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New Economic Hub Proposal In West Java Based On Toll Road Connectivity Using Community Detection, Ichwanul Muslim Karo Karo, Mohd Farhan Bin Md. Fudzee, Shahreen Binti Kasim, Azizul Azhar Ramli Oct 2025

New Economic Hub Proposal In West Java Based On Toll Road Connectivity Using Community Detection, Ichwanul Muslim Karo Karo, Mohd Farhan Bin Md. Fudzee, Shahreen Binti Kasim, Azizul Azhar Ramli

Baghdad Science Journal

A region's economic activity has a significant impact on the growth of its surroundings. Adequate connectivity (e.g., toll roads, railways, airlines and others) are essential to the inter-regional economy and encourage new economic hub. Indonesia is intensively constructing toll road infrastructure and West Java province has the highest number of planned/operating it. This study aims to identify new economic hubs in West Java based on connectivity between regencies/cities with toll roads. The new hubs are identified by using a community detection approach. To support the idea, this study illustrates cities/regencies as vertices and connectivity of cities/regencies with toll roads as …


Face Recognition Using Optimized Multi-Task Cascaded Cnn In Artificial Intelligence Systems, Sami Abduljabbar Rashid, Mustafa Maad Hamdi, Salah Ayad Jassim, Lukman Audah, Baraa Saad Abdulhakeem, Mohammed Salah Abood, Ahmed Adil Nafea Oct 2025

Face Recognition Using Optimized Multi-Task Cascaded Cnn In Artificial Intelligence Systems, Sami Abduljabbar Rashid, Mustafa Maad Hamdi, Salah Ayad Jassim, Lukman Audah, Baraa Saad Abdulhakeem, Mohammed Salah Abood, Ahmed Adil Nafea

Baghdad Science Journal

Improving the accuracy level of face recognition system is still an open research area where it consists of certain limitations to attain maximum accuracy. In earlier days, several algorithms are developed using machine learning and deep learning models, but still, they need improvement in terms of accuracy. For that purpose, in this article a novel CNN model called the optimized multi cascaded CNN (OPT-MTC-CNN) in the artificial intelligence system is developed, which helps to overcome the accuracy issues in face recognition system. The algorithms that are incorporated in this model are Fully Convolutional Network (FCN), Convolutional Neural Network (CNN), and …


Cover And Contents Oct 2025

Cover And Contents

Turkish Journal of Biology

No abstract provided.


Microplastic Pollution In Marine Ecosystems: Sources, Impacts, Andstakeholder-Based Solutions, Seren Acarer Arat Oct 2025

Microplastic Pollution In Marine Ecosystems: Sources, Impacts, Andstakeholder-Based Solutions, Seren Acarer Arat

Turkish Journal of Biology

Microplastics (MPs) are plastic particles of anthropogenic origin with a size range of 1–5000 μm. Marine MP pollution is increasingly recognized as a significant global environmental challenge. MPs, which enter marine ecosystems from land- and marine-based sources, pose physical, chemical, and biological risks due to the adsorption of various pollutants and the formation of biofilm layers. MPs are found in various organisms from lower to higher trophic levels of the marine food web. The negative effects of MPs on marine organisms depend on their abundance, their characteristics, and the exposure time of organisms to MPs. MPs can adversely affect various …


Application Of Biological And Green Nanomaterials In Wastewater Treatment: Techniques For The Effective Removal Of Dyes, Heavy Metals, And Organic Pollutants, Emi̇ne Sena Kazan Kaya, Zeynep Ci̇ğeroğlu, Tansel Kemerli̇ Kalbaran, Başak Temur Ergan, Zeynep Mi̇ne Şenol, Meral Yildirim Yalçin Oct 2025

Application Of Biological And Green Nanomaterials In Wastewater Treatment: Techniques For The Effective Removal Of Dyes, Heavy Metals, And Organic Pollutants, Emi̇ne Sena Kazan Kaya, Zeynep Ci̇ğeroğlu, Tansel Kemerli̇ Kalbaran, Başak Temur Ergan, Zeynep Mi̇ne Şenol, Meral Yildirim Yalçin

Turkish Journal of Biology

Background/aim: Wastewater from industrial, agricultural, and residential sources poses significant environmental and public health risks due to the presence of dyes, heavy metals, and organic pollutants. Conventional treatment methods are often inadequate for the complete removal of these pollutants. Therefore, the development of sustainable, environmentally friendly, and highly efficient treatment techniques has become increasingly important. The aim of this review is to evaluate the application of biological and green nanomaterials in wastewater treatment and to compare their effectiveness against different types of pollutants (dyes, heavy metals, and organics).

Materials and methods: This review provides detailed information on the removal of …


A Review Of Deep Learning Architectures For Plant Disease Detection​, Yasi̇n Kaya, Ercan Gürsoy Oct 2025

A Review Of Deep Learning Architectures For Plant Disease Detection​, Yasi̇n Kaya, Ercan Gürsoy

Turkish Journal of Biology

Background/aim: The rapid advancement of deep learning (DL) has revolutionized plant disease detection by enabling highly accurate, image-based diagnostic solutions. This review provides a comprehensive synthesis of DL-based methodologies for plant disease detection, systematically structured around the key stages of the modeling pipeline, encompassing data acquisition, preprocessing, augmentation, classification, detection, segmentation, and deployment.

Materials and methods: The review focuses on evaluating convolutional neural network (CNN) architectures such as VGG, ResNet, EfficientNet, and DenseNet across diverse experimental contexts. Classification strategies are categorized according to their integration of visualization techniques (e.g., saliency maps, Grad-CAM) to enhance model interpretability, emphasizing the pivotal role …


Green Carbon Dots In The Era Of Ai: Sustainable Synthesis, Intelligent Drug Delivery, Advanced Diagnostics, And Bioimaging, Emi̇ne Sezer, Fulden Ulucan Karnak, Si̇nan Akgöl Oct 2025

Green Carbon Dots In The Era Of Ai: Sustainable Synthesis, Intelligent Drug Delivery, Advanced Diagnostics, And Bioimaging, Emi̇ne Sezer, Fulden Ulucan Karnak, Si̇nan Akgöl

Turkish Journal of Biology

Background/aim: Green carbon dots (GCDs) are a rapidly developing class of nanomaterials that are revolutionizing various scientific disciplines due to their unique optical properties, low toxicity, and sustainable synthesis. This review offers a comprehensive roadmap for the field, emphasizing the synergy between GCDs and artificial intelligence (AI).

Materials and methods: We begin by detailing the sustainable synthesis of GCDs, highlighting green chemistry principles and the transformative role of AI in optimizing their production. Subsequently, we explore the critical characterization of GCDs, including their structural, optical, and biocompatibility assessment. The core of this study explores the diverse biomedical applications of GCDs, …


Applications Of Transfer Learning In Sunflower Disease Detection: Advances, Challenges, And Future Directions, Yonis Gulzar Oct 2025

Applications Of Transfer Learning In Sunflower Disease Detection: Advances, Challenges, And Future Directions, Yonis Gulzar

Turkish Journal of Biology

Background/aim: Sunflower (Helianthus annuus) is a crop of high economic and nutritional importance that continues to suffer significant yield losses due to foliar diseases. Traditional image-based and laboratory detection techniques remain limited by subjectivity, cost, and scalability. Transfer learning (TL) has recently emerged as an effective approach to overcoming these challenges involving the reuse of pretrained deep models for plant pathology tasks. Presented here is a systematic examination of recent TL-based studies on sunflower disease classification to identify prevailing trends, research gaps, and future opportunities.

Materials and methods: A structured Scopus query was employed to retrieve peer-reviewed articles published between …


Principles Of Environmentally Sustainable Agriculture For Building Resilient And Resource-Efficient Food Systems, Ramazan Çakmakçi, Songül Çakmakçi, Muhammet Fati̇h Çakmakçi Oct 2025

Principles Of Environmentally Sustainable Agriculture For Building Resilient And Resource-Efficient Food Systems, Ramazan Çakmakçi, Songül Çakmakçi, Muhammet Fati̇h Çakmakçi

Turkish Journal of Biology

As the demand for greater quantities of higher-quality food grows with population expansion, climate change, urbanization, and unsustainable agricultural practices accelerate the loss of arable land, ultimately threatening agricultural sustainability. Population growth necessitates a transition to nutritious, safe, and healthy food production systems that ensure higher yields, less reduced waste, improved social outcomes, and the integration of economic, social, and environmental sustainability principles. Urgent global challenges such as resource depletion, biodiversity loss, and climate change necessitate the protection of ecosystems and the sustainable use of natural resources. Agricultural systems must enhance food production and supply productivity, strengthen system resilience, and …


Artificial Intelligence In Medical And Biological Research: Promise And Perils Of Chatgpt And Deepseek In Advancing Healthcare, Mahmut Enes Kayaalp, Onur Gülteki̇n, Serhat Akçaalan, Hami̇t Çağlayan Kahraman, Hüseyi̇n Nevzat Topçu, Gülşah Kavrul Kayaalp Oct 2025

Artificial Intelligence In Medical And Biological Research: Promise And Perils Of Chatgpt And Deepseek In Advancing Healthcare, Mahmut Enes Kayaalp, Onur Gülteki̇n, Serhat Akçaalan, Hami̇t Çağlayan Kahraman, Hüseyi̇n Nevzat Topçu, Gülşah Kavrul Kayaalp

Turkish Journal of Biology

Background/aim: Artificial intelligence (AI), particularly large language models (LLMs) such as ChatGPT and DeepSeek, is being increasingly applied in clinical care, research, and education. The aim of this review is to examine how these tools may transform the conduct of medical and biological research and to define their limitations.

Materials and methods: A narrative synthesis of the literature was performed, encompassing studies published between 2020 and 2025. Peer-reviewed journals, systematic reviews, and high-impact original research articles were included to ensure an evidence-based overview. The principle applications, validation metrics, and clinical implications across orthopedics, oncology, cardiology, internal medicine, and the biological …


A Systematic Review Of Machine Learning In Heart Disease Prediction, Tathagat Banerjee, İshak Paçal Oct 2025

A Systematic Review Of Machine Learning In Heart Disease Prediction, Tathagat Banerjee, İshak Paçal

Turkish Journal of Biology

Background/aim: Cardiovascular diseases (CVDs) are a leading cause of global mortality, prompting the need for advanced predictive tools. While machine learning (ML) offers a powerful solution, there are significant challenges to clinical translation. This systematic review synthesizes the current state of ML in heart disease prediction, evaluating algorithmic performance, data utilization, and key translational challenges.

Materials and methods: Following PRISMA guidelines, a systematic search of literature published up to 2025 was conducted. From an initial pool of over 2500 records, a rigorous screening process yielded 65 studies for in-depth qualitative synthesis.

Results: Analysis showed that ensemble learning models dominate prediction …


Flavonoids And Phenolic Compounds: A Promising Avenue For Neurodegenerative Disease Therapy, Tesli̇me Özge Şahi̇n, Özge Cemali̇, Merve Özdemi̇r, Şeri̇fe Ayten, Duygu Ağagündüz Oct 2025

Flavonoids And Phenolic Compounds: A Promising Avenue For Neurodegenerative Disease Therapy, Tesli̇me Özge Şahi̇n, Özge Cemali̇, Merve Özdemi̇r, Şeri̇fe Ayten, Duygu Ağagündüz

Turkish Journal of Biology

Background/aim: Neurodegenerative diseases such as Alzheimer’s, Parkinson’s, Huntington’s, and ALS are characterized by a progressive loss of nerve cells, for which no definitive cure currently exists. These conditions share common pathological mechanisms, including chronic neuroinflammation, oxidative stress, protein aggregation, and mitochondrial dysfunction. Flavonoids and other plant-derived phenolic compounds have recently attracted attention for the treatment of such conditions due to their antiinflammatory and antioxidant properties. This review explores the neuroprotective mechanisms of flavonoids and evaluates their potential for the prevention and treatment of neurodegenerative diseases.

Materials and methods: A literature search of the Web of Science, PubMed, and ScienceDirect databases …


Cover And Contents Oct 2025

Cover And Contents

Turkish Journal of Biology

No abstract provided.


Hsa_Circ_0001776 Regulates The Progression Of Acute Myeloid Leukemia Through The Mir-1269b/Pten Axis, Yaoyao Wang, Xiancong Yang, Simin Rong, Xiaoxu Lan, Chenhui Ti, Weimiao Sun, Baohui Yin, Youjie Li, Yunxiao Sun Oct 2025

Hsa_Circ_0001776 Regulates The Progression Of Acute Myeloid Leukemia Through The Mir-1269b/Pten Axis, Yaoyao Wang, Xiancong Yang, Simin Rong, Xiaoxu Lan, Chenhui Ti, Weimiao Sun, Baohui Yin, Youjie Li, Yunxiao Sun

Turkish Journal of Biology

Background/aim: Acute myeloid leukemia (AML) is a malignant neoplasm arising from bone marrow hematopoietic stem cells. It is a common subtype of childhood leukemia and remains challenging to cure. Emerging evidence suggests that circular RNAs (circRNAs), a class of noncoding RNAs, play key regulatory roles in tumor biology. Among their various functions, circRNAs often act as ‘sponges’ for microRNAs (miRNAs), modulating gene expression posttranscriptionally. This study investigates the functional role and clinical relevance of hsa_circ_0001776 in AML.

Materials and methods: Three AML cell lines and 22 peripheral blood samples were analyzed. Differential expression analysis of circRNAs in a GSE dataset …


Royal Jelly With Ellagic Acid Inhibits The Glycolytic Pathway And Induces Apoptosis Through Multiple Pathways In Colorectal Cancer, Tuğba Kul Köprülü Oct 2025

Royal Jelly With Ellagic Acid Inhibits The Glycolytic Pathway And Induces Apoptosis Through Multiple Pathways In Colorectal Cancer, Tuğba Kul Köprülü

Turkish Journal of Biology

Background/aim: Developing novel chemotherapeutics with high anticancer efficacy and low toxicity remains a critical challenge in oncology. Natural products have shown promise due to their multitargeted activity and favorable safety profiles. The present study investigates the combined anticancer effects of royal jelly (RJ) and ellagic acid (EA), two potent antioxidants of animal and plant origin.

Materials and methods: Royal jelly (RJ) and ellagic acid (EA) were applied to HT29 (ATCC HTB-38, Human colorectal adenocarcinoma), HCT116 (ATCC CCL-247, Human colorectal carcinoma) and BEAS-2B (ATCC CRL-3588, human bronchial epithelium) cell lines, and their antiproliferative effects were evaluated using a xCELLigence Real-Time Cell …


Differential Modulation Of Cisplatin Efficacy By Montelukast Sodium And Desloratadine In Lung Cancer, Seha Akduman, Büşra Yüksel, Di̇dem Teci̇mel, Ömer Faruk Bayrak, Di̇dem Seven, Fi̇kretti̇n Şahi̇n Oct 2025

Differential Modulation Of Cisplatin Efficacy By Montelukast Sodium And Desloratadine In Lung Cancer, Seha Akduman, Büşra Yüksel, Di̇dem Teci̇mel, Ömer Faruk Bayrak, Di̇dem Seven, Fi̇kretti̇n Şahi̇n

Turkish Journal of Biology

Background/aim: Despite advances in treatment, achieving effective and durable responses with chemotherapy remains a significant challenge in lung cancer management. This study investigates the effects of montelukast sodium (MLS) and desloratadine (DES), alone and in combination with cisplatin (CIS), on cell viability, apoptosis, cell cycle distribution, and antioxidant gene expression in A549 and DMS114 lung cancer cell lines.

Materials and methods: Cells were treated with CIS, MLS, DES, and their combinations for 24–72 h. Cell viability was assessed via MTS assay; apoptosis and cell cycle progression were analyzed by flow cytometry. The expression of antioxidant-related genes (GPX4, GSR, GCLC) was …


Evaluating Sh-Sy5y Cells As A Dopaminergic Neuronal Model: Morphological, Transcriptomic, And Proteomic Insights, Eylül Ece İşlek Camadan, Mehmet Sarihan, Murat Kasap, Gürler Akpinar, Eli̇fcan Koçyi̇ği̇t Oct 2025

Evaluating Sh-Sy5y Cells As A Dopaminergic Neuronal Model: Morphological, Transcriptomic, And Proteomic Insights, Eylül Ece İşlek Camadan, Mehmet Sarihan, Murat Kasap, Gürler Akpinar, Eli̇fcan Koçyi̇ği̇t

Turkish Journal of Biology

Background/aim: The SH-SY5Y neuroblastoma cell line is a popular in vitro model for neurodegenerative disease research, especially Parkinson’s disease (PD) research, but its use is complicated by limitations like the persistence of neuroblastoma-like features, unstable differentiation, mitochondrial dysfunction, and cellular stress. To address these limitations, this study tested a blended, nine-day differentiation protocol that sequentially applied all-trans retinoic acid (RA), brain-derived neurotrophic factor (BDNF), and dibutyryl cyclic adenosine monophosphate (dbcAMP). By evaluating key neuronal, dopaminergic, and PD-related markers, the research aims to determine if these differentiated SH-SY5Y cells are a suitable model for studying PD.

Materials and methods: A blended …


The Effects Of The Combined Use Of Carbon Quantum Dots And Antibacterial Agents On Pathogenic Bacteria, Derya Doğanay, İbrahi̇m Serkan Avşar, Şevval Maral Özcan Aykol, Gamze Çamlik, Besa Bi̇lakaya, İsmai̇l Tuncer Deği̇m Oct 2025

The Effects Of The Combined Use Of Carbon Quantum Dots And Antibacterial Agents On Pathogenic Bacteria, Derya Doğanay, İbrahi̇m Serkan Avşar, Şevval Maral Özcan Aykol, Gamze Çamlik, Besa Bi̇lakaya, İsmai̇l Tuncer Deği̇m

Turkish Journal of Biology

Background/aim: This study evaluates the challenges associated with overcoming antimicrobial resistance and innovative approaches to combat multidrug-resistant (MDR) bacterial infections.

Materials and methods: Novel codoped carbon quantum dots (CCQDs) were synthesized using citric acid as the carbon source and L-cysteine as the nitrogen codoping atom. The formulation in which citric acid was retained was designated as CCQDs-1, whereas the purified version, from which citric acid was removed, was termed CCQDs-2. The antibacterial properties of CCQDs-1 and CCQDs-2 were compared using the agar well diffusion method. This study comprehensively characterizes these nanomaterials and evaluates their antibacterial potential, both alone and in …


Dramatic Biases In Terrestrial Nitrogen Fixation In Earth System Models Revealed By Natural Isotope Signatures, Maoyuan Fang, Shushi Peng, Philippe Ciais, Daniel S. Goll, Benjamin Z. Houlton, Ying-Ping Wang, Yilong Wang, Pan Liu, Joshua B. Fisher, Pierre Regnier Oct 2025

Dramatic Biases In Terrestrial Nitrogen Fixation In Earth System Models Revealed By Natural Isotope Signatures, Maoyuan Fang, Shushi Peng, Philippe Ciais, Daniel S. Goll, Benjamin Z. Houlton, Ying-Ping Wang, Yilong Wang, Pan Liu, Joshua B. Fisher, Pierre Regnier

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Biological nitrogen fixation (BNF) is the primary input of new reactive nitrogen to natural terrestrial ecosystems. However, this flux is poorly constrained due to its unclear drivers and associated control mechanisms. Here, we extend the existing theory of nitrogen (N) isotope mass balance to estimate BNF rates and then use a Bayesian approach to constrain the BNF rates in natural terrestrial ecosystems by using measurements of natural N-isotope ratios (δ15N) in plants (δP) and soil (δS). Together with pairwise δP and δS measurements from 18 forest sites covering diverse climates and thousands …


Ameliorating Effect Of Haematococcus Pluvialis Powder On Lps-Induced Barrier Damage In Hok Cells, Xie Jinmei, Chen Cailian, Zhang Yong, Zheng Yunjian, Xie Xi Oct 2025

Ameliorating Effect Of Haematococcus Pluvialis Powder On Lps-Induced Barrier Damage In Hok Cells, Xie Jinmei, Chen Cailian, Zhang Yong, Zheng Yunjian, Xie Xi

Food and Machinery

[Objective] To investigate the protective effect of Haematococcus pluvialis (H.pluvialis) powder on lipopolysaccharide (LPS)-induced oral epithelial damage. [Methods] The effects of different doses of H.pluvialis on the viability of human oral keratinocytes (HOKs) were assessed. In LPS-induced HOKs, changes in the tight junction-associated proteins ZO-1 and Occludin, mitochondrial morphology, reactive oxygen species (ROS), mitochondrial membrane potential (MMP), mitochondrial superoxide (MitoSOX), and mitochondrial permeability transition pore (MPTP) were evaluated. [Results] Compared with the LPS model group, high-dose H.pluvialis significantly upregulated the expression levels of Occludin and ZO-1 to 151.56% and 170.52%, respectively (P < 0.05), and promoted their membrane localization. In addition, H.pluvialis markedly improved LPS-induced excessive ROS and MitoSOX production, the reduction in MMP, and the increase in MPTP in HOKs. [Conclusion] H.pluvialis may alleviate LPS-induced barrier damage in HOKs by improving mitochondrial dysfunction and reducing oxidative stress, suggesting its potential as a functional food for oral mucosal barrier repair.


Research Progress On Active Ingredients And Functions Of Hericium Erinaceus, Wang Kaixuan, Lin Junfang, Guo Liqiong, Zhou Fenglong, Wang Na, Zhong Jingru Oct 2025

Research Progress On Active Ingredients And Functions Of Hericium Erinaceus, Wang Kaixuan, Lin Junfang, Guo Liqiong, Zhou Fenglong, Wang Na, Zhong Jingru

Food and Machinery

Hericium erinaceus has a long history in China as a medicinal and edible fungus. With delicious tastes, it also contains various active ingredients. In the current era of increasing emphasis on dietary health, Hericium erinaceus can be an ideal choice for a balanced diet. Based on previous research, this paper comprehensively summarizes the active ingredients contained in Hericium erinaceus, including terpenes, ketones, ergothioneine, and polysaccharides. The specific types and different active functions of corresponding ingredients are elaborated, while the prospect is also given on the future development of active ingredients.


Complexity Measures For Self-Similar And Chemical Graphs Using Entropies And Generalized Fractal Dimensions, J. Bhuvaneswari, D. Easwaramoorthy Oct 2025

Complexity Measures For Self-Similar And Chemical Graphs Using Entropies And Generalized Fractal Dimensions, J. Bhuvaneswari, D. Easwaramoorthy

Baghdad Science Journal

Nonlinear analysis finds numerous applications in understanding the intricate characteristics of generalized Sierpinski graphs or chemical graphs. It aids in discerning the fractal patterns inherent in self-similar structures, deciphering the dynamic interactions within chemical bonds, and assessing the complexity of molecular arrangements. Furthermore, it plays a crucial role in unraveling the emergent behaviors of complex systems, offering insights applicable to diverse fields such as materials science, chemistry, biology, network theory, and beyond. In this paper, the complexity of generalized Sierpinski graphs and chemical graphs is analyzed using fractal-based nonlinear measures computed iteratively. Nonlinear measures assess intricate relationships within graphs by …


Cd7 Regulates The Persistence Of Terminally Exhausted Cd8 T Cells During Chronic Infection, Sean Hyslop, Colby J Hofferek, Maria V Stegantseva, Emerald Kan, Kelli A Mccord, Victor M Alvarez, Amanda Y Xia, Jacob P Conarty, Andreas Wieland, William H Hudson Oct 2025

Cd7 Regulates The Persistence Of Terminally Exhausted Cd8 T Cells During Chronic Infection, Sean Hyslop, Colby J Hofferek, Maria V Stegantseva, Emerald Kan, Kelli A Mccord, Victor M Alvarez, Amanda Y Xia, Jacob P Conarty, Andreas Wieland, William H Hudson

Faculty, Staff and Students Publications

CD8+ T cell exhaustion limits immune responses during cancer and chronic infection. We identify CD7 as a tissue-specific regulator of terminally exhausted CD8+ T cells during chronic infection. CD7 expression progressively increases during exhaustion, reaching its highest levels on a subset of CD101+Tim3low terminally exhausted cells that arise in the liver. Transcriptomic analysis revealed that CD7-deficient terminally exhausted cells display altered expression of co-stimulatory, translational, and effector genes, correlating with markedly reduced persistence and increased apoptotic susceptibility. Importantly, CD7 is preferentially upregulated on PD-1+CD39+ tumor-infiltrating lymphocytes (TILs) in human head and neck squamous cell carcinoma (HNSCC), suggesting CD7 may play …


The Roles Of Sirt1 In Breast And Gynecologic Malignancies, Jianmin Ding, Matthew T Ye, Songlin Zhang Oct 2025

The Roles Of Sirt1 In Breast And Gynecologic Malignancies, Jianmin Ding, Matthew T Ye, Songlin Zhang

Faculty, Staff and Students Publications

Sirtuin 1 (SIRT1), an NAD+-dependent histone deacetylase, exerts complex and context-dependent effects in breast and gynecological cancers. By deacetylating histone and non-histone proteins such as p53, FOXO, and NF-κB, SIRT1 regulates essential processes including DNA repair, apoptosis, metabolism, and stress response. In breast cancer, SIRT1 may act as a tumor suppressor in early stages by maintaining genomic stability but promotes epithelial–mesenchymal transition, metastasis, and chemoresistance in aggressive subtypes such as triple-negative breast cancer. Similarly, in gynecological cancers, SIRT1 displays dual roles: promoting proliferation via estrogen signaling and p53/FOXO1 inhibition in Type I endometrial cancer yet potentially supporting DNA repair in …


Selective Rna Sequestration In Biomolecular Condensates Directs Cell Fate Transitions, Patrizia Pessina, Mika Nevo, Junchao Shi, Srikanth Kodali, Eduard Casas, Yingzhi Cui, Alicia L Richards, Emily J Park, Xi Chen, Florencia Levin-Ferreyra, Alejandra Rivera Tostado, Erica Stevenson, Nevan J Krogan, Danielle L Swaney, Qilong Ying, Qi Chen, Justin Brumbaugh, Bruno Di Stefano Oct 2025

Selective Rna Sequestration In Biomolecular Condensates Directs Cell Fate Transitions, Patrizia Pessina, Mika Nevo, Junchao Shi, Srikanth Kodali, Eduard Casas, Yingzhi Cui, Alicia L Richards, Emily J Park, Xi Chen, Florencia Levin-Ferreyra, Alejandra Rivera Tostado, Erica Stevenson, Nevan J Krogan, Danielle L Swaney, Qilong Ying, Qi Chen, Justin Brumbaugh, Bruno Di Stefano

Faculty, Staff and Students Publications

Controlling stem cell differentiation is a longstanding goal in biomedical research. Here we explore how cell fate is influenced by RNA condensates, specifically P-bodies, which modulate gene expression posttranscriptionally. We profiled the transcriptomes of biomolecular condensates in diverse developmental contexts spanning multiple vertebrate species. Our analyses revealed conserved, cell type-specific sequestration of untranslated RNAs encoding cell fate regulators. P-body RNA contents do not reflect active gene expression in each cell type but are enriched for translationally repressed transcripts characteristic of the preceding developmental stage. Mechanistically, P-body contents are controlled by microRNAs and can be profoundly reshaped by perturbing AGO2 or …


Molecular And Cellular Characterization Of Planarian Stem Cell Microenvironments, Frederick G Mann, Carolyn E Brewster, Dung M Vuu, Mol Mir, Riley Galton, Shao-Fu Nien, Enya R Dewars, Carlos Guerrero-Hernández, Jason A Morrison, Mary C Mckinney, Lucinda E Maddera, Melainia L Mcclain, Kate E Hall, Seth Malloy, Shiyuan Chen, Brian D Slaughter, Sean A Mckinney, Stephanie H Nowotarski, Anoja Perera, Blair W Benham-Pyle, Alejandro Sánchez Alvarado Oct 2025

Molecular And Cellular Characterization Of Planarian Stem Cell Microenvironments, Frederick G Mann, Carolyn E Brewster, Dung M Vuu, Mol Mir, Riley Galton, Shao-Fu Nien, Enya R Dewars, Carlos Guerrero-Hernández, Jason A Morrison, Mary C Mckinney, Lucinda E Maddera, Melainia L Mcclain, Kate E Hall, Seth Malloy, Shiyuan Chen, Brian D Slaughter, Sean A Mckinney, Stephanie H Nowotarski, Anoja Perera, Blair W Benham-Pyle, Alejandro Sánchez Alvarado

Faculty, Staff and Students Publications

Stem cell niches are essential for regulating stem cell self-renewal and differentiation during tissue repair and regeneration. However, the mechanisms supporting stem cell function in highly regenerative organisms, such as the freshwater planarian Schmidtea mediterranea, remain unclear. Using spatial transcriptomics, we identified two cell types associated with planarian stem cells: secretory cells we term "hecatonoblasts" and intestinal cells. Surprisingly, while hecatonoblasts were in close physical proximity to stem cells in the mesenchyme, they were dispensable for regeneration. In contrast, intestinal cells, despite lacking direct contact with stem cells, regulated both their position and function during regeneration. Electron microscopy revealed diverse …


Rainwater Harvesting For Domestic Use In Suburb Areas Of Dar Es Salaam, Tanzania: A Case Study Of Wazo Hill, Scholastica S. Ishengoma, Mahir Mohammed Said, Neema O. Msuya Oct 2025

Rainwater Harvesting For Domestic Use In Suburb Areas Of Dar Es Salaam, Tanzania: A Case Study Of Wazo Hill, Scholastica S. Ishengoma, Mahir Mohammed Said, Neema O. Msuya

Tanzania Journal of Science

Despite the increasing reliance of rainwater harvesting in semi-urban areas, there is a lack of comprehensive localized data on the safety of harvested rainwater, particularly in areas such as Wazo Hill where communities predominantly depend on it. This study evaluates the quality of harvested rooftop rainwater intended for human consumption and assesses its compliance with the World health Organization (WHO) and Draft East Africa Standards (DEAS) for drinking water. Rainwater samples were collected from various catchment surfaces and storage systems located in Wazo Hill, Tanzania. A stratified random sampling technique was employed to select the households equipped with rainwater harvesting …


Dissecting The Intrinsic And Extrinsic Regulators Of Prostate Cancer Dormancy In The Bone Microenvironment, Mostafa M. Nasr Oct 2025

Dissecting The Intrinsic And Extrinsic Regulators Of Prostate Cancer Dormancy In The Bone Microenvironment, Mostafa M. Nasr

USF Tampa Graduate Theses and Dissertations

Metastatic disease is the primary driver of cancer-related mortality. In prostate cancer (PCa), patient survival decreases dramatically once the disease spreads to distant organs, with over 80% of metastases occurring in the bone. This dissemination is often followed by a clinically silent period of tumor dormancy that can last for years, creating a critical reservoir of cells poised for lethal relapse. A significant barrier to understanding and targeting this dormant phase has been the lack of robust experimental models. This thesis first addresses this challenge by establishing a novel stress-induced model of PCa dormancy, validated across multiple murine and human …


Early Intratracheal Budesonide To Reduce Bronchopulmonary Dysplasia In Extremely Preterm Infants: The Budesonide In Babies (Bib) Randomized Clinical Trial, Namasivayam Ambalavanan, Waldemar A Carlo, Kayla J Nowak, Laura Elizabeth Wiener, Shirley S Cosby, Abhay J Bhatt, Kristi L Watterberg, Brenda B Poindexter, Martin Keszler, Carl T D'Angio, Luc P Brion, Vivek Narendran, Carrie A Rau, C Michael Cotten, Matthew M Laughon, Abhik Das, Matthew A Rysavy, Anna Maria Hibbs, Janell Fuller, Karen M Puopolo, Anup Katheria, Ravi M Patel, Jennifer R Bermick, Abbot R Laptook, Irina Prelipcean, Myra H Wyckoff, Ryan Moore, Stephanie L Merhar, Robin K Ohls, Bradley A Yoder, Marta Perez, Sarvin Ghavam, Lauritz R Meyer, Valerie Y Chock, Sara B Demauro, Wesley M Jackson, Deepali Handa, Michele C Walsh Oct 2025

Early Intratracheal Budesonide To Reduce Bronchopulmonary Dysplasia In Extremely Preterm Infants: The Budesonide In Babies (Bib) Randomized Clinical Trial, Namasivayam Ambalavanan, Waldemar A Carlo, Kayla J Nowak, Laura Elizabeth Wiener, Shirley S Cosby, Abhay J Bhatt, Kristi L Watterberg, Brenda B Poindexter, Martin Keszler, Carl T D'Angio, Luc P Brion, Vivek Narendran, Carrie A Rau, C Michael Cotten, Matthew M Laughon, Abhik Das, Matthew A Rysavy, Anna Maria Hibbs, Janell Fuller, Karen M Puopolo, Anup Katheria, Ravi M Patel, Jennifer R Bermick, Abbot R Laptook, Irina Prelipcean, Myra H Wyckoff, Ryan Moore, Stephanie L Merhar, Robin K Ohls, Bradley A Yoder, Marta Perez, Sarvin Ghavam, Lauritz R Meyer, Valerie Y Chock, Sara B Demauro, Wesley M Jackson, Deepali Handa, Michele C Walsh

Faculty, Staff and Student Publications

Importance: Extremely preterm infants are at high risk for bronchopulmonary dysplasia (BPD) and death. Multiple small randomized clinical trials showed that a combination of budesonide with surfactant compared with surfactant alone reduced BPD or death.

Objective: To determine if early intratracheal administration of a combination of budesonide (0.25 mg/kg) mixed with surfactant, compared with surfactant alone, reduces physiologic BPD or death by 36 weeks' postmenstrual age in extremely preterm infants.

Design, setting, and participants: This double-masked randomized clinical trial was conducted from April 2021 to June 2024 in the 17 centers of the United States Neonatal Research Network. Infants 22 …


Effects Of Coffee Preparation Processes On Colloidal Particle Formation And Antioxidant Properties, Gao Guanzhen, Rao Pingfan, Xu Yao, Zhou Jianwu, Shan Yunhui Oct 2025

Effects Of Coffee Preparation Processes On Colloidal Particle Formation And Antioxidant Properties, Gao Guanzhen, Rao Pingfan, Xu Yao, Zhou Jianwu, Shan Yunhui

Food and Machinery

[Objective] To investigate the effects of grinding size and extraction temperature on the chemical composition, colloidal properties, and antioxidant activity of coffee colloidal particles, and to elucidate their formation and characteristics. [Methods] Coffee infusions were prepared from whole beans, medium-ground (0.9 mm), and fine-ground (0.3 mm) coffee beans using hot brewing (100 ℃, 3 min) and cold brewing (4 ℃, 24 h). The content of total solids, total sugars, proteins, total polyphenols, and lipids were determined. The colloidal properties were characterized using a nanoparticle size and zeta potential analyzer. The infusions were separated into a filtrate (true solution phase) and …