Digital Commons Network^™

From Athens To Jerusalem: Platonism, Richard Owen, And The Road Not Taken In Biology, Michael A. Flannery

Libraries Professional Work

Tertullian provocatively asked (circa 200 AD), “What indeed has Athens to do with Jerusalem? What concord is there between the Academy and the Church?” The relationship between formal philosophy and religion has been a contentious battleground ever since. It has historically come into sharpest focus in biology generally, and evolutionary theory specifically. Charles Darwin clearly won the day in the short-term. His evolutionary functionalism looked like an inglorious abandonment of time-honored metaphysical realism for positivist empirical reductionism with a concomitant horizontalization of perspective that has secularized and flattened the intellectual landscape. But more recently the rise of evo-devo (evolutionary developmental …

Assessing The Effectiveness Of Wetland Reserve Easements As Habitat For Birds In The Mississippi Alluvial Valley Of Eastern Arkansas, Colin K. Dobson

Student Theses and Dissertations

Globally, wetland habitats suffered major declines during the 20th century. In the 1990s, the United States government created the Wetland Reserve Program (later consolidated into the Agricultural Conservation Easement Program), to combat the loss of wetlands. Despite success in attracting landowners, minimal monitoring of properties enrolled into the program (easements) has occurred. In this study, we monitored avian communities at easements, compared avian diversity at easements to agriculture and bottomland forests, and quantified microhabitat, site-specific, and surrounding landscape features at easements. We also studied the demographic rates of an indicator species of bottomland forests, the Prothonotary Warbler (Protonotaria citrea) at …

Conformational Cycling Of The Wntless Transporter Drives Trafficking And Secretion Of Wnt Morphogens, Yunhui Ge, Taciani De Almeida Magalhaes, Hongjiang Wu, Dick J H Van Den Boomen, Thu Uyen Nguyen, Tongyi Dou, Gaya P Yadav, Sukyeong Lee, Zhao Wang, Andrew Lemoff, Xuemei Luo, Sumitha S Menon, Min Zhang, Jin Wang, Zhicheng Jin, Jiansen Jiang, Adrian Salic, Pengxiang Huang

Faculty, Staff and Students Publications

Wnt proteins are lipid-modified morphogens fundamental in development and disease. During Wnt biogenesis, the G-protein-coupled receptor (GPCR)-like transporter Wntless (WLS) escorts lipidated Wnts from the endoplasmic reticulum to the plasma membrane, then transfers them to extracellular carriers, forming active and soluble morphogen-carrier complexes. To dissect the mechanisms involved, we solve cryo-EM structures of Wnt-bound WLS and unliganded WLS, and perform structure-guided functional experiments. Wnts engage WLS via three conserved hairpins, which are all required for Wnt trafficking to the cell surface and carrier-mediated secretion. Wnt release from cells is driven by dramatic conformational changes in the WLS transmembrane domain, reminiscent …

Neddylation Maintains Oocyte Quality By Stabilizing Mitochondrial Transcription, Avery A Ahmed, Tessa E Steenwinkel, Bethany K Patton, Peixin Jiang, Matthew D Meyer, Jaspreet K Rishi, Mei Leng, Alexander B Saltzman, Elizabeth S Anaya, Momal Sharif, Laurie J Mckenzie, Laura Detti, Anna Malovannaya, Sean M Hartig, Stephanie A Pangas

Faculty, Staff and Students Publications

Age-related decline in oocyte quality increases the risk of infertility, miscarriage, and birth defects. Mitochondrial dysfunction is a key contributor to this decline. Here, we report that oocyte-specific deletion of Uba3, which encodes the catalytic subunit of the E1 NEDDylation-activating complex, causes sterility in mice. Fully grown, germinal vesicle–stage Uba3 conditional knockout oocytes exhibit mitochondrial dysfunction, including elevated reactive oxygen species, impaired oxidative phosphorylation, and depletion of mitochondrially encoded RNA transcripts. Proteomic analysis identified alterations in mitochondrial-associated proteins, including enrichment of mitochondrial matrix and respiratory chain components and reduced abundance of electron transport chain complexes. These defects were associated …

Enhancer Rna Transcription Near Segmentation Gene Enhancers Can Be Analyzed In Situ Using Fish, Christine Mau, Benjamin Schmid, Ezzat El-Sherif

School of Integrative Biological & Chemical Sciences Faculty Publications

Enhancer RNAs (eRNAs) are non-coding transcripts produced at enhancer regions, which appear to be involved in transcriptional regulation. Up to date, these have been primarily investigated using labor- and cost-intensive genomic techniques. However, the precise mechanisms by which eRNA transcription or eRNA transcripts themselves mediate transcriptional regulation remain unclear. Here, we present a novel experimental approach that allows us to analyze characteristics of eRNA transcription in fixed and live whole Drosophila melanogaster embryos. We employ the anterior–posterior patterning genes as a model system to investigate the dynamics of eRNA expression, utilizing an imaging-based approach. We combined high-sensitivity fluorescence in situ …

3d Em Uncovers Mitochondrial Network Remodeling In Residual Triple Negative Breast Cancer After Conventional Chemotherapy Treatments, Mariah J Berner, Heather K Beasley, Benjamin Rodriguez, Audra Lane, Steven W Wall, Andrea G Marshall, Zer Vue, Larry Vang, Mokryun L Baek, Mason Killion, Faben Zeleke, Bryanna Shao, Dominique Parker, Autumn Peterson, Julie Sterling Rhoades, Lacey E Dobrolecki, Amber Crabtree, Annet Kirabo, Sepiso K Masenga, Prasanna Katti, Prasanna Venkhatesh, Chandravanu Dash, Michael T Lewis, Antentor Hinton, Gloria V Echeverria

Faculty, Staff and Students Publications

Mitochondria are hubs of metabolism and signaling. We previously demonstrated the importance of mitochondrial structure and function in chemotherapy-refractory triple-negative breast cancer (TNBC). Herein, we present the first 3D analysis of mitochondrial networks in human tumor tissues. Using serial block face scanning electron microscopy, we reconstructed 3,750 mitochondria and 800 lipid droplets (LDs) in naive and residual tumors persisting after conventional chemotherapies in two orthotopic patient-derived xenografts (PDX). Chemotherapies administered as monotherapy or in combination produced residual tumors that harbored mitochondria with significantly increased areas, volumes, and perimeters. We observed substantial reduction of mitochondrial intratumor heterogeneity following all treatments. Further, …

Technical Disclosure: A Unified Planetary Scale Architecture For Non-Equilibrium Thermodynamics, Cryptographic Governance, And Automated Labor Sovereignty, Christopher L. Eckes

Defensive Publications Series

This disclosure details a unified macro-system architecture designed to facilitate, manage, and scale the physical, administrative, and labor operations of a planetary-scale infrastructure array. Current technological ecosystems are fundamentally bottlenecked by active thermal throttling, localized supply-chain speculation, and closed digital rights management (DRM) frameworks that fragment development.

This multi-domain framework resolves these limitations through a three-layer topology:

1. The Physical Layer: Passive geometric routing of multi-variant heat-flux fields, non-chemical acoustic standing-wave cellular matrices, and turbine-free direct-loop magnetohydrodynamic (MHD) induction.
2. The Coordination Layer: Zero-knowledge edge-confined cognitive scaffolding, non-fiat logistical hypergraphs (M-EHN), and transparent game-theoretic defensive de-escalation matrices.
3. The Execution Layer: Open-standard computer-aided …

The Overdrive Anomaly: A Philosophical And Technical Appeal For Aligned Cognitive Scaffolding In Tomorrow's Stewards, Christopher L. Eckes

Defensive Publications Series

This appeal exposes a critical structural risk in the trajectory of modern global technology: the destabilizing asymmetry between exponential physical infrastructure and linear human cognitive development. By optimizing resources exclusively for external execution milestones—such as aerospace transit, automated manufacturing, and centralized compute networks—modern innovation paradigms treat human agency as a passive, downstream variable.

This paper demonstrates that without the systemic deployment of cryptographically secure, localized cognitive mentorship and sovereign security scaffolding, accelerating technological matrices will induce widespread psychological alienation and cognitive fragmentation. We present a formal, non-negotiable appeal to the global engineering community to reprioritize individual psychological sovereignty as the …

Systemic Integration Of Lifelong Agentic Mentorship, Contextual Scaffolding, And Sovereign Guardian Protocols In K-12 Pedagogy, Christopher L. Eckes

Defensive Publications Series

This specification details the architecture for a non-centralized, lifelong educational operating system that integrates machine learning as an individualized cognitive accelerator, psychometric auditor, and sovereign security layer. This protocol systematically replaces age-segregated, standardized instructional rotations with an immutable Dual-Focus Baseline Matrix paired with a localized Lifelong Cognitive Mentor.

By tracking an individual's development continuously from the primary entry point (K-1) through adulthood, the system implements Probabilistic Scaffolding—balancing automated aptitude mapping with deliberately engineered "negative learning" spaces. Furthermore, it incorporates an active Guardian Sensor Layerutilizing real-time linguistic and behavioral anomaly detection to insulate the child from predatory coercion and manipulative algorithm …

Contribution Of Animals To Biomedical Advancements In The Current Era: A Narrative Review, Leena Rajathy Port Louis, Mani Rajarathinam, Prithiviraj Nagarajan, Divya Sekar, Nisha Perumal

The Thai Journal of Pharmaceutical Sciences

Animal research has played a major role in the development of vaccinations and therapies for illnesses such as tetanus, polio, meningitis, hepatitis, and Severe Acute Respiratory Syndrome Coronavirus 2. For every prescription drug available today, animal testing and research have contributed immensely. This narrative review aims to explore the contribution of animals to biomedical advancements in the current era, which involved a search of peer-reviewed literature using electronic databases such as Scopus, Web of Science, and PubMed. In current biomedical research, animals help develop new treatments for long-term illnesses such as cancer, HIV, and Alzheimer’s. Animals also aid in the …

Anti-Inflammatory Activities Of Muntingia Calabura L. In Monosodium Urate-Induced Acute Gout Arthritis: Regulation Of Nlrp3 And Il-1Β, Nita Parisa, Eva Rianty, Nia Savitri Tamzil, Debby Handayati Harahap, Veny Larasati, Bintang Arroyantri Prananjaya, Theodorus Theodorus

The Thai Journal of Pharmaceutical Sciences

Background: Acute gout arthritis, which is caused by hyperuricemia, is a common inflammatory joint disease, leading to monosodium urate (MSU) crystal deposition. These crystals trigger inflammation, causing pain and significantly impairing the patient’s quality of life. Colchicine is commonly used to treat and prevent acute gout arthritis, but it has several side effects. Cherry tree (Muntingia calabura L.) leaves, which possess anti-inflammatory properties, show promise as an alternative treatment. The potential benefit of the leaves may be due to the flavonoid content.
Objectives: This study aimed to assess the anti-inflammatory activities of cherry tree leaves in an MSU-induced acute …

Microwave-Assisted Extraction Optimization And Bioactivity Assessment Of Flavonoid-Rich Extract From Lantana Camara L. Leaves In Zebrafish Epilepsy Model, Prem Kumar B R, Shwetha Krishnamurthy, Gouri Nair, Sundara Saravanan Kamatchi

The Thai Journal of Pharmaceutical Sciences

Background: Lantana camara L. (Verbanaceae) is known for its bioactive compounds and has been reported for its potential therapeutic applications. Flavonoids from natural sources are acknowledged for their antioxidant and neuroprotective properties, suggesting a possible role in seizure management.
Objectives: This study intended to optimize the microwaveassisted extraction (MAE) of flavonoid-rich extract from L. camara L. leaves utilizing a designof- experiment approach and evaluate its antiepileptic property using the zebrafish model.
Materials and Methods: Four solvents (ethyl acetate, acetone, ethanol, and water) were initially used, with ethanol yielding the highest total flavonoid content (TFC). A central composite design was employed …

Samannachan: A Thai Traditional Herbal Recipe With Cytotoxic Potential Against Breast, Cervical, And Ovarian Cancers, Perika Monkanna, Srisopa Ruangnoo, Pakakrong Thongdeeying, Arunporn Itharat, Pranporn Kuropakornpong, Reawfang Sriyom, Apinya Wiboonwattanakit, Kanyarat Namphonsan, Paponpachara Pibanpaknitee, Neal M. Davies

The Thai Journal of Pharmaceutical Sciences

Background: Samannachan (SMC) is a Thai traditional herbal recipe that has been used since 2005 at Khampramong Temple, Sakon Nakhon, to treat more than 6,000 cancer patients. However, scientific evidence supporting cytotoxic effects remains limited.
Objectives: The objective of the study is to evaluate the cytotoxicity of the SMC recipe and its ten herbal components against breast, cervical, and ovarian cancer cells compared to normal cells.
Methods: Cytotoxic activity was assessed using the sulforhodamine B (SRB) assay on breast (MCF-7, T47D, MDA-MB-231), cervical (HeLa), and ovarian (SK-OV-3) cancer cell lines, as well as on non-cancerous human keratinocytes (HaCaT). Both aqueous …

Real-Time Iot-Enabled Dissolved Oxygen Monitoring And Automated Wastewater Recirculation In Constructed Wetlands, Sivasankar Pandiarajan, Vanitha Sankararajan, Devarinti Chandu

Mansoura Engineering Journal

Wastewater treatment is necessary for environmental conservation and combating water pollution. This study demonstrates real-time dissolved oxygen (DO) monitoring in constructed wetland treatment. The system would ensure an adequate supply of oxygen through automated water circulation whenever the level is below 4 mg/L, and shut down when it reaches the normal level. From experiments conducted, it was observed that within three automated circulation processes, it is possible to increase DO concentrations from 0.5 mg/L to 5.0 mg/L. Additionally, Total Dissolved Solids reduced from 1,380 ppm to 920 ppm. pH also stabilized from 8.38 to 7.9. In this system, data is …

When The Weeds Strike Back: Rethinking Aphis's Regulation Of Genetically Engineered Plants Post-National Family Farm Coalition V. Vilsack, Reagan Powers

Tennessee Journal of Law and Policy

No abstract provided.

Philosophical Meditations On The Covid-19 Pandemic: What Have We Learned So Far?, Gregory Fernando Pappas

Dewey Studies

No abstract provided.

Get It Together: Education In A Dangerous Time, John Lupinacci

Dewey Studies

No abstract provided.

The Mask As Metaphor: Deweyan Reflections In The Time Of A Pandemic, Todd Lekan

Dewey Studies

No abstract provided.

Racial Justice And The Image Of Public Health, Marilyn Fischer

Dewey Studies

No abstract provided.

Knowledge, Attitude, And Practice Regarding Vitamin D Among Adults In Western Libya: Assessment And Socio-Demographic Influences, Abdounasser Albasher Omar, Kawther Adaila, Mofida M. Alfaid, Abdurrahman M Sweidan, Ruqayah Kasheem, Samia Emhemmed Abadi, Abdulnabi Ali Abushita, Hafsa A. Alemam

Al-Bahir

Vitamin D deficiency is a widespread public health concern, necessitating a clear understanding of knowledge, attitudes, and practices (KAP) among populations. Therefore, this study was conducted to assess Libyan citizens' knowledge, attitude, and practice (KAP) regarding vitamin D in the western region of Libya. This study was carried out between June and September of 2021. A questionnaire was distributed across the study area and the complete responses were 314, with 62.7% were females and 37.3% were males.  The scores were calculated as percentages and statistically tested. Additionally, the impact of some socio-demographic factors (age, gender, education level, job, and salary) …

Oral Health Knowledge Across Cultural Boundaries: A Physiology And Hygiene Textbook From The Tamsui Middle School During The Japanese Colonial Period, Chun-Pin Chiang

Articles in Press

No abstract provided.

Biological Performance Enhancement Of Ni-Free Zr-Based Bulk Metallic Glass For Dental Implants Via Nitrogen Plasma Immersion Ion Implantation, Her-Hsiung Huang

Articles in Press

No abstract provided.

Prognostic Impact Of The Preoperative Naples Prognostic Score On Overall And Progression-Free Survival In Surgically Treated Oral Squamous Cell Carcinoma: A Retrospective Cohort Study From A Taiwanese Medical Center, Wei-Chin Chang

Articles in Press

No abstract provided.

Ameliorating Chromium-Induced Stress In Maize Through Phosphorus And Melatonin Application, Zunaira Zafar, Shoaib Ahmad, Muhammad Akhtar, Shafaqat Ali, Sarah Owdah Alomrani, Muhammad Ali Alshehri

Turkish Journal of Agriculture and Forestry

Chromium (Cr+6)  toxicity is a significant environmental stress factor that severely hampers plant growth and productivity. This study aimed to evaluate whether the combined application of phosphorus fertilizer and melatonin could alleviate chromium induced stress in maize  (Zea mays L.).  A foliar spray of melatonin (50 µM) was applied alongside two phosphorus sources—phosphoric acid (PA) and diammonium phosphate (DAP), each at 60% of the recommended rate. Two maize cultivars (FH-1046 and YH-1898) were grown under chromium stress (0, 15, and 30 mg kg–1) to assess treatment effects. The results demonstrated that FH-1046 plants treated with PA + melatonin under noncontaminated …

Unveiling Resistance Mechanisms To Fusarium Wilt Through Comparative Transcriptome Analysis Of Cicer Arietinum And Cicer Reticulatum, Özlem Tuna, Yasi̇n Kaymaz, Talap Talapov, Canan Can, Muhammed Bahatti̇n Tanyolaç, Duygu Ateş

Turkish Journal of Agriculture and Forestry

Developing resistant chickpea cultivars is essential for managing Fusarium wilt caused by Fusarium oxysporum, a major pathogen responsible for substatial yield losses. In this study, we conducted RNA-seq–based transcriptome analysis to characterize gene expression changes in resistant and susceptible genotypes of Cicer arietinum L. and C. reticulatum following inoculation with Fusarium oxysporum f. sp. ciceris race 0. Susceptible genotypes exhibited markedly higher numbers of differentially expressed genes compared with resistant genotypes. Defense-related genes were induced in all plants upon infection; however, resistant genotypes specifically upregulated genes functioning in the apoplast or extracellular region while downregulating intracellular processes—a pattern not observed …

Ozonated Water Delays The Microbial Growth And Sensory Quality Loss Of Capia Pepper Fruit During Cold Storage, Yasi̇n Şi̇mşek, Mehmet Ali̇ Koyuncu, Derya Erbaş

Turkish Journal of Agriculture and Forestry

The aim of the present research was to evaluate, for the first time, the effect of ozonated water treatments on the postharvest quality of capia pepper (Capsicum annuum L. ‘Kaptan’). The peppers were harvested at the optimum time and transported to the laboratory immediately. Uniform and quality fruit was selected and precooled. After precooling, the fruit was divided into four groups. The first three groups were immersed in ozonated water at three different concentrations (1.0, 2.0 and 3.0 ppm) for 15 min. The last group (control) was immersed in distilled water for 15 min. The peppers were kept at room …

Plant Extract-Enriched Mineral Beverages: Effects Of Temperature And Ultrasound Processing On Bioactive Content, Eli̇f Feyza Topdaş, İsa Arslan Karakütük, Memnune Şengül

Turkish Journal of Agriculture and Forestry

Functional beverages derived from herbal extracts have potential health benefits. There is a growing interest in these beverages because they are a sustainable and health-promoting alternative to conventional flavored drinks. This study aimed to produce phenolic rich mineralized herbal beverages using lyophilized purple basil, lavender, and thyme extracts at two different concentrations (2% and 4%). Changes in the physicochemical properties (pH, electrical conductivity, color, and viscosity), total phenolic content (TPC), total flavonoid content (TFC), total antioxidant capacity (2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2’-Azino-bis(3-ethylbenzothiazoline 6-sulfonic acid (ABTS) radical scavenging assays), and individual phenolic compounds were determined for beverages stored at 4, 25, and …

Ecological Risk Assessment Of Heavy Metal-Microplastic Interactions In Agricultural Soils Irrigated With Secondary Treated Wastewater, Senar Aydin, Osman Mücevher, Arzu Ulvi̇, Fatma Bedük, Özen Merken, Ci̇han Uzun, Mehmet Emi̇n Aydin

Turkish Journal of Agriculture and Forestry

The increased reuse of treated wastewater (TWW) for irrigation in arid and semiarid regions raises environmental concerns regarding microplastics (MPs), specifically their capacity to adsorb and transport heavy metals. This study assesses the quantity of MPs and associated metals (Cd, Cr, Cu, Pb, Ni, and Co) in agricultural soils irrigated with TWW in the Konya region of Türkiye. To this end, a total of 202 soil samples were collected from TWW-irrigated (180) and nonirrigated control fields (22) at two depths (0–10 and 10–20 cm). MPs were extracted from the samples using a density separation technique, identified microscopically, and analyzed for …

The Core Microbiome Of Fluvisols From The Vistula River Valley: Relationships Between Bacteria And Basic Soil Properties, Karolina Furtak, Anna Marzec-Grządziel, Jarosław Grządziel, Jacek Niedźwiecki

Turkish Journal of Agriculture and Forestry

Fluvisols develop in river valleys through the accumulation of alluvial sediments. They are characterised by high fertility and are extensively used for agriculture. This study aimed to identify the core microbiome of fluvisols in the Vistula Valley and to examine its relationship with the basic physicochemical properties of the soils. Six types of fluvisol (very light, light, medium, and heavy) from four locations in Lublin province were analysed, with samples collected in 2018 and 2022. The microbiome structure was determined by sequencing the V3–V4 region of the 16S rRNA gene and was compared with soil parameters such as pH, electrical …

Effects Of Fenugreek And Shatavari On Vasomotor And Hormonal Balance In Ovariectomized Rats, Füsun Erten, Beşi̇r Er, Cemal Orhan, Abhijeet A. Morde, Muralidhara Padigaru, Kazi̇m Şahi̇n

Turkish Journal of Agriculture and Forestry

Trigonella foenum-graecum L. (fenugreek, TFG) and Asparagus racemosus Willd. (shatavari, AR) have been extensively used in Ayurvedic, Unani, and traditional folk medicine to support women’s health. TFG seeds are traditionally employed as galactagogues and hormonal modulators, while AR roots are valued as rejuvenating tonics with phytoestrogenic activity, prescribed for menopausal complaints and reproductive well-being. Both plants also exhibit antioxidant and hepatoprotective effects, suggesting their potential as safe, nonhormonal alternatives to conventional hormone replacement therapy. This study investigated the dose-dependent effects of TFG and AR, administered individually or in combination, on vasomotor symptoms, hormonal balance, oxidative stress, and neuroendocrine markers in …