawati Wanandi, Linda Erlina, Resda Akhra Syahrani

Makara Journal of Science

Survivin is an antiapoptotic protein that is highly expressed in cancer cells. We investigated the dual roles of the Bacu-lovirus IAP Repeats (BIR) domain within survivin, encompassing both apoptosis and proliferation, through an in silico study. The protein-protein interaction (PPI) network of survivin was analyzed using Cytoscape software. Functional enrichment (FE) analysis and data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to identify the implicated signaling pathways. The binding affinity of the BIR domain with the targeted proteins was visualized via molecular docking analysis. Drawing insights from the PPI network and FE analysis, we identified two …

Antibacterial Activity Of Endophytic Actinobacteria Isolated From Ziziphus Mauritiana Against Multidrug-Resistant Strains, Hafifatunil Khairani, Jepri Agung Priyanto, Muhammad Eka Prastya, Dwi Retnowati

Makara Journal of Science

Increasing resistance to existing antibiotics has led to a need for new alternative sources. Among the possibilities that need to be explored is the endophytic actinobacteria associated with Ziziphus mauritiana. The present study aimed to evaluate the antibacterial activity of endophytic actinobacteria isolated from Z. mauritiana against five multidrug-resistant bacterial strains. Thirty actinobacteria isolates were obtained from the roots, stem, and leaves of the plant using the serial dilution technique. Using a double-layer agar test, we found that colonies from five of the 30 isolates (16%) exhibited antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and the M18 strain of Bacillus …

Emg-Based Intraoperative Neuromonitoring Using Advanced Machine Learning Approaches, Abdalla Nabil Elsharkawy, Nourhan Zayed

Mechanical Engineering

Intraoperative neuromonitoring (IONM) plays a critical role in minimizing nerve damage during surgeries by providing real-time feedback on neural integrity. This study evaluated models associated with deep learning and machine learning models for electromyography classification of signal during intraoperative neuromonitoring (IONM). The CNNLSTM model achieved the highest accuracy (85.2%), outperforming traditional models like KNN (53%), RF (62%), and CNN (76%). This demonstrates the degree to which the CNN-LSTM model can gain insight into temporal and spatial dependencies throughout the EMG signals, which makes it optimal for real-time classification in IONM applications. This implies that deep learning techniques can improve surgical …

Stress As A Means Of Success: Investigating The Effect Of Stress Appraisals On Willpower, Ego Depletion, And Physiological Responses In College Students, Anna Minor

Honors College Theses

Stress impacts our emotions, cognition, behavior, and health. Although stress is abundant and unavoidable, recent research suggests our perception of stress can strongly influence its outcomes. The Biopsychosocial Model of Challenge and Threat (BPS) states that we appraise a stressful scenario in one of two ways: challenge or threat. A challenge appraisal involves a positive perception of stress and is associated with lower physiological output while a threat appraisal involves a negative perception of stress and increased physiological arousal. The current research seeks to apply the BPS to a cognitive task and consider its relation to willpower, ego depletion, and …

Suppression Of Stress Granule Formation Is A Vulnerability Imposed By Mutant P53., Elizabeth A. Thoenen, Atul Ranjan, Alejandro Parrales, Shigeto Nishikawa, Dan A. Dixon, Sugako Oka, Tomoo Iwakuma

Manuscripts, Articles, Book Chapters and Other Papers

Missense mutations in the TP53 (p53) gene have been linked to malignant progression. However, our in-silico analyses reveal that hepatocellular carcinoma (HCC) patients with mutant p53 (mutp53) have better overall survival compared to those with p53-null (p53^null) HCC, unlike other cancer types. Given the historical use of sorafenib (SOR) monotherapy for advanced HCC, we hypothesize that mutp53 increases sensitivity to SOR, a multikinase inhibitor that induces endoplasmic reticulum (ER) stress. Here we show that mutp53 inhibits stress granule (SG) formation by binding to an ER stress sensor, PKR-like ER kinase (PERK), and a key SG component, GAP SH3 …

Neurophisology Biosignals Of Cognitive Training Classification In Virtual Reality Environment Using Deep Learning Model, Nourhan Zayed, Mohamed Reda

Mechanical Engineering

This research investigates the potential of neurophysiological biosignals fusion, such as electroencephalogram (EEG) and Eye Tracking signals (ET), to classify cognitive states during virtual reality (VR) training, specifically for the rehabilitation of neurodegenerative diseases. By analyzing EEG data collected from participants engaged in VR-based cognitive exercises, we aim to identify patterns associated with different cognitive states and develop a robust classification system. A Convolutional Neural Network (CNN) model was developed to predict task performance utilizing neurophysiological inputs in an immersive world. This system could be used to monitor cognitive function, assess treatment efficacy, and provide real-time feedback to adapt the …

Predicting The Invasiveness Of Alpine Newts In The Uk, Alexandra North, Luke James Sutton, Jason L. Brown, Trenton W.J. Garner, Richard Billington, John W Wilkinson, Robert Puschendorf, Manuela Truebano

School of Biological and Marine Sciences

Predicting invasion risk to novel environments is essential for risk management and conservation decision making but the evolutionary lineage at which to make these predictions is often unclear. Here we predict the current suitability across the United Kingdom (UK) for the alpine newt Ichthyosaura alpestris, a species with a complex evolutionary history, a broad native range, a growing number of introduced populations and anecdotal reports of ecological consequences to native amphibian communities. We use species distribution and ecological niche modelling to predict environmental suitability of the alpine newt in the UK at both the species-level and lineage-level and to quantify …

The Neuromarketing: Bridging Neuroscience And Marketing For Enhanced Consumer Engagement, Guo Song, Md Abu Issa Gazi, Abdul Waaje, Md Mustaqim Roshid, Rejaul Karim, Md Atikur Rahaman

Michigan Tech Publications

This review paper examines the influence of neuromarketing on consumer behavior research, emphasizing its origins, methodologies, impacts, and implications for customer engagement. This paper conducts a thorough narrative literature review on neuromarketing, analyzing the application of diverse neuroscientific techniques, including functional magnetic resonance imaging (fMRI), electroencephalography (EEG), positron emission tomography (PET), magnetoencephalography (MEG), and facial coding/eye tracking, to assess cerebral responses and forecast consumer behavior. Recent scholarly investigations underscore how neuromarketing utilizes contemporary breakthroughs to transform consumer behavior research by offering enhanced insights into cognition and emotion. These sophisticated tools have contested conventional study methodologies, facilitating a more comprehensive comprehension …

Prophylaxis, Clinical Management, And Monitoring Of Datopotamab Deruxtecan-Associated Oral Mucositis/Stomatitis, Funda Meric-Bernstam, Aditya Bardia, Paolo Bossi, Giampaolo Bianchini, Frances Gatlin, Rajesh V Lalla, Barbara Melosky, Naoki Niikura, Timothy A Yap, Sophie S Kim, Rachana Rajagopalan, Rick M Fairhurst, Stephanie L Graff, Hope S Rugo

Faculty, Staff and Student Publications

Oral mucositis/stomatitis (hereafter stomatitis) is a common dose-limiting toxicity seen with various classes of cancer treatment. Symptoms associated with stomatitis, primarily oral pain, may impact patient quality of life and may lead to dose delay and reduction or treatment discontinuation. Datopotamab deruxtecan (Dato-DXd) is a novel trophoblast cell surface antigen 2-directed antibody-drug conjugate undergoing clinical investigation in multiple solid tumor types. Stomatitis is among the most reported adverse events associated with Dato-DXd, with most cases being grades 1-2. This article reviews the incidence of stomatitis seen with Dato-DXd, including in the phase III pivotal studies TROPION-Lung01 and TROPION-Breast01 (in patients …

Advances In Extracellular Matrix-Associated Diagnostics And Therapeutics, Morten Karsdal, Thomas R Cox, Amelia L Parker, Nicholas Willumsen, Jannie Marie Bülow Sand, Gisli Jenkins, Henrik H Hansen, Anouk Oldenburger, Kerstin E Geillinger-Kaestle, Anna Thorsø Larsen, Darcey Black, Federica Genovese, Alexander Eckersley, Andrea Heinz, Alexander Nyström, Signe Holm Nielsen, Lucas Bennink, Lars Johannsson, Anne-Christine Bay-Jensen, Dana E Orange, Scott Friedman, Mads Røpke, Vincent Fiore, Detlef Schuppan, Florian Rieder, Benjamin Simona, Lee Borthwick, Mark Skarsfeldt, Haakan Wennbo, Paresh Thakker, Ruedi Stoffel, Graham W Clarke, Raghu Kalluri, Darren Ruane, Faiez Zannad, Joachim Høg Mortensen, Dovile Sinkeviciute, Fred Sundberg, Molly Coseno, Christian Thudium, Adam P Croft, Dinesh Khanna, Michael Cooreman, Andre Broermann, Diana Julie Leeming, Ali Mobasheri, Sylvie Ricard-Blum

Faculty, Staff and Student Publications

The extracellular matrix (ECM) is the common denominator of more than 50 chronic diseases. Some of these chronic pathologies lead to enhanced tissue formation and deposition, whereas others are associated with increased tissue degradation, and some exhibit a combination of both, leading to severe tissue alterations. To develop effective therapies for diseases affecting the lung, liver, kidney, skin, intestine, musculoskeletal system, heart, and solid tumors, we need to modulate the ECM's composition to restore its organization and function. Across diverse organ diseases, there are common denominators and distinguishing factors in this fibroinflammatory axis, which may be used to foster new …

A Phase I/Ii Trial Of Avelumab Combinations With Ivuxolimab, Utomilumab, And Radiation Therapy In Patients With Advanced Gastrointestinal Malignancies, Jibran Ahmed, Anne Knisely, Carlos Torrado, Bettzy Stephen, Yali Yang, Juhee Song, Anas Alshawa, Abdulrazzak Zarifa, Anuja Jhingran, Eugene J Koay, Van Karlyle Morris, Milind Javle, Robert A Wolff, Funda Meric-Bernstam, Shubham Pant, Jordi Rodon, Aung Naing

Faculty, Staff and Student Publications

Background: Checkpoint agonists utomilumab (4-1BB agonist) and ivuxolimab (OX40 agonist) enhance Teffector cell function. Preclinical studies suggest that combining these drugs with avelumab (anti-PD-L1 antibody) can potentially synergize this effect. In addition, tissue abscopal effects of radiation therapy may improve antigen presentation, complementing PD-L1 blockade. We conducted a single institution, open-label, multi-arm, non-randomized, phase 1/2 clinical trial of avelumab in combination with ivuxolimab, with or without utomilumab, and radiation therapy in patients with advanced solid tumors. Herein, we present a subgroup analysis in patients with gastrointestinal (GI) tumors (pancreatic, colon, gastric, and hepatocellular).

Methods: The primary objectives of this study …