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35 pages, 1857 KB  
Review
Antioxidant Activity and Oxidative Stability of Flaxseed and Its Processed Products: A Review
by Yuliya Frolova, Roman Sobolev and Alla Kochetkova
Sci 2025, 7(4), 155; https://doi.org/10.3390/sci7040155 (registering DOI) - 2 Nov 2025
Abstract
Flaxseed (Linum usitatissimum) is one of the most important crops worldwide due to its nutritional and functional properties. Given the diversity of flax and its processed products, this review aimed to systematize and analyze data on their antioxidant properties, oxidative stability, [...] Read more.
Flaxseed (Linum usitatissimum) is one of the most important crops worldwide due to its nutritional and functional properties. Given the diversity of flax and its processed products, this review aimed to systematize and analyze data on their antioxidant properties, oxidative stability, and content of biologically active substances. The literature search was conducted using the following databases: Scopus and The Lens. This review examines the approaches to studying the antioxidant properties, oxidative stability, and content of biologically active substances of flax and its processed products, which are used in the food industry, highlighting the advantages and limitations of the methods employed. For the analysis of AOA and OS in flaxseeds and their processing products, the most common approach is the in vitro model. For AOA assessment, non-standardized methods such as DPPH, FRAP, and ABTS•+ are most frequently used, while standard methods for determining OS (PV, AV, p-AnV, CDs, CTs, TBARSs, OSI) are employed. However, these parameters are integral and cannot fully explain the underlying processes. In our opinion, the most promising directions for further research are the standardization of methods for analyzing the antioxidant activity (AOA) of flaxseed and its processing products. Furthermore, expanding the methodological framework will lead to a better understanding of the mechanisms of oxidative processes and how to inhibit them. An expanded set of AOA assessment methods will allow researchers not only to study the action of antioxidants but also to predict it. This is particularly relevant since the same antioxidant can exhibit both antioxidant and pro-oxidant effects. Full article
(This article belongs to the Section Chemistry Science)
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13 pages, 609 KB  
Review
The miR-200 Family in Non-Small-Cell Lung Cancer: Molecular Mechanisms, Clinical Applications, and Therapeutic Implications
by Nobuaki Kobayashi, Yukihito Kajita, Fangfei Yang, Nobuhiko Fukuda, Kohei Somekawa, Ayami Kaneko and Seigo Katakura
Genes 2025, 16(11), 1312; https://doi.org/10.3390/genes16111312 (registering DOI) - 2 Nov 2025
Abstract
Non-small-cell lung cancer (NSCLC) remains a leading cause of cancer-related mortality worldwide, demanding improved biomarkers and therapeutic approaches. This review synthesizes the extensive evidence positioning the miR-200 family as a master regulator of NSCLC progression. We detail the core molecular circuitry centered on [...] Read more.
Non-small-cell lung cancer (NSCLC) remains a leading cause of cancer-related mortality worldwide, demanding improved biomarkers and therapeutic approaches. This review synthesizes the extensive evidence positioning the miR-200 family as a master regulator of NSCLC progression. We detail the core molecular circuitry centered on the bistable, double-negative feedback loop between miR-200 and the ZEB1/ZEB2 transcription factors, which governs epithelial–mesenchymal transition (EMT). This review connects this central mechanism to critical clinical challenges, including the development of resistance to EGFR-targeted therapies and the regulation of immune evasion through PD-L1 expression and CD8+ T cell infiltration. We evaluate the strong clinical evidence for the miR-200 family’s utility as a diagnostic, prognostic, and predictive biomarker. Finally, we explore emerging therapeutic strategies that target this network, including miRNA replacement, epigenetic reactivation, and rational combinations with immunotherapy and targeted agents. We synthesize evidence positioning the miR-200/ZEB feedback circuit as a central regulatory node in NSCLC that links EMT with therapeutic resistance and immune evasion. Beyond summarizing associations, we interpret how this circuitry could inform biomarker development and rational combinations with targeted and immune therapies. Given heterogeneous study designs and non-standardized assays, translational claims remain provisional; we outline immediate priorities for assay harmonization and biomarker-stratified trials. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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19 pages, 8412 KB  
Article
A Thymus-Independent Artificial Organoid System Supports Complete Thymopoiesis from Rhesus Macaque-Derived Hematopoietic Stem and Progenitor Cells
by Callie Wilde, Saleem Anwar, Yu-Tim Yau, Sunil Badve, Yesim Gokmen Polar, John D. Roback, Rama Rao Amara, R. Paul Johnson and Sheikh Abdul Rahman
Biomedicines 2025, 13(11), 2692; https://doi.org/10.3390/biomedicines13112692 (registering DOI) - 1 Nov 2025
Abstract
Background: T cell regeneration in the thymus is intrinsically linked to the T cell-biased lineage differentiation of hematopoietic stem and progenitor cells (HSPCs). Although nonhuman primates (NHPs) serve as indispensable models for studying thymic output under physiological and pathological conditions, a non-animal technology [...] Read more.
Background: T cell regeneration in the thymus is intrinsically linked to the T cell-biased lineage differentiation of hematopoietic stem and progenitor cells (HSPCs). Although nonhuman primates (NHPs) serve as indispensable models for studying thymic output under physiological and pathological conditions, a non-animal technology facilitating efficient TCR-selected T cell development and evaluating T cell output from NHP-derived HSPCs has been lacking. To address this gap, we established a rhesus macaque-specific artificial thymic organoid (RhATO) modeling primary thymus-tissue-free thymopoiesis. Methods: The RhATO was developed by expressing Rhesus macaque (RM) Delta-like Notch ligand 1 in mouse bone marrow stromal cell line (MS5-RhDLL1). The bone marrow-derived HSPCs were aggregated with MS5-RhDLL1 and cultured forming 3D artificial thymic organoids. These organoids were maintained under defined cytokine conditions to support complete T cell developmental ontogeny. T cell developmental progression was assessed by flow cytometry, and TCR-selected subsets were analyzed for phenotypic and functional properties. Results: RhATOs recapitulated the complete spectrum of thymopoietic events, including emergence of thymus-seeding progenitors, CD4+CD3 immature single-positive and CD4+CD8+ double-positive early thymocytes, and mature CD4+ or CD8+ single-positive subsets. These subsets expressed CD38, consistent with the recent thymic emigrant phenotype, and closely mirrored canonical T cell ontogeny described in humans. RhATO-derived T cells were TCR-selected and demonstrated cytokine expression upon stimulation. Conclusions: This study provides the first demonstration of an NHP-specific artificial thymic technology that faithfully models thymopoiesis. RhATO represents a versatile ex vivo platform for studying T cell development, immunopathogenesis, and generating TCR selected T cells. Full article
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25 pages, 6936 KB  
Article
Sustainable Cyclodextrin Modification and Alginate Incorporation: Viscoelastic Properties, Release Behavior, and Morphology in Bulk and Microbead Hydrogel Systems
by Maja Čič, Nejc Petek, Iztok Dogša, Andrijana Damjanović, Boštjan Genorio, Nataša Poklar Ulrih and Ilja Gasan Osojnik Črnivec
Gels 2025, 11(11), 875; https://doi.org/10.3390/gels11110875 (registering DOI) - 1 Nov 2025
Abstract
Incorporating cyclodextrins (CDs) into ionically crosslinked polysaccharide matrices offers a promising strategy for developing well-defined, safe-by-design and biocompatible carrier systems with tunable rheological properties. In this study, β-cyclodextrin (β-CD) was functionalized with citric acid (CDC) and maleic anhydride (CDM) using [...] Read more.
Incorporating cyclodextrins (CDs) into ionically crosslinked polysaccharide matrices offers a promising strategy for developing well-defined, safe-by-design and biocompatible carrier systems with tunable rheological properties. In this study, β-cyclodextrin (β-CD) was functionalized with citric acid (CDC) and maleic anhydride (CDM) using solvent-free synthesis to improve compatibility with alginate hydrogels. The modified CDs were characterized by FTIR, 1H NMR, DLS, zeta potential, and MS, confirming successful esterification (4.0 and 3.4 –OH substitution for CDC and CDM, respectively) and stable aqueous dispersion. Rheological measurements showed that native CD accelerated gelation (within approximately 30 s), while CDC and CDM delayed crosslinking (by 2 to 13 min) and reduced gel strength, narrowing the linear viscoelastic range to 0.015–0.089% strain due to competition between polycarboxylated CDs and alginate chains for Ca2+ ions. Vibrational prilling produced alginate microbeads with diameters of 800–1000 µm and a simultaneous increase in size and CD concentration. Hydrogels demonstrated high CD retention (>80% after 28 h) and slightly greater release of CDC and CDM than native CD. Overall, solvent-free modification of CDs with citric and maleic acids provides a sustainable approach to tailoring the gelation kinetics, viscoelasticity, and release behavior of alginate-based hydrogels, offering a versatile, food- and health-compliant platform for controlled delivery of bioactive compounds. Full article
(This article belongs to the Special Issue Gel-Related Materials: Challenges and Opportunities (2nd Edition))
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15 pages, 4510 KB  
Article
Hapten-Specific Cellular Immune Responses in the Elicitation and Sensitization Phases of Murine Contact Hypersensitivity
by Kornél Molnár, Gábor Kovács, Bence Kormos, Petra Aradi and Zoltán Jakus
Biomolecules 2025, 15(11), 1540; https://doi.org/10.3390/biom15111540 (registering DOI) - 1 Nov 2025
Abstract
Contact dermatitis (CD) is a common inflammatory skin condition with irritant etiology or a delayed-type hypersensitivity called allergic contact dermatitis (ACD). Contact hypersensitivity (CHS) is a widely used rodent model of ACD and similarly consists of two phases: sensitization and elicitation. To trigger [...] Read more.
Contact dermatitis (CD) is a common inflammatory skin condition with irritant etiology or a delayed-type hypersensitivity called allergic contact dermatitis (ACD). Contact hypersensitivity (CHS) is a widely used rodent model of ACD and similarly consists of two phases: sensitization and elicitation. To trigger CHS, low-molecular-weight haptens, such as DNFB or TNCB, are commonly applied. However, the characterization of the induced immune response remains incomplete. Our aim was to characterize the immune response after first and repeated exposures to model haptens. First exposure to DNFB or TNCB led to significant ear swelling, with DNFB causing a more pronounced effect. DNFB enhanced neutrophil infiltration, whereas TNCB led to macrophage, dendritic cell, and helper T cell accumulation. Repeated DNFB exposure did not aggravate edema significantly, while TNCB re-exposure enhanced edema formation and induced neutrophil granulocyte, dendritic cell, and helper and cytotoxic T cell accumulation. Our results demonstrate that a hapten-specific immune response is induced during both phases of CHS. A detailed understanding of allergen-specific immune responses is crucial for the appropriate selection of the model and for gaining deeper insight into the mechanisms of inflammatory skin diseases. These findings may contribute to the targeted selection of haptens. Full article
(This article belongs to the Section Molecular Medicine)
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25 pages, 2193 KB  
Article
Immunomodulatory Effects of Juzentaihoto on Fas-Mediated Apoptosis: Insights from Cancer Patients and In Vitro Models
by Quang Trung Ngo, Jorge Luis Espinoza, Hongyang Li, Masafumi Inokuchi, Yosuke Nakanishi, Eriko Morishita, Takamasa Katagiri, Akihiro Kawahara, Tomokazu Yoshizaki, Akiyoshi Takami and Keiko Ogawa-Ochiai
Pharmaceuticals 2025, 18(11), 1658; https://doi.org/10.3390/ph18111658 (registering DOI) - 1 Nov 2025
Abstract
Background/Objectives: Juzentaihoto (JTT), a traditional Kampo formula composed of ten medicinal herbs, is widely prescribed in Japan for immune enhancement and general health maintenance. This exploratory, open-label pilot study aimed to evaluate the feasibility and immunomodulatory effects of JTT in cancer patients and [...] Read more.
Background/Objectives: Juzentaihoto (JTT), a traditional Kampo formula composed of ten medicinal herbs, is widely prescribed in Japan for immune enhancement and general health maintenance. This exploratory, open-label pilot study aimed to evaluate the feasibility and immunomodulatory effects of JTT in cancer patients and to explore its potential mechanisms of action. Methods: Ten cancer patients received oral JTT (7.5 g/day) for 14 days, while healthy volunteers served as a reference group. Peripheral natural killer (NK) cell phenotypes and CD95 expression were analyzed by flow cytometry, and serum Fas ligand (FasL) concentrations were measured by ELISA. Complementary in vitro assays using PBS-extracted, autoclaved JTT were conducted to assess Fas/FasL-mediated apoptosis in Jurkat and primary T cells by flow cytometry and Western blotting for cleaved caspase-8 and -3. Additional experiments with staurosporine (intrinsic apoptosis) and TRAIL in OSC-19 carcinoma cells were performed to determine pathway specificity. Results: In patients, most NK-cell markers showed no statistically significant within-subject changes, although a trend-level increase in NKp46 and a significant reduction in NK-cell CD95 expression (paired p = 0.014) were observed. Between-group differences primarily reflected baseline disparities between cancer patients and healthy controls. In vitro, JTT (50–100 µg/mL) partially attenuated FasL-induced apoptosis and reduced cleaved caspase-3 without affecting cleaved caspase-8, suggesting selective downstream modulation of the extrinsic pathway. Conclusions: Within the limitations of a small, non-randomized cohort without placebo, these findings are hypothesis-generating and indicate that JTT selectively modulates Fas-mediated lymphocyte apoptosis without promoting tumor immune evasion. Further randomized trials and mechanistic studies incorporating co-culture or 3D tumor–immune models are warranted to confirm these observations and identify active constituents. Full article
(This article belongs to the Special Issue Natural Products as an Alternative for Treatment of Human Diseases)
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12 pages, 3149 KB  
Article
Phase-Controlled Synthesis of Alloyed (CdS)x(CuInS2)1−x Nanocrystals with Tunable Band Gap
by Bingqian Zu, Song Chen, Liping Bao, Yingjie Liu and Liang Wu
Nanomaterials 2025, 15(21), 1661; https://doi.org/10.3390/nano15211661 (registering DOI) - 1 Nov 2025
Abstract
Phase and band gap engineering of (CdS)x(CuInS2)1−x nanomaterials is critical for their potential applications in photovoltaics and photocatalysis, yet it remains a challenge. Here, we report a precursor-mediated colloidal method for phase-control synthesis of alloyed (CdS)x(CuInS [...] Read more.
Phase and band gap engineering of (CdS)x(CuInS2)1−x nanomaterials is critical for their potential applications in photovoltaics and photocatalysis, yet it remains a challenge. Here, we report a precursor-mediated colloidal method for phase-control synthesis of alloyed (CdS)x(CuInS2)1−x nanocrystals with tunable band gap. When CuCl, InCl3, and Cd(AC)2·2H2O are used as the respective cation sources, wurtzite-structured alloyed (CdS)x(CuInS2)1−x nanocrystals can be synthesized with a tunable optical band gap ranging from 1.56 to 2.45 eV by directly controlling the molar ratio of the Cd precursor. Moreover, using Cu(S2CNEt2)2, In(S2CNEt2)3, and Cd(S2CNEt2)2 as cation sources results in alloyed (CdS)x(CuInS2)1−x nanocrystals with a zinc-blende structure, demonstrating that the optical band gap of these nanocrystals can be compositionally tuned from 1.50 to 1.84 eV through precisely adjusting the molar ratio of Cd precursor. The results were validated through a comprehensive characterization approach employing XRD, TEM, HRTEM, STEM-EDS, XPS, UV-vis-NIR absorption spectroscopy, and Mott–Schottky analysis. Full article
(This article belongs to the Special Issue Preparation and Characterization of Nanomaterials)
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41 pages, 887 KB  
Review
Advances in Photocatalytic Degradation of Crystal Violet Using ZnO-Based Nanomaterials and Optimization Possibilities: A Review
by Vladan Nedelkovski, Milan Radovanović and Milan Antonijević
ChemEngineering 2025, 9(6), 120; https://doi.org/10.3390/chemengineering9060120 (registering DOI) - 1 Nov 2025
Abstract
The photocatalytic degradation of Crystal Violet (CV) using ZnO-based nanomaterials presents a promising solution for addressing water pollution caused by synthetic dyes. This review highlights the exceptional efficiency of ZnO and its modified forms—such as doped, composite, and heterostructured variants—in degrading CV under [...] Read more.
The photocatalytic degradation of Crystal Violet (CV) using ZnO-based nanomaterials presents a promising solution for addressing water pollution caused by synthetic dyes. This review highlights the exceptional efficiency of ZnO and its modified forms—such as doped, composite, and heterostructured variants—in degrading CV under both ultraviolet (UV) and solar irradiation. Key advancements include strategic bandgap engineering through doping (e.g., Cd, Mn, Co), innovative heterojunction designs (e.g., n-ZnO/p-Cu2O, g-C3N4/ZnO), and composite formations with graphene oxide, which collectively enhance visible-light absorption and minimize charge recombination. The degradation mechanism, primarily driven by hydroxyl and superoxide radicals, leads to the complete mineralization of CV into non-toxic byproducts. Furthermore, this review emphasizes the emerging role of Artificial Neural Networks (ANNs) as superior tools for optimizing degradation parameters, demonstrating higher predictive accuracy and scalability compared to traditional methods like Response Surface Methodology (RSM). Potential operational challenges and future directions—including machine learning-driven optimization, real-effluent testing potential, and the development of solar-active catalysts—are further discussed. This work not only consolidates recent breakthroughs in ZnO-based photocatalysis but also provides a forward-looking perspective on sustainable wastewater treatment strategies. Full article
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21 pages, 1765 KB  
Review
A Critical Review of Recent Inorganic Redox Flow Batteries Development from Laboratories to Industrial Applications
by Chivukula Kalyan Sundar Krishna and Yansong Zhao
Batteries 2025, 11(11), 402; https://doi.org/10.3390/batteries11110402 (registering DOI) - 1 Nov 2025
Abstract
Redox flow batteries (RFBs) are an emerging class of large-scale energy storage devices, yet the commercial benchmark—vanadium redox flow batteries (VRFBs)—is highly constrained by a modest open-circuit potential (1.26 V) while posing an expensive and volatile material procurement costs. This review focuses on [...] Read more.
Redox flow batteries (RFBs) are an emerging class of large-scale energy storage devices, yet the commercial benchmark—vanadium redox flow batteries (VRFBs)—is highly constrained by a modest open-circuit potential (1.26 V) while posing an expensive and volatile material procurement costs. This review focuses on recent progress in diversifying redox-active species to overcome these limits, highlighting chemistries that increase overall cell voltage, energy density, and efficiency while maintaining long cycle life and safety. The study dwells deeper into manganese-based systems (e.g., Mn/Ti, Mn/V, Mn/S, M/Zn) that leverage Mn’s high positive potential while addressing Mn(III) disproportionation reactions; iron-based hybrids (Fe/Cr, Fe/Zn, Fe/Pb, Fe/V, Fe/S, Fe/Cd) that exploit the low cost, and its abundance, along with membrane and electrolyte strategies to prevent the potential issue involving crossover; cerium-anchored catholytes (Ce/Pb, V/Ce, Eu/Ce, Ce/S, Ce/Zn) that deliver high operational voltage by implementing an acid-base media, along with selective zeolite membranes; and halide systems (Zn–I, Zn–Br, Sn–Br, polysulfide–bromine/iodide) that combine fast redox kinetics and high solubility with advances such as carbon-coated membranes, bromine complexation, and ambipolar electrolytes. Across these various families of RFBs, the review highlights the modifications made to the flow-fields, membranes, and electrodes by utilizing a zero-gap serpentine flow field, sulfonated poly(ether ether ketone) (SPEEK) membranes, carbon-modified and zeolite separators, electrolyte additives to enhance the voltage (VE%), and thereby energy (EE%) efficiency, while reducing the overall system cost. These modifications to the existing RFB technology offer a promising alternative to traditional approaches, paving the way for improved performance and widespread adoption of RFB technology in large-scale grid-based energy storage solutions. Full article
(This article belongs to the Special Issue Batteries: 10th Anniversary)
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9 pages, 3739 KB  
Protocol
Protocol to Establish Estrogen Receptor-Negative Heterozygous BRCA1 Organoids
by Madhura Deshpande and Jeannine Gerhardt
Methods Protoc. 2025, 8(6), 127; https://doi.org/10.3390/mps8060127 (registering DOI) - 1 Nov 2025
Abstract
Cancer development in BRCA1 carriers is a multi-step process, which is triggered by several factors and mechanisms that are not clearly understood. Most BRCA1 carriers develop triple-negative breast cancer (TNBC)—estrogen receptor (ER)-, progesterone receptor (PR)-, and HER2 -negative cancers—which originates from ER/PR/HER2-negative breast [...] Read more.
Cancer development in BRCA1 carriers is a multi-step process, which is triggered by several factors and mechanisms that are not clearly understood. Most BRCA1 carriers develop triple-negative breast cancer (TNBC)—estrogen receptor (ER)-, progesterone receptor (PR)-, and HER2 -negative cancers—which originates from ER/PR/HER2-negative breast progenitor cells. Due to a lack of ER/PR/HER2-negative cell models with BRCA mutations, the processes inducing cancer development in BRCA carriers have not been comprehensively studied. Thus, studies characterizing ER/PR/HER2-negative cells carrying a BRCA1 germline mutation are needed to gain more in-depth knowledge about the steps leading to cancer initiation in BRCA1 carriers. To study the cancer development in these patients, we established a protocol for the generation of human ER/PR/HER2-negative breast organoids carrying a BRCA1 germline mutation. We confirmed that these organoids are unresponsive to estrogen, can self-renew, and express the stem/progenitor marker CD44. In addition, we observed that these organoids contain outgrowths that resemble the mature ductal and lobular units of the mammary gland, thus making it a suitable model system to study how cancer develops in ER/PR/HER2-negative mammary cells that carry a BRCA1 germline mutation. Full article
(This article belongs to the Section Molecular and Cellular Biology)
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17 pages, 758 KB  
Systematic Review
Evaluating the Safety and Efficacy of PD-1 Inhibitors in HIV Patients Diagnosed with Lung Cancer: A Systematic Review
by Helal F. Hetta, Yasser Alatawi, Fawaz E. Alanazi, Abdullah Alattar, Reem Alshaman, Hanan Alshareef, Zinab Alatawi, Majd S. Alatawi, Jumana H. Albalawi, Ghadeer A. Alosaimi, Reem Sayad and Wedad M. Nageeb
Pharmaceuticals 2025, 18(11), 1654; https://doi.org/10.3390/ph18111654 (registering DOI) - 1 Nov 2025
Abstract
Background and Aim: People with HIV (PWH) have historically been excluded from cancer immunotherapy trials due to concerns over immune dysregulation and safety. This systematic review evaluates the safety, efficacy, and immunologic outcomes of Programmed death-1 (PD-1) inhibitors in PWH diagnosed with [...] Read more.
Background and Aim: People with HIV (PWH) have historically been excluded from cancer immunotherapy trials due to concerns over immune dysregulation and safety. This systematic review evaluates the safety, efficacy, and immunologic outcomes of Programmed death-1 (PD-1) inhibitors in PWH diagnosed with non-small-cell lung cancer (NSCLC). Methods: Following PRISMA guidelines, a systematic search was conducted across PubMed, Scopus, Web of Science, and Medline through January 2025. Studies were included if they reported outcomes of ICIs in PWH with NSCLC. Data extraction included progression-free survival (PFS), overall survival (OS), immune-related adverse events (irAEs), antitumor response, HIV viral control, and immunologic parameters. Study quality was assessed using the Joanna Briggs Institute (JBI) checklist. Results: Six cohort studies (n = 762 patients) met inclusion criteria. ICIs used included nivolumab, pembrolizumab, atezolizumab, and durvalumab, with treatment durations ranging from 3.1 to 5.4 months. Median PFS ranged from 3.0 to 6.3 months, and OS ranged from 10.0 to 66.0 months. Overall response rates (ORRs) varied from 13% to 75%, and disease control rates (DCRs) ranged from 47% to 62.5%. irAEs occurred in 25% to 75% of patients, with 6–20% experiencing grade 3–4 events. Corticosteroids were required in 13–29% of patients, and treatment discontinuation due to toxicity occurred in up to 30%. Most patients had controlled HIV, with CD4 counts typically above 300 cells/μL and undetectable viral loads. Conclusions: ICIs appear safe and effective in PWH with NSCLC, with toxicity and efficacy outcomes comparable to the general population. While immunotherapy should not be withheld based solely on HIV status, better standardization in reporting HIV-related variables is needed to optimize patient selection and management. Full article
(This article belongs to the Special Issue Comprehensive Strategies in Cancer Immunotherapy)
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21 pages, 7362 KB  
Article
Integrative Bioinformatics Analysis Reveals Key Regulatory Genes and Therapeutic Targets in Ulcerative Colitis Pathogenesis
by Sheikh Atikur Rahman, Mst. Tania Khatun, Mahendra Singh, Viplov Kumar Biswas, Forkanul Hoque, Nurun Nesa Zaman, Anzana Parvin, Mohammad Khaja Mafij Uddin, Md. Mominul Islam Sheikh, Most Morium Begum, Rakesh Arya and Hossain Md. Faruquee
Genes 2025, 16(11), 1296; https://doi.org/10.3390/genes16111296 (registering DOI) - 1 Nov 2025
Abstract
Background: Ulcerative colitis (UC), a chronic and relapsing form of inflammatory bowel disease (IBD), arises from a multifactorial interplay of genetic predisposition, immune dysregulation, and environmental triggers. Despite advances in understanding UC pathogenesis, the identification of reliable biomarkers and key regulatory genes remains [...] Read more.
Background: Ulcerative colitis (UC), a chronic and relapsing form of inflammatory bowel disease (IBD), arises from a multifactorial interplay of genetic predisposition, immune dysregulation, and environmental triggers. Despite advances in understanding UC pathogenesis, the identification of reliable biomarkers and key regulatory genes remains essential for unraveling disease mechanisms. Such insights are crucial for improving diagnostic precision and developing personalized therapeutic strategies. Methods: In this study, gene expression profiles from publicly available microarray and RNA-sequencing datasets were systematically analyzed using advanced bioinformatics tools. Differentially expressed genes (DEGs) were identified through statistical comparisons, and functional enrichment analyses were performed to explore their biological relevance. A total of 141 overlapping DEGs were extracted from three GEO datasets, and 20 key DEGs were further prioritized via protein–protein interaction (PPI) network construction. Hub genes, relevant signaling pathways, associated transcription factors (TFs), and microRNAs (miRNAs) linked to disease progression were identified. Potential therapeutic compounds were also predicted through computational drug–gene interaction analysis. Results: The analysis revealed a panel of novel biomarkers-TLR2, IFNG, CD163, CXCL9, CCL4, PRF1, TLR8, ARG1, LILRB2, FPR2, and PPARG-that function as key hub genes implicated in ulcerative colitis (UC) pathogenesis. These genes were associated with critical biological processes including signal transduction, inflammatory and immune responses, proteolysis, lipid transport, and cholesterol/triglyceride homeostasis. Furthermore, transcription factors (FOXC1, GABPA, GATA2, SUPT5H) and microRNAs (hsa-miR-34a-5p, hsa-miR-335-5p, hsa-miR-24-3p, hsa-miR-23a-5p, hsa-miR-26a-5p) revealed key regulatory networks influencing post-transcriptional gene regulation. Molecular docking analysis predicted Apremilast and Golotimod as promising therapeutic candidates for UC intervention. Conclusions: In conclusion, this study enhances our understanding of ulcerative colitis pathogenesis by identifying key biomarkers and therapeutic targets, paving the way for future advancements in personalized diagnosis and treatment strategies. Full article
(This article belongs to the Special Issue Computational Genomics and Bioinformatics of Cancer)
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14 pages, 878 KB  
Article
Genome Selection for Fleece Traits in Inner Mongolia Cashmere Goats Based on GWAS Prior Marker Information
by Huanfeng Yao, Na Wang, Yu Li, Gang He, Jin Ning, Shuai Kang, Yongbin Liu, Jinquan Li, Qi Lv, Ruijun Wang, Yanjun Zhang, Rui Su and Zhiying Wang
Animals 2025, 15(21), 3184; https://doi.org/10.3390/ani15213184 (registering DOI) - 31 Oct 2025
Abstract
The Inner Mongolia Cashmere goat (IMCG) industry is a major contributor to global cashmere production, with fleece traits serving as key economic indicators that directly impact both income and the long-term sustainability of the industry. When genome-wide SNPs are used to estimate kinship [...] Read more.
The Inner Mongolia Cashmere goat (IMCG) industry is a major contributor to global cashmere production, with fleece traits serving as key economic indicators that directly impact both income and the long-term sustainability of the industry. When genome-wide SNPs are used to estimate kinship matrices, the traditional animal model implicitly assumes that all SNPs have the same effect-size distribution. However, in practice, there are differences in the genetic mechanisms and complexity of different traits. We conducted a genome-wide association study (GWAS) on 2299 IMCGs genotyped with 67,021 SNPs, which were obtained after imputation. The traits measured included cashmere yield (CY), wool length (WL), cashmere length (CL), and cashmere diameter (CD), with a total of 33,564 records collected. The top 5% to 20% of the significant SNPs from the GWAS were used as biological prior information. We then assigned proportional weights based on their contribution to the overall genetic variance and further integrated them with the remaining loci to construct a kinship relationship matrix for estimating genetic parameters and genomic breeding value. By incorporating prior marker information from the GWAS, it was found that the heritability estimates for CY, WL, CL, and CD were 0.26, 0.37, 0.09, and 0.35, respectively. For CY and CL, integrating the top 5% of prior SNP markers yielded the highest genomic prediction accuracies of 0.742 and 0.673, representing improvements of 16.67% and 19.75% over models that did not utilize prior information. In contrast, for WL and CD, the highest accuracies of 0.851 and 0.780 were achieved by integrating the top 10% of prior SNP markers, reflecting improvements of 9.81% and 10.14%, respectively. Compared with the conventional GBLUP method, this method of integrating GWAS-derived prior markers for genomic genetic evaluation can significantly improve the accuracy of genomic prediction for fleece traits in IMCGs. This approach facilitates accurate selection for fleece traits in IMCGs, enabling accelerated genetic progress through long-term breeding programs. Full article
(This article belongs to the Section Animal Genetics and Genomics)
21 pages, 4934 KB  
Article
Effects of Arbuscular Mycorrhizal Fungi and Metal-Tolerant Pseudomonas fluorescens on Mitigating Cadmium and Zinc Stress in Tomato
by Leilei Zhang, Gabriele Bellotti, Hajar Salehi, Edoardo Puglisi and Luigi Lucini
Plants 2025, 14(21), 3353; https://doi.org/10.3390/plants14213353 (registering DOI) - 31 Oct 2025
Abstract
Heavy metal (HM) contamination in agricultural soils poses a significant threat to soil health and plant productivity. This study investigates the impact of cadmium (Cd) and zinc (Zn) stress on tomato plants (Solanum lycopersicum) and explores the mitigation potential of microbial [...] Read more.
Heavy metal (HM) contamination in agricultural soils poses a significant threat to soil health and plant productivity. This study investigates the impact of cadmium (Cd) and zinc (Zn) stress on tomato plants (Solanum lycopersicum) and explores the mitigation potential of microbial biostimulants (MBs), including arbuscular mycorrhizal fungi (AMF) and Pseudomonas fluorescens So_08 (PGPR), over a 52-day period using multi-omics approaches. Root exudate profiling revealed distinct metabolic changes under HM stress, which compromised soil–plant interactions. Cd stress reduced the secretion of phenylpropanoids (sum LogFC: −45.18), lipids (sum LogFC: −27.67), and isoprenoids (sum LogFC: −11−67), key metabolites in antioxidative defense, while also suppressing rhizosphere fungal populations. Conversely, Zn stress enhanced lipid exudation (such as sphingolipids and sterols, as sum LogFC of 8.72 and 9.99, respectively) to maintain membrane integrity and reshaped rhizobacterial communities. The MBs application mitigated HM-induced stress by enhancing specialized metabolite syntheses, including cinnamic acids, terpenoids, and flavonoids, which promoted crop resilience. MBs also reshaped microbial diversity, fostering beneficial species like Portibacter spp., Alkalitalea saponilacus under Cd stress, and stimulating rhizobacteria like Aggregatilinea spp. under Zn stress. Specifically, under Cd stress, bacterial diversity remained relatively stable, suggesting their resilience to Cd. However, fungal communities exhibited greater sensitivity, with a decline in diversity in Cd-treated soils and partial recovery when MBs were applied. Conversely, Zn stress caused decline in bacterial α-diversity, while fungal diversity was maintained, indicating that Zn acts as an ecological filter that suppresses sensitive bacterial taxa and favors Zn-tolerant fungal species. Multi-omics data integration combined with network analysis highlighted key features associated with improved nutrient availability and reduced HM toxicity under MB treatments, including metabolites and microbial taxa linked to sulfur cycling, nitrogen metabolism, and iron reduction pathways. These findings demonstrate that MBs can modulate plant metabolic responses and restore rhizosphere microbial communities under Cd and Zn stress, with PGPR showing broader metabolomic recovery effects and AMF influencing specific metabolite pathways. This study provides new insights into plant–microbe interactions in HM-contaminated environments, supporting the potential application of biostimulants for sustainable soil remediation and plant health improvement. Full article
(This article belongs to the Section Plant–Soil Interactions)
18 pages, 754 KB  
Systematic Review
Exploring the Cardiovascular Impacts of Agmatine: A Systematic Review
by Oana-Mădălina Manole, Gabriela Rusu-Zota, Amin Bazyani and Viviana Onofrei
Med. Sci. 2025, 13(4), 255; https://doi.org/10.3390/medsci13040255 (registering DOI) - 31 Oct 2025
Abstract
Background: Agmatine (AG) is an endogenous neurotransmitter discovered in 1910. It acts on imidazoline I1 and I2 receptors, alpha-2 adrenoceptors, N-methyl-D-aspartate receptors (NMDAR), and serotonergic receptors and modulates nitric oxide synthase (NOS) subtypes. It has neuroprotective, anxiolytic, antidepressant, anticonvulsant, and anti-inflammatory properties and [...] Read more.
Background: Agmatine (AG) is an endogenous neurotransmitter discovered in 1910. It acts on imidazoline I1 and I2 receptors, alpha-2 adrenoceptors, N-methyl-D-aspartate receptors (NMDAR), and serotonergic receptors and modulates nitric oxide synthase (NOS) subtypes. It has neuroprotective, anxiolytic, antidepressant, anticonvulsant, and anti-inflammatory properties and is involved in cognitive functions and withdrawal. The cardiovascular effects of AG began to be explored after the hypotensive effect of clonidine, an imidazoline agonist, was demonstrated. The current study aimed to systematize the effects of AG on the cardiovascular system obtained in previous preclinical studies. Methods: We searched three databases, PubMed, Cochrane, and Embase, using the keywords “agmatine” and “cardiac” or “vascular.” Results: Sixty studies were eligible and included in the analysis. Initially identified as Clonidine Displacing Substance (CDS), AG has demonstrated dual effects—an increase or decrease in blood pressure or in heart rate. Conclusions: The effects exerted by AG depend on the dose and route of administration, as well as on the receptors involved and the pathophysiological pathway used. Full article
(This article belongs to the Section Cardiovascular Disease)
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