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24 pages, 1681 KiB  
Article
A Hybrid Quantum–Classical Architecture with Data Re-Uploading and Genetic Algorithm Optimization for Enhanced Image Classification
by Aksultan Mukhanbet and Beimbet Daribayev
Computation 2025, 13(8), 185; https://doi.org/10.3390/computation13080185 (registering DOI) - 1 Aug 2025
Abstract
Quantum machine learning (QML) has emerged as a promising approach for enhancing image classification by exploiting quantum computational principles such as superposition and entanglement. However, practical applications on complex datasets like CIFAR-100 remain limited due to the low expressivity of shallow circuits and [...] Read more.
Quantum machine learning (QML) has emerged as a promising approach for enhancing image classification by exploiting quantum computational principles such as superposition and entanglement. However, practical applications on complex datasets like CIFAR-100 remain limited due to the low expressivity of shallow circuits and challenges in circuit optimization. In this study, we propose HQCNN–REGA—a novel hybrid quantum–classical convolutional neural network architecture that integrates data re-uploading and genetic algorithm optimization for improved performance. The data re-uploading mechanism allows classical inputs to be encoded multiple times into quantum states, enhancing the model’s capacity to learn complex visual features. In parallel, a genetic algorithm is employed to evolve the quantum circuit architecture by optimizing gate sequences, entanglement patterns, and layer configurations. This combination enables automatic discovery of efficient parameterized quantum circuits without manual tuning. Experiments on the MNIST and CIFAR-100 datasets demonstrate state-of-the-art performance for quantum models, with HQCNN–REGA outperforming existing quantum neural networks and approaching the accuracy of advanced classical architectures. In particular, we compare our model with classical convolutional baselines such as ResNet-18 to validate its effectiveness in real-world image classification tasks. Our results demonstrate the feasibility of scalable, high-performing quantum–classical systems and offer a viable path toward practical deployment of QML in computer vision applications, especially on noisy intermediate-scale quantum (NISQ) hardware. Full article
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27 pages, 872 KiB  
Article
Effect of Monomer Mixture Composition on TiCl4-Al(i-C4H9)3 Catalytic System Activity in Butadiene–Isoprene Copolymerization: A Theoretical Study
by Konstantin A. Tereshchenko, Rustem T. Ismagilov, Nikolai V. Ulitin, Yana L. Lyulinskaya and Alexander S. Novikov
Computation 2025, 13(8), 184; https://doi.org/10.3390/computation13080184 (registering DOI) - 1 Aug 2025
Abstract
Divinylisoprene rubber, a copolymer of butadiene and isoprene, is used as raw material for rubber technical products, combining isoprene rubber’s elasticity and butadiene rubber’s wear resistance. These properties depend quantitatively on the copolymer composition, which depends on the kinetics of its synthesis. This [...] Read more.
Divinylisoprene rubber, a copolymer of butadiene and isoprene, is used as raw material for rubber technical products, combining isoprene rubber’s elasticity and butadiene rubber’s wear resistance. These properties depend quantitatively on the copolymer composition, which depends on the kinetics of its synthesis. This work aims to theoretically describe how the monomer mixture composition in the butadiene–isoprene copolymerization affects the activity of the TiCl4–Al(i-C4H9)3 catalytic system (expressed by active sites concentration) via kinetic modeling. This enables development of a reliable kinetic model for divinylisoprene rubber synthesis, predicting reaction rate, molecular weight, and composition, applicable to reactor design and process intensification. Active sites concentrations were calculated from experimental copolymerization rates and known chain propagation constants for various monomer compositions. Kinetic equations for active sites formation were based on mass-action law and Langmuir monomolecular adsorption theory. An analytical equation relating active sites concentration to monomer composition was derived, analyzed, and optimized with experimental data. The results show that monomer composition’s influence on active sites concentration is well described by a two-step kinetic model (physical adsorption followed by Ti–C bond formation), accounting for competitive adsorption: isoprene adsorbs more readily, while butadiene forms more stable active sites. Full article
(This article belongs to the Special Issue Feature Papers in Computational Chemistry)
22 pages, 5209 KiB  
Article
Analytical Inertia Identification of Doubly Fed Wind Farm with Limited Control Information Based on Symbolic Regression
by Mengxuan Shi, Yang Li, Xingyu Shi, Dejun Shao, Mujie Zhang, Duange Guo and Yijia Cao
Appl. Sci. 2025, 15(15), 8578; https://doi.org/10.3390/app15158578 (registering DOI) - 1 Aug 2025
Abstract
The integration of large-scale wind power clusters significantly reduces the inertia level of the power system, increasing the risk of frequency instability. Accurately assessing the equivalent virtual inertia of wind farms is critical for grid stability. Addressing the dual bottlenecks in existing inertia [...] Read more.
The integration of large-scale wind power clusters significantly reduces the inertia level of the power system, increasing the risk of frequency instability. Accurately assessing the equivalent virtual inertia of wind farms is critical for grid stability. Addressing the dual bottlenecks in existing inertia assessment methods, where physics-based modeling requires full control transparency and data-driven approaches lack interpretability for inertia response analysis, thus failing to reconcile commercial confidentiality constraints with analytical needs, this paper proposes a symbolic regression framework for inertia evaluation in doubly fed wind farms with limited control information constraints. First, a dynamic model for the inertia response of DFIG wind farms is established, and a mathematical expression for the equivalent virtual inertia time constant under different control strategies is derived. Based on this, a nonlinear function library reflecting frequency-active power dynamic is constructed, and a symbolic regression model representing the system’s inertia response characteristics is established by correlating operational data. Then, sparse relaxation optimization is applied to identify unknown parameters, allowing for the quantification of the wind farm’s equivalent virtual inertia. Finally, the effectiveness of the proposed method is validated in an IEEE three-machine nine-bus system containing a doubly fed wind power cluster. Case studies show that the proposed method can fully utilize prior model knowledge and operational data to accurately assess the system’s inertia level with low computational complexity. Full article
13 pages, 1293 KiB  
Article
Integration of an OS-Based Machine Learning Score (AS Score) and Immunoscore as Ancillary Tools for Predicting Immunotherapy Response in Sarcomas
by Isidro Machado, Raquel López-Reig, Eduardo Giner, Antonio Fernández-Serra, Celia Requena, Beatriz Llombart, Francisco Giner, Julia Cruz, Victor Traves, Javier Lavernia, Antonio Llombart-Bosch and José Antonio López Guerrero
Cancers 2025, 17(15), 2551; https://doi.org/10.3390/cancers17152551 (registering DOI) - 1 Aug 2025
Abstract
Background: Angiosarcomas (ASs) represent a heterogeneous and highly aggressive subset of tumors that respond poorly to systemic treatments and are associated with short progression-free survival (PFS) and overall survival (OS). The aim of this study was to develop and validate an immune-related [...] Read more.
Background: Angiosarcomas (ASs) represent a heterogeneous and highly aggressive subset of tumors that respond poorly to systemic treatments and are associated with short progression-free survival (PFS) and overall survival (OS). The aim of this study was to develop and validate an immune-related prognostic model—termed the AS score—using data from two independent sarcoma cohorts. Methods: A prognostic model was developed using a previously characterized cohort of 25 angiosarcoma samples. Candidate genes were identified via the Maxstat algorithm (Maxstat v0.7-25 for R), combined with log-rank testing. The AS score was then computed by weighing normalized gene expression levels according to Cox regression coefficients. For external validation, transcriptomic data from TCGA Sarcoma cohort (n = 253) were analyzed. The Immunoscore—which reflects the tumor immune microenvironment—was inferred using the ESTIMATE package (v1.0.13) in R. All statistical analyses were performed in RStudio (v 4.0.3). Results: Four genes—IGF1R, MAP2K1, SERPINE1, and TCF12—were ultimately selected to construct the prognostic model. The resulting AS score enabled the classification of angiosarcoma cases into two prognostically distinct groups (p = 0.00012). Cases with high AS score values, which included both cutaneous and non-cutaneous forms, exhibited significantly poorer outcomes, whereas cases with low AS scores were predominantly cutaneous. A significant association was observed between the AS score and the Immunoscore (p = 0.025), with higher Immunoscore values found in high-AS score tumors. Validation using TCGA sarcoma cohort confirmed the prognostic value of both the AS score (p = 0.0066) and the Immunoscore (p = 0.0029), with a strong correlation between their continuous values (p = 2.9 × 10−8). Further survival analysis, integrating categorized scores into four groups, demonstrated robust prognostic significance (p = 0.00021). Notably, in tumors with a low Immunoscore, AS score stratification was not prognostic. In contrast, among cases with a high Immunoscore, the AS score effectively distinguished outcomes (p < 0.0001), identifying a subgroup with poor prognosis but potential sensitivity to immunotherapy. Conclusions: This combined classification using the AS score and Immunoscore has prognostic relevance in sarcoma, suggesting that angiosarcomas with an immunologically active microenvironment (high Immunoscore) and poor prognosis (high AS score) may be prime candidates for immunotherapy and this approach warrants prospective validation. Full article
(This article belongs to the Special Issue Genomics and Transcriptomics in Sarcoma)
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29 pages, 6541 KiB  
Article
Lacticaseibacillus paracasei L21 and Its Postbiotics Ameliorate Ulcerative Colitis Through Gut Microbiota Modulation, Intestinal Barrier Restoration, and HIF1α/AhR-IL-22 Axis Activation: Combined In Vitro and In Vivo Evidence
by Jingru Chen, Linfang Zhang, Yuehua Jiao, Xuan Lu, Ning Zhang, Xinyi Li, Suo Zheng, Bailiang Li, Fei Liu and Peng Zuo
Nutrients 2025, 17(15), 2537; https://doi.org/10.3390/nu17152537 (registering DOI) - 1 Aug 2025
Abstract
Background: Ulcerative colitis (UC), characterized by chronic intestinal inflammation, epithelial barrier dysfunction, and immune imbalance demands novel ameliorative strategies beyond conventional approaches. Methods: In this study, the probiotic properties of Lactobacillus paracasei L21 (L. paracasei L21) and its ability to ameliorate colitis [...] Read more.
Background: Ulcerative colitis (UC), characterized by chronic intestinal inflammation, epithelial barrier dysfunction, and immune imbalance demands novel ameliorative strategies beyond conventional approaches. Methods: In this study, the probiotic properties of Lactobacillus paracasei L21 (L. paracasei L21) and its ability to ameliorate colitis were evaluated using an in vitro lipopolysaccharide (LPS)-induced intestinal crypt epithelial cell (IEC-6) model and an in vivo dextran sulfate sodium (DSS)-induced UC mouse model. Results: In vitro, L. paracasei L21 decreased levels of pro-inflammatory cytokines (TNF-α, IL-1β, IL-8) while increasing anti-inflammatory IL-10 levels (p < 0.05) in LPS-induced IEC-6 cells, significantly enhancing the expression of tight junction proteins (ZO-1, occludin, claudin-1), thereby restoring the intestinal barrier. In vivo, both viable L. paracasei L21 and its heat-inactivated postbiotic (H-L21) mitigated weight loss, colon shortening, and disease activity indices, concurrently reducing serum LPS and proinflammatory mediators. Interventions inhibited NF-κB signaling while activating HIF1α/AhR pathways, increasing IL-22 and mucin MUC2 to restore goblet cell populations. Gut microbiota analysis showed that both interventions increased the abundance of beneficial gut bacteria (Lactobacillus, Dubococcus, and Akkermansia) and improved faecal propanoic acid and butyric acid levels. H-L21 uniquely exerted an anti-inflammatory effect, marked by the regulation of Dubosiella, while L. paracasei L21 marked by the Akkermansia. Conclusions: These results highlight the potential of L. paracasei L21 as a candidate for the development of both probiotic and postbiotic formulations. It is expected to provide a theoretical basis for the management of UC and to drive the development of the next generation of UC therapies. Full article
(This article belongs to the Special Issue Probiotics, Postbiotics, Gut Microbiota and Gastrointestinal Health)
29 pages, 5505 KiB  
Article
Triaxial Response and Elastoplastic Constitutive Model for Artificially Cemented Granular Materials
by Xiaochun Yu, Yuchen Ye, Anyu Yang and Jie Yang
Buildings 2025, 15(15), 2721; https://doi.org/10.3390/buildings15152721 (registering DOI) - 1 Aug 2025
Abstract
Because artificially cemented granular (ACG) materials employ diverse combinations of aggregates and binders—including cemented soil, low-cement-content cemented sand and gravel (LCSG), and concrete—their stress–strain responses vary widely. In LCSG, the binder dosage is typically limited to 40–80 kg/m3 and the sand–gravel skeleton [...] Read more.
Because artificially cemented granular (ACG) materials employ diverse combinations of aggregates and binders—including cemented soil, low-cement-content cemented sand and gravel (LCSG), and concrete—their stress–strain responses vary widely. In LCSG, the binder dosage is typically limited to 40–80 kg/m3 and the sand–gravel skeleton is often obtained directly from on-site or nearby excavation spoil, endowing the material with a markedly lower embodied carbon footprint and strong alignment with current low-carbon, green-construction objectives. Yet, such heterogeneity makes a single material-specific constitutive model inadequate for predicting the mechanical behavior of other ACG variants, thereby constraining broader applications in dam construction and foundation reinforcement. This study systematically summarizes and analyzes the stress–strain and volumetric strain–axial strain characteristics of ACG materials under conventional triaxial conditions. Generalized hyperbolic and parabolic equations are employed to describe these two families of curves, and closed-form expressions are proposed for key mechanical indices—peak strength, elastic modulus, and shear dilation behavior. Building on generalized plasticity theory, we derive the plastic flow direction vector, loading direction vector, and plastic modulus, and develop a concise, transferable elastoplastic model suitable for the full spectrum of ACG materials. Validation against triaxial data for rock-fill materials, LCSG, and cemented coal–gangue backfill shows that the model reproduces the stress and deformation paths of each material class with high accuracy. Quantitative evaluation of the peak values indicates that the proposed constitutive model predicts peak deviatoric stress with an error of 1.36% and peak volumetric strain with an error of 3.78%. The corresponding coefficients of determination R2 between the predicted and measured values are 0.997 for peak stress and 0.987 for peak volumetric strain, demonstrating the excellent engineering accuracy of the proposed model. The results provide a unified theoretical basis for deploying ACG—particularly its low-cement, locally sourced variants—in low-carbon dam construction, foundation rehabilitation, and other sustainable civil engineering projects. Full article
(This article belongs to the Special Issue Low Carbon and Green Materials in Construction—3rd Edition)
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21 pages, 3686 KiB  
Article
Genome-Wide Analyses of the XTH Gene Family in Brachypodium distachyon and Functional Analyses of the Role of BdXTH27 in Root Elongation
by Hongyan Shen, Qiuping Tan, Wenzhe Zhao, Mengdan Zhang, Cunhao Qin, Zhaobing Liu, Xinsheng Wang, Sendi An, Hailong An and Hongyu Wu
Int. J. Mol. Sci. 2025, 26(15), 7457; https://doi.org/10.3390/ijms26157457 (registering DOI) - 1 Aug 2025
Abstract
Xyloglucan endotransglucosylase/hydrolases (XTHs) are a class of cell wall-associated enzymes involved in the construction and remodeling of cellulose/xyloglucan crosslinks. However, knowledge of this gene family in the model monocot Brachypodium distachyon is limited. A total of 29 BdXTH genes were identified from the [...] Read more.
Xyloglucan endotransglucosylase/hydrolases (XTHs) are a class of cell wall-associated enzymes involved in the construction and remodeling of cellulose/xyloglucan crosslinks. However, knowledge of this gene family in the model monocot Brachypodium distachyon is limited. A total of 29 BdXTH genes were identified from the whole genome, and these were further divided into three subgroups (Group I/II, Group III, and the Ancestral Group) through evolutionary analysis. Gene structure and protein motif analyses indicate that closely clustered BdXTH genes are relatively conserved within each group. A highly conserved amino acid domain (DEIDFEFLG) responsible for catalytic activity was identified in all BdXTH proteins. We detected three pairs of segmentally duplicated BdXTH genes and five groups of tandemly duplicated BdXTH genes, which played vital roles in the expansion of the BdXTH gene family. Cis-elements related to hormones, growth, and abiotic stress responses were identified in the promoters of each BdXTH gene, and when roots were treated with two abiotic stresses (salinity and drought) and four plant hormones (IAA, auxin; GA3, gibberellin; ABA, abscisic acid; and BR, brassinolide), the expression levels of many BdXTH genes changed significantly. Transcriptional analyses of the BdXTH genes in 38 tissue samples from the publicly available RNA-seq data indicated that most BdXTH genes have distinct expression patterns in different tissues and at different growth stages. Overexpressing the BdXTH27 gene in Brachypodium led to reduced root length in transgenic plants, which exhibited higher cellulose levels but lower hemicellulose levels compared to wild-type plants. Our results provide valuable information for further elucidation of the biological functions of BdXTH genes in the model grass B. distachyon. Full article
(This article belongs to the Section Molecular Plant Sciences)
23 pages, 3427 KiB  
Article
Visual Narratives and Digital Engagement: Decoding Seoul and Tokyo’s Tourism Identity Through Instagram Analytics
by Seung Chul Yoo and Seung Mi Kang
Tour. Hosp. 2025, 6(3), 149; https://doi.org/10.3390/tourhosp6030149 (registering DOI) - 1 Aug 2025
Abstract
Social media platforms like Instagram significantly shape destination images and influence tourist behavior. Understanding how different cities are represented and perceived on these platforms is crucial for effective tourism marketing. This study provides a comparative analysis of Instagram content and engagement patterns in [...] Read more.
Social media platforms like Instagram significantly shape destination images and influence tourist behavior. Understanding how different cities are represented and perceived on these platforms is crucial for effective tourism marketing. This study provides a comparative analysis of Instagram content and engagement patterns in Seoul and Tokyo, two major Asian metropolises, to derive actionable marketing insights. We collected and analyzed 59,944 public Instagram posts geotagged or location-tagged within Seoul (n = 29,985) and Tokyo (n = 29,959). We employed a mixed-methods approach involving content categorization using a fine-tuned convolutional neural network (CNN) model, engagement metric analysis (likes, comments), Valence Aware Dictionary and sEntiment Reasoner (VADER) sentiment analysis and thematic classification of comments, geospatial analysis (Kernel Density Estimation [KDE], Moran’s I), and predictive modeling (Gradient Boosting with SHapley Additive exPlanations [SHAP] value analysis). A validation analysis using balanced samples (n = 2000 each) was conducted to address Tokyo’s lower geotagged data proportion. While both cities showed ‘Person’ as the dominant content category, notable differences emerged. Tokyo exhibited higher like-based engagement across categories, particularly for ‘Animal’ and ‘Food’ content, while Seoul generated slightly more comments, often expressing stronger sentiment. Qualitative comment analysis revealed Seoul comments focused more on emotional reactions, whereas Tokyo comments were often shorter, appreciative remarks. Geospatial analysis identified distinct hotspots. The validation analysis confirmed these spatial patterns despite Tokyo’s data limitations. Predictive modeling highlighted hashtag counts as the key engagement driver in Seoul and the presence of people in Tokyo. Seoul and Tokyo project distinct visual narratives and elicit different engagement patterns on Instagram. These findings offer practical implications for destination marketers, suggesting tailored content strategies and location-based campaigns targeting identified hotspots and specific content themes. This study underscores the value of integrating quantitative and qualitative analyses of social media data for nuanced destination marketing insights. Full article
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12 pages, 1252 KiB  
Article
Low Dietary Folate Increases Developmental Delays in the Litters of Mthfr677TT Mice
by Karen E. Christensen, Marie-Lou Faquette, Vafa Keser, Alaina M. Reagan, Aaron T. Gebert, Teodoro Bottiglieri, Gareth R. Howell and Rima Rozen
Nutrients 2025, 17(15), 2536; https://doi.org/10.3390/nu17152536 (registering DOI) - 1 Aug 2025
Abstract
Background/Objectives: Low folate intake before and during pregnancy increases the risk of neural tube defects and other adverse outcomes. Gene variants such as MTHFR 677C>T (rs1801133) may increase risks associated with suboptimal folate intake. Our objective was to use BALB/cJ Mthfr677C>T [...] Read more.
Background/Objectives: Low folate intake before and during pregnancy increases the risk of neural tube defects and other adverse outcomes. Gene variants such as MTHFR 677C>T (rs1801133) may increase risks associated with suboptimal folate intake. Our objective was to use BALB/cJ Mthfr677C>T mice to evaluate the effects of the TT genotype and low folate diets on embryonic development and MTHFR protein expression in pregnant mice. Methods: Female 677CC (mCC) and 677TT (mTT) mice were fed control (2 mg folic acid/kg (2D)), 1 mg folic acid/kg (1D) and 0.3 mg folic acid/kg (0.3D) diets before and during pregnancy. Embryos and maternal tissues were collected at embryonic day 10.5. Embryos were examined for developmental delays and defects. Methyltetrahydrofolate (methylTHF) and total homocysteine (tHcy) were measured in maternal plasma, and MTHFR protein expression was evaluated in maternal liver. Results: MethylTHF decreased due to the experimental diets and mTT genotype. tHcy increased due to 0.3D and mTT genotype; mTT 0.3D mice had significantly higher tHcy than the other groups. MTHFR expression was lower in mTT liver than mCC. MTHFR protein expression increased due to low folate diets in mCC mice, whereas in mTT mice, MTHFR expression increased only due to 1D. Developmental delays were increased in the litters of mTT mice fed 1D and 0.3D. Conclusions: The Mthfr677C>T mouse models the effects of the MTHFR 677TT genotype in humans and provides a folate-responsive model for examination of the effects of folate intake and the MTHFR 677C>T variant during gestation. Full article
(This article belongs to the Section Micronutrients and Human Health)
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14 pages, 1399 KiB  
Article
GSTM5 as a Potential Biomarker for Treatment Resistance in Prostate Cancer
by Patricia Porras-Quesada, Lucía Chica-Redecillas, Beatriz Álvarez-González, Francisco Gutiérrez-Tejero, Miguel Arrabal-Martín, Rosa Rios-Pelegrina, Luis Javier Martínez-González, María Jesús Álvarez-Cubero and Fernando Vázquez-Alonso
Biomedicines 2025, 13(8), 1872; https://doi.org/10.3390/biomedicines13081872 (registering DOI) - 1 Aug 2025
Abstract
Background/Objectives: Androgen deprivation therapy (ADT) is widely used to manage prostate cancer (PC), but the emergence of treatment resistance remains a major clinical challenge. Although the GST family has been implicated in drug resistance, the specific role of GSTM5 remains poorly understood. [...] Read more.
Background/Objectives: Androgen deprivation therapy (ADT) is widely used to manage prostate cancer (PC), but the emergence of treatment resistance remains a major clinical challenge. Although the GST family has been implicated in drug resistance, the specific role of GSTM5 remains poorly understood. This study investigates whether GSTM5, alone or in combination with clinical variables, can improve patient stratification based on the risk of early treatment resistance. Methods: In silico analyses were performed to examine GSTM5’s role in protein interactions, molecular pathways, and gene expression. The rs3768490 polymorphism was genotyped in 354 patients with PC, classified by ADT response. Descriptive analysis and logistic regression models were applied to evaluate associations between genotype, clinical variables, and ADT response. GSTM5 expression related to the rs3768490 genotype and ADT response was also analyzed in 129 prostate tissue samples. Results: The T/T genotype of rs3768490 was significantly associated with a lower likelihood of early ADT resistance in both individual (p = 0.0359, Odd Ratios (OR) = 0.18) and recessive models (p = 0.0491, OR = 0.21). High-risk classification according to D’Amico was strongly associated with early progression (p < 0.0004; OR > 5.4). Combining genotype and clinical risk improved predictive performance, highlighting their complementary value in stratifying patients by treatment response. Additionally, GSTM5 expression was slightly higher in T/T carriers, suggesting a potential protective role against ADT resistance. Conclusions: The T/T genotype of rs3768490 may protect against ADT resistance by modulating GSTM5 expression in PC. These preliminary findings highlight the potential of integrating genetic biomarkers into clinical models for personalized treatment strategies, although further studies are needed to validate these observations. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Tumors: Advancing Genetic Studies)
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21 pages, 3146 KiB  
Article
TnP as a Multifaceted Therapeutic Peptide with System-Wide Regulatory Capacity
by Geonildo Rodrigo Disner, Emma Wincent, Carla Lima and Monica Lopes-Ferreira
Pharmaceuticals 2025, 18(8), 1146; https://doi.org/10.3390/ph18081146 (registering DOI) - 1 Aug 2025
Abstract
Background: The candidate therapeutic peptide TnP demonstrates broad, system-level regulatory capacity, revealed through integrated network analysis from transcriptomic data in zebrafish. Our study primarily identifies TnP as a multifaceted modulator of drug metabolism, wound healing, proteolytic activity, and pigmentation pathways. Results: Transcriptomic profiling [...] Read more.
Background: The candidate therapeutic peptide TnP demonstrates broad, system-level regulatory capacity, revealed through integrated network analysis from transcriptomic data in zebrafish. Our study primarily identifies TnP as a multifaceted modulator of drug metabolism, wound healing, proteolytic activity, and pigmentation pathways. Results: Transcriptomic profiling of TnP-treated larvae following tail fin amputation revealed 558 differentially expressed genes (DEGs), categorized into four functional networks: (1) drug-metabolizing enzymes (cyp3a65, cyp1a) and transporters (SLC/ABC families), where TnP alters xenobiotic processing through Phase I/II modulation; (2) cellular trafficking and immune regulation, with upregulated myosin genes (myhb/mylz3) enhancing wound repair and tlr5-cdc42 signaling fine-tuning inflammation; (3) proteolytic cascades (c6ast4, prss1) coupled to autophagy (ulk1a, atg2a) and metabolic rewiring (g6pca.1-tg axis); and (4) melanogenesis-circadian networks (pmela/dct-fbxl3l) linked to ubiquitin-mediated protein turnover. Key findings highlight TnP’s unique coordination of rapid (protease activation) and sustained (metabolic adaptation) responses, enabled by short network path lengths (1.6–2.1 edges). Hub genes, such as nr1i2 (pxr), ppara, and bcl6aa/b, mediate crosstalk between these systems, while potential risks—including muscle hypercontractility (myhb overexpression) or cardiovascular effects (ace2-ppp3ccb)—underscore the need for targeted delivery. The zebrafish model validated TnP-conserved mechanisms with human relevance, particularly in drug metabolism and tissue repair. TnP’s ability to synchronize extracellular matrix remodeling, immune resolution, and metabolic homeostasis supports its development for the treatment of fibrosis, metabolic disorders, and inflammatory conditions. Conclusions: Future work should focus on optimizing tissue-specific delivery and assessing genetic variability to advance clinical translation. This system-level analysis positions TnP as a model example for next-generation multi-pathway therapeutics. Full article
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27 pages, 471 KiB  
Article
Multi-Granulation Covering Rough Intuitionistic Fuzzy Sets Based on Maximal Description
by Xiao-Meng Si and Zhan-Ao Xue
Symmetry 2025, 17(8), 1217; https://doi.org/10.3390/sym17081217 (registering DOI) - 1 Aug 2025
Abstract
Rough sets and fuzzy sets are two complementary approaches for modeling uncertainty and imprecision. Their integration enables a more comprehensive representation of complex, uncertain systems. However, existing rough fuzzy sets models lack the expressive power to fully capture the interactions among structural uncertainty, [...] Read more.
Rough sets and fuzzy sets are two complementary approaches for modeling uncertainty and imprecision. Their integration enables a more comprehensive representation of complex, uncertain systems. However, existing rough fuzzy sets models lack the expressive power to fully capture the interactions among structural uncertainty, cognitive hesitation, and multi-level granular information. To address these limitations, we achieve the following: (1) We propose intuitionistic fuzzy covering rough membership and non-membership degrees based on maximal description and construct a new single-granulation model that more effectively captures both the structural relationships among elements and the semantics of fuzzy information. (2) We further extend the model to a multi-granulation framework by defining optimistic and pessimistic approximation operators and analyzing their properties. Additionally, we propose a neutral multi-granulation covering rough intuitionistic fuzzy sets based on aggregated membership and non-membership degrees. Compared with single-granulation models, the multi-granulation models integrate multiple levels of information, allowing for more fine-grained and robust representations of uncertainty. Finally, a case study on real estate investment was conducted to validate the effectiveness of the proposed models. The results show that our models can more precisely represent uncertainty and granularity in complex data, providing a flexible tool for knowledge representation in decision-making scenarios. Full article
(This article belongs to the Section Mathematics)
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19 pages, 6096 KiB  
Article
Functional Characterization of Two Glutamate Dehydrogenase Genes in Bacillus altitudinis AS19 and Optimization of Soluble Recombinant Expression
by Fangfang Wang, Xiaoying Lv, Zhongyao Guo, Xianyi Wang, Yaohang Long and Hongmei Liu
Curr. Issues Mol. Biol. 2025, 47(8), 603; https://doi.org/10.3390/cimb47080603 (registering DOI) - 1 Aug 2025
Abstract
Glutamate dehydrogenase (GDH) is ubiquitous in organisms and crucial for amino acid metabolism, energy production, and redox balance. The gdhA and gudB genes encoding GDH were identified in Bacillus altitudinis AS19 and shown to be regulated by iron. However, their functions remain unclear. [...] Read more.
Glutamate dehydrogenase (GDH) is ubiquitous in organisms and crucial for amino acid metabolism, energy production, and redox balance. The gdhA and gudB genes encoding GDH were identified in Bacillus altitudinis AS19 and shown to be regulated by iron. However, their functions remain unclear. In this study, gdhA and gudB were analyzed using bioinformatics tools, such as MEGA, Expasy, and SWISS-MODEL, expressed with a prokaryotic expression system, and the induction conditions were optimized to increase the yield of soluble proteins. Phylogenetic analysis revealed that GDH is evolutionarily conserved within the genus Bacillus. GdhA and GudB were identified as hydrophobic proteins, not secreted or membrane proteins. Their structures were primarily composed of irregular coils and α-helices. SWISS-MODEL predicts GdhA to be an NADP-specific GDH, whereas GudB is an NAD-specific GDH. SDS-PAGE analysis showed that GdhA was expressed as a soluble protein after induction with 0.2 mmol/L IPTG at 24 °C for 16 h. GudB was expressed as a soluble protein after induction with 0.1 mmol/L IPTG at 16 °C for 12 h. The proteins were confirmed by Western blot and mass spectrometry. The enzyme activity of recombinant GdhA was 62.7 U/mg with NADPH as the coenzyme. This study provides a foundation for uncovering the functions of two GDHs of B. altitudinis AS19. Full article
(This article belongs to the Section Bioinformatics and Systems Biology)
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19 pages, 1771 KiB  
Article
Steady Radial Diverging Flow of a Particle-Laden Fluid with Particle Migration
by C. Q. Ru
Fluids 2025, 10(8), 200; https://doi.org/10.3390/fluids10080200 - 1 Aug 2025
Abstract
The steady plane radial diverging flow of a viscous or inviscid particle-fluid suspension is studied using a novel two-fluid model. For the initial flow field with a uniform particle distribution, our results show that the relative velocity of particles with respect to the [...] Read more.
The steady plane radial diverging flow of a viscous or inviscid particle-fluid suspension is studied using a novel two-fluid model. For the initial flow field with a uniform particle distribution, our results show that the relative velocity of particles with respect to the fluid depends on their inlet velocity ratio at the entrance, the mass density ratio and the Stokes number of particles, and the particles heavier (or lighter) than the fluid will move faster (or slower) than the fluid when their inlet velocities are equal (then Stokes drag vanishes at the entrance). The relative motion of particles with respect to the fluid leads to particle migration and the non-uniform distribution of particles. An explicit expression is obtained for the steady particle distribution eventually attained due to particle migration. Our results demonstrated and confirmed that, for both light particles (gas bubbles) and heavy particles, depending on the particle-to-fluid mass density ratio, the volume fraction of particles attains its maximum or minimum value near the entrance of the radial flow and after then monotonically decreases or increases with the radial coordinate and converges to an asymptotic value determined by the particle-to-fluid inlet velocity ratio. Explicit solutions given here could help quantify the steady particle distribution in the decelerating radial flow of a particle-fluid suspension. Full article
(This article belongs to the Special Issue 10th Anniversary of Fluids—Recent Advances in Fluid Mechanics)
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16 pages, 875 KiB  
Article
Association of Bioelectrical Impedance Analysis Parameters with Malnutrition in Patients Undergoing Maintenance Hemodialysis: A Cross-Sectional Study
by Minh D. Pham, Thang V. Dao, Anh T. X. Vu, Huong T. Q. Bui, Bon T. Nguyen, An T. T. Nguyen, Thuy T. T. Ta, Duc M. Cap, Toan D. Le, Phuc H. Phan, Ha N. Vu, Tuan D. Le, Toan Q. Pham, Thang V. Le, Thuc C. Luong, Thang B. Ta and Tuyen V. Duong
Medicina 2025, 61(8), 1396; https://doi.org/10.3390/medicina61081396 - 1 Aug 2025
Abstract
Background and Objectives: Malnutrition is one of the most common complications in patients undergoing hemodialysis (HD) and is closely linked to increased morbidity and mortality. This study aimed to investigate the nutritional status of HD patients and the clinical relevance of bioelectrical impedance [...] Read more.
Background and Objectives: Malnutrition is one of the most common complications in patients undergoing hemodialysis (HD) and is closely linked to increased morbidity and mortality. This study aimed to investigate the nutritional status of HD patients and the clinical relevance of bioelectrical impedance analysis (BIA) parameters such as the percent body fat (PBF), skeletal muscle mass index (SMI), extracellular water-to-total body water ratio (ECW/TBW), and phase angle (PhA) in assessing malnutrition in Vietnamese HD patients. Materials and Methods: This cross-sectional study was conducted among 184 patients undergoing hemodialysis in Hanoi, Vietnam. The BIA parameters were measured by the InBody S10 body composition analyzer, while malnutrition was assessed by the geriatric nutritional risk index (GNRI), with a GNRI <92 classified as a high risk of malnutrition. The independent BIA variables for predicting malnutrition and its cut-off values were explored using logistic regression models and a receiver operating characteristic (ROC) curve analysis, respectively. Results: Among the study population, 42.9% (79/184) of patients were identified as being at a high risk of malnutrition. The multivariate logistic regression analysis revealed that a higher ECW/TBW was independently associated with an increased risk of malnutrition, while the PBF, SMI, and PhA expressed significant and inverse associations with the malnutrition risk after adjusting for multiple confounders. The cut-off values for predicting the high risk of malnutrition in overall HD patients were determined to be 20.45%, 7.75 kg/m2, 5.45°, and 38.03% for the PBF, the SMI, the PhA, and the ECW/TBW ratio, respectively. Conclusions: BIA parameters, including the PBF, SMI, PhA, and ECW/TBW ratio, could serve as indicators of malnutrition in general Vietnamese patients with HD. Full article
(This article belongs to the Special Issue End-Stage Kidney Disease (ESKD))
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